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Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

Aksenov, Alexander A. Laponogov, Ivan Zhang, Zheng Doran, Sophie L. F. Belluomo, Ilaria Veselkov, Dennis Bittremieux, Wout Nothias, Louis Felix Nothias-Esposito, Melissa Maloney, Katherine N. Misra, Biswapriya B. Melnik, Alexey V. Smirnov, Aleksandr Du, Xiuxia Jones, Kenneth L., II Dorrestein, Kathleen Panitchpakdi, Morgan Ernst, Madeleine van der Hooft, Justin J. J. Gonzalez, Mabel Carazzone, Chiara Amezquita, Adolfo Callewaert, Chris Morton, James T. Quinn, Robert A. Bouslimani, Amina Orio, Andrea Albarracin Petras, Daniel Smania, Andrea M. Couvillion, Sneha P. Burnet, Meagan C. Nicora, Carrie D. Zink, Erika Metz, Thomas O. Artaev, Viatcheslav Humston-Fulmer, Elizabeth Gregor, Rachel Meijler, Michael M. Mizrahi, Itzhak Eyal, Stav Anderson, Brooke Dutton, Rachel Lugan, Raphael Le Boulch, Pauline Guitton, Yann Prevost, Stephanie Poirier, Audrey Dervilly, Gaud Le Bizec, Bruno Fait, Aaron Persi, Noga Sikron Song, Chao Gashu, Kelem Coras, Roxana Guma, Monica Manasson, Julia Scher, Jose U. Barupal, Dinesh Kumar Alseekh, Saleh Fernie, Alisdair R. Mirnezami, Reza Vasiliou, Vasilis Schmid, Robin Borisov, Roman S. Kulikova, Larisa N. Knight, Rob Wang, Mingxun Hanna, George B. Dorrestein, Pieter C. Veselkov, Kirill

Nature Biotechnology, 2020-11-9

https://doi.org/10.1038/s41587-020-0700-3

Gaud Dervilly-Pinel

Dervilly-Pinel Gaud / Pinel Gaud

ORCID: 0000-0002-1867-0008

https://www.researchgate.net/profile/Gaud_Pinel

Hydrophilic interaction (HILIC) and reverse phase liquid chromatography (RPLC)–high resolution MS for characterizing lipids profile disruption in serum of anabolic implanted bovines 10.1007/s11306-015-0847-y

Measurement of phthalates diesters in food using gas chromatography-tandem mass spectrometry 10.1016/j.foodchem.2015.09.045

Analysis of glucuronide and sulfate steroids in urine by ultra-high-performance supercritical-fluid chromatography hyphenated tandem mass spectrometry 10.1007/s00216-015-8573-x

Clinical biochemical and hormonal profiling in plasma: a promising strategy to predict growth hormone abuse in cattle 10.1007/s00216-015-8548-y

Determination of a large set of β-adrenergic agonists in animal matrices based on ion mobility and mass separations 10.1021/acs.analchem.5b01831

Direct analysis in real time - high resolution mass spectrometry (DART-HRMS): a high throughput strategy for identification and quantification of anabolic steroid esters 10.1002/dta.1727

Potential of mass spectrometry metabolomics for chemical food safety 10.4155/bio.14.267

Short-term effects of a perinatal exposure to the HBCDD α-isomer in rats: Assessment of early motor and sensory development, spontaneous locomotor activity and anxiety in pups 10.1016/j.ntt.2015.08.005

Spatial Distribution of Lactococcus lactis Colonies Modulates the Production of Major Metabolites during the Ripening of a Model Cheese 10.1128/AEM.02621-15

Basics of mass spectrometry based metabolomics 10.1002/pmic.201400255

Development and validation of a specific and sensitive gas chromatography tandem mass spectrometry method for the determination of bisphenol A residues in a large set of food items 10.1016/j.chroma.2014.07.105

High throughput identification and quantification of anabolic steroid esters by atmospheric solids analysis probe mass spectrometry for efficient screening of drug preparations 10.1021/ac501072g

Monitoring the endogenous steroid profile disruption in urine and blood upon nandrolone administration: An efficient and innovative strategy to screen for nandrolone abuse in entire male horses 10.1002/dta.1520

Fast and multiresidue determination of twenty glucocorticoids in bovine milk using ultra high performance liquid chromatography-tandem mass spectrometry 10.1016/j.chroma.2013.04.019

Human dietary exposure to polycyclic aromatic hydrocarbons: results of the second French Total Diet Study 10.1016/j.envint.2012.12.011

Recombinant bovine growth hormone identification and the kinetic of elimination in rainbow trout treated by LC-MS/MS 10.1080/19440049.2013.787650

Ultra high performance liquid chromatography/tandem mass spectrometry based identification of steroid esters in serum and plasma: an efficient strategy to detect natural steroids abuse in breeding and racing animals 10.1016/j.chroma.2013.02.010

Metabolomics in food analysis: application to the control of forbidden substances 10.1002/dta.1349

Molecularly imprinted polymer applied to the selective isolation of urinary steroid hormones: an efficient tool in the control of natural steroid hormones abuse in cattle 10.1016/j.chroma.2012.10.067

5α-Estrane-3β,17β-diol and 5β-estrane-3α,17β-diol: definitive screening biomarkers to sign nandrolone abuse in cattle? 10.1016/j.jsbmb.2011.05.005

Assessment of two complementary liquid chromatography coupled to high resolution mass spectrometry metabolomics strategies for the screening of anabolic steroid treatment in calves 10.1016/j.aca.2011.02.008

Development and validation of an enzyme-linked immunosorbent assay for the detection of circulating antibodies raised against growth hormone as a consequence of rbST treatment in cows 10.1016/j.aca.2011.01.035

Toward a criterion for suspect thiouracil administration in animal husbandry 10.1080/19440049.2011.565483

Estranediols profiling in calves' urine after 17β-nandrolone laureate ester administration 10.1016/j.jsbmb.2010.01.012

Criteria to distinguish between natural situations and illegal use of boldenone, boldenone esters and boldione in cattle. 2. Direct measurement of 17β-boldenone sulpho-conjugate in calf urine by liquid chromatography-high resolution and tandem mass spectrometry 10.1016/j.steroids.2009.04.010

Detection and identification of 20-hydroxyecdysone metabolites in calf urine by liquid chromatography-high resolution or tandem mass spectrometry measurements and establishment of their kinetics of elimination after 20-hydroxyecdysone administration 10.1016/j.aca.2008.10.015

Development of a metabolomic approach based on liquid chromatography-high resolution mass spectrometry to screen for clenbuterol abuse in calves 10.1039/b901813a

Development of a metabonomic approach based on LC-ESI-HRMS measurements for profiling of metabolic changes induced by recombinant equine growth hormone in horse urine 10.1007/s00216-009-2912-8

Elimination kinetic of recombinant somatotropin in bovine 10.1016/j.aca.2008.09.003

Options for veterinary drug analysis using mass spectrometry 10.1016/j.chroma.2009.07.007

Detection of 20-hydroxyecdysone in calf urine by comparative liquid chromatography/high-resolution mass spectrometry and liquid chromatography/tandem mass spectrometry measurements: application to the control of the potential misuse of ecdysteroids in cattle 10.1002/rcm.3816

Detection of secondary biomarker of met-eGH as a strategy to screen for somatotropin misuse in horseracing 10.1039/b713712e

Direct determination of recombinant bovine somatotropin in plasma from a treated goat by liquid chromatography/high-resolution mass spectrometry 10.1002/rcm.3712

Elimination kinetic of 17β-estradiol 3-benzoate and 17β-nandrolone laureate ester metabolites in calves' urine 10.1016/j.jsbmb.2007.09.024

Evidence that urinary excretion of thiouracil in adult bovine submitted to a cruciferous diet can give erroneous indications of the possible illegal use of thyrostats in meat production 10.1080/02652030600806370

Unambiguous identification of thiouracil residue in urine collected in non-treated bovine by tandem and high-resolution mass spectrometry 10.1002/rcm.2711

Discrimination of recombinant and pituitary-derived bovine and porcine growth hormones by peptide mass mapping 10.1021/jf030536e

Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics 10.1016/j.copbio.2016.08.004

Selective androgen receptor modulators: comparative excretion study of bicalutamide in bovine urine and faeces 10.1002/dta.2113

Impact of storage conditions on the urinary metabolomics fingerprint 10.1016/j.aca.2016.11.055

Chapter 11 Analytical Strategies to Control the Illegal Use of Banned Growth Promoters in Meat Producing Animals 10.1016/s0166-526x(08)00011-1

Recombinant bovine somatotropin misuse in cattle 10.1016/j.aca.2004.07.063

First insights into serum metabolomics of trenbolone/estradiol implanted bovines; screening model to predict hormone-treated and control animals’ status 10.1007/s11306-015-0775-x

First mass spectrometry metabolic fingerprinting of bacterial metabolism in a model cheese 10.1016/j.foodchem.2013.03.094

Production of polyclonal antibodies directed to recombinant methionyl bovine somatotropin 10.1016/j.aca.2012.11.041

Water-extractable Arabinoxylan from Pearled Flours of Wheat, Barley, Rye and Triticale. Evidence for the Presence of Ferulic Acid Dimers and their Involvement in Gel Formation 10.1006/jcrs.2001.0392

Detection of recombinant bovine somatotropin in milk and effect of industrial processes on its stability 10.1016/j.aca.2010.04.030

Multi-residue method for the determination of thyreostats in urine samples using liquid chromatography coupled to tandem mass spectrometry after derivatisation with 3-iodobenzylbromide 10.1016/j.chroma.2005.06.055

Generation and processing of urinary and plasmatic metabolomic fingerprints to reveal an illegal administration of recombinant equine growth hormone from LC-HRMS measurements 10.1007/s11306-010-0233-8

Experimental evidence for a semi-flexible conformation for arabinoxylans 10.1016/s0008-6215(00)00300-1

Analytical strategies to detect enobosarm administration in bovines 10.1080/19440049.2016.1258122

Evaluation of specific gravity as normalization strategy for cattle urinary metabolome analysis 10.1007/s11306-013-0604-z

LC-HRMS based metabolomics screening model to detect various β-agonists treatments in bovines 10.1007/s11306-014-0705-3

LC–HRMS fingerprinting as an efficient approach to highlight fine differences in cheese metabolome during ripening 10.1007/s11306-014-0769-0

Global urine fingerprinting by LC-ESI(+)-HRMS for better characterization of metabolic pathway disruption upon anabolic practices in bovine 10.1007/s11306-014-0685-3

Screening halogenated environmental contaminants in biota based on isotopic pattern and mass defect provided by high resolution mass spectrometry profiling 10.1016/j.aca.2016.06.053

Assessment of the short-term neurobehavioral toxicity of a perinatal exposure to the hexabromocyclododecane (HBCDD) α-isomer in rats 10.1016/j.ntt.2015.04.078

Comparison of different liquid chromatography stationary phases in LC-HRMS metabolomics for the detection of recombinant growth hormone doping control 10.1002/jssc.201100223

Urinary signature of pig carcasses with boar taint by liquid chromatography-high-resolution mass spectrometry 10.1080/19440049.2016.1265152

Investigation of the distribution of arabinose residues on the xylan backbone of water-soluble arabinoxylans from wheat flour 10.1016/j.carbpol.2003.09.004

Specificity of monoclonal antibodies generated against arabinoxylans of cereal grains 10.1016/j.carbpol.2004.05.016

Analytical strategies to detect use of recombinant bovine somatotropin in food-producing animals 10.1016/j.trac.2013.08.006

Aminoaciduria Caused by Fanconi Syndrome in a Heifer 10.1111/jvim.14605

Tissue Distribution and Transfer to Eggs of Ingested α-Hexabromocyclododecane (α-HBCDD) in Laying Hens (Gallus domesticus) 10.1021/acs.jafc.5b05574

Specific characterization of non-steroidal selective androgen peceptor modulators using supercritical fluid chromatography coupled to ion-mobility mass spectrometry: application to the detection of enobosarm in bovine urine 10.1002/dta.1951

Toward a New European Threshold to Discriminate Illegally Administered from Naturally Occurring Thiouracil in Livestock 10.1021/jf504475f

APCI as an innovative ionization mode compared with EI and CI for the analysis of a large range of organophosphate esters using GC-MS/MS 10.1002/jms.3899

Identification of Recombinant Equine Growth Hormone in Horse Plasma by LC−MS/MS: A Confirmatory Analysis in Doping Control 10.1021/ac801234f

Identification of Cows Treated with Recombinant Bovine Somatotropin 10.1021/jf903032q

Micropollutants and chemical residues in organic and conventional meat 10.1016/j.foodchem.2017.04.013

Enantiomer-specific accumulation and depuration of α-hexabromocyclododecane (α-HBCDD) in chicken (Gallus gallus) as a tool to identify contamination sources 10.1016/j.chemosphere.2017.04.031

Serum-based metabolomics characterization of pigs treated with ractopamine 10.1007/s11306-017-1212-0

Hens can ingest extruded polystyrene in rearing buildings and lay eggs contaminated with hexabromocyclododecane 10.1016/j.chemosphere.2017.07.117

Analysis of thyreostats: A history of 35 years 10.1016/j.aca.2008.08.027

Effects of pan cooking on micropollutants in meat 10.1016/j.foodchem.2017.03.049

Targeted and untargeted profiling of biological fluids to screen for anabolic practices in cattle 10.1016/j.trac.2010.06.010

Accumulation of Α-hexabromocyclododecane (Α-HBCDD) in tissues of fast- and slow-growing broilers (Gallus domesticus) 10.1016/j.chemosphere.2017.03.064

Metabolomics analysis of liver reveals profile disruption in bovines upon steroid treatment 10.1007/s11306-017-1220-0

Past, present and future of mass spectrometry in the analysis of residues of banned substances in meat-producing animals 10.1002/jms.1272

Solid-phase microextraction set-up for the analysis of liver volatolome to detect livestock exposure to micropollutants 10.1016/j.chroma.2017.03.008

Isolation and characterization of high molar mass water-soluble arabinoxylans from barley and barley malt 10.1016/S0144-8617(01)00172-2

Current applications and perspectives of ion mobility spectrometry to answer chemical food safety issues 10.1016/j.trac.2017.07.006

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics 10.1007/s11306-017-1233-8

Mass spectrometry-based metabolomics applied to the chemical safety of food 10.1016/j.trac.2010.11.003

Isolation of homogeneous fractions from wheat water-soluble arabinoxylans. Influence of the structure on their macromolecular characteristics 10.1021/jf990222k

Field investigation to determine the environmental source of PCBs in a pig farm 10.1016/j.foodchem.2017.10.105

Classification of trace elements in tissues from organic and conventional French pig production 10.1016/j.meatsci.2018.02.008

Collision Cross Section (CCS) Database: An Additional Measure to Characterize Steroids 10.1021/acs.analchem.7b05117

Ochratoxin A determination in swine muscle and liver from French conventional or organic farming production systems 10.1016/j.jchromb.2018.05.040

Occurence of legacy and novel brominated flame retardants in food and feed in France for the period 2014 to 2016 10.1016/j.chemosphere.2018.05.122

Comprehensive steroid profiling by liquid chromatography coupled to high resolution mass spectrometry 10.1016/j.jsbmb.2018.06.003

Collision cross section (CCS) as a complementary parameter to characterize human and veterinary drugs 10.1016/j.aca.2018.09.065

Potential of ion mobility-mass spectrometry for both targeted and non-targeted analysis of phase II steroid metabolites in urine 10.1016/j.acax.2019.100006

Toward the characterisation of non-intentionally added substances migrating from polyester-polyurethane lacquers by comprehensive gas chromatography-mass spectrometry technologies 10.1016/j.chroma.2019.05.024

Assessment of Dechlorane Plus and related compounds in foodstuffs and estimates of daily intake from Lebanese population 10.1016/j.chemosphere.2019.06.148

Ammonium Fluoride as Suitable Additive for HILIC-Based LC-HRMS Metabolomics 10.3390/metabo9120292

Optimized characterization of short-, medium, and long-chain chlorinated paraffins in liquid chromatography-high resolution mass spectrometry 10.1016/j.chroma.2020.460927

A role for metabolomics in the antidoping toolbox? 10.1002/dta.2788

Combining mass spectrometric platforms for lipidome investigation - Application to the characterisation of disruptions in the lipid profile of pig serum upon β-agonist treatment 10.1101/2020.03.20.997189

Applying metabolomics to detect growth hormone administration in athletes: Proof of concept 10.1002/dta.2798

Characterization of Steroids through Collision Cross Sections: Contribution of Quantum Chemistry Calculations 10.1021/acs.analchem.0c00357

Addressing Main Challenges Regarding Short- and Medium-Chain Chlorinated Paraffin Analysis Using GC/ECNI-MS and LC/ESI-MS Methods 10.1021/jasms.0c00155

Combined Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry Approaches for Metabolomics 10.1021/acs.analchem.0c04371

Nontargeted LC/ESI-HRMS Detection of Polyhalogenated Compounds in Marine Mammals Stranded on French Atlantic Coasts 10.1021/acsestwater.0c00091

Dechlorane Plus and Related Compounds in Food—A Review 10.3390/ijerph18020690

Data analysis strategies for the characterization of chemical contaminant mixtures. Fish as a case study 10.1016/j.envint.2021.106610

Extending the Lipidome Coverage by Combining Different Mass Spectrometric Platforms: An Innovative Strategy to Answer Chemical Food Safety Issues 10.3390/foods10061218

Enantiomeric fraction of hexabromocyclododecanes in foodstuff from the Belgian market 10.1016/j.chemosphere.2020.127607

Rapid evaporative ionisation mass spectrometry and chemometrics for high-throughput screening of growth promoters in meat producing animals 10.1080/19440049.2017.1421778

A multidimensional H-1 NMR lipidomics workflow to address chemical food safety issues 10.1007/s11306-018-1360-x

Ion Mobility Spectrometry in Food Analysis: Principles, Current Applications and Future Trends 10.3390/molecules24152706

Modeling the fragmentation patterns of triacylglycerides in mass spectrometry allows the quantification of the regioisomers with a minimal number of standards 10.1016/j.aca.2019.01.017

Exposure assessment for dioxin-like PCBs intake from organic and conventional meat integrating cooking and digestion effects 10.1016/j.fct.2017.10.032

When LC-HRMS metabolomics gets ISO17025 accredited and ready for official controls - Application to the screening of forbidden compounds in livestock 10.1080/19440049.2018.1496280

Elucidation of non-intentionally added substances migrating from polyester-polyurethane lacquers using automated LC-HRMS data processing 10.1007/s00216-018-0968-z

HaloSeeker 1.0: A user-friendly software to highlight halogenated chemicals in nontargeted high-resolution mass spectrometry data sets 10.1021/acs.analchem.8b05103

Undernutrition combined with dietary mineral oil hastens depuration of stored dioxin and polychlorinated biphenyls in ewes. 2. Tissue distribution, mass balance and body burden 10.1371/journal.pone.0230628

Interlaboratory and Interplatform Study of Steroids Collision Cross Section by Traveling Wave Ion Mobility Spectrometry 10.1021/acs.analchem.9b05247

Levels of persistent organic pollutants (POPs) in foods from the first regional Sub-Saharan Africa Total Diet Study 10.1016/j.envint.2019.105413

Braviporc - Retardateurs de flammes bromés dans produits avicoles et porcins : état des lieux, modalités de transfert et facteurs de risques 10.15454/1.5191155195255698E12

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS 10.1101/2020.01.13.905091

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Do farming conditions influence brominated flame retardant levels in pig and poultry products? 10.1017/S1751731119003392

Occurrence of Dechlorane Plus and related compounds in catfish (Silurus spp.) from rivers in France 10.1016/j.chemosphere.2018.05.101

Nandrolone and estradiol biomarkers identification in bovine urine applying a liquid chromatography high‐resolution mass spectrometry metabolomics approach 10.1002/dta.3126

Rob Knight

Knight Rob

ORCID: 0000-0002-0975-9019

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt.3893

Current understanding of the human microbiome. 10.1038/nm.4517

Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. 10.1080/19490976.2021.1961203

Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. 10.1038/s41396-021-00935-9

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. 10.1101/2020.11.13.370387

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. 10.1101/2020.08.17.238444

Methods for phylogenetic analysis of microbiome data. 10.1038/s41564-018-0156-0

Publisher Correction: Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-018-0114-x

Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-017-0072-8

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. 10.1371/journal.pcbi.1009056

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. 10.1101/gr.275777.121

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. 10.1101/2021.07.16.452756

Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 10.1038/s41396-021-01016-7

Structure-based protein function prediction using graph convolutional networks. 10.1038/s41467-021-23303-9

Challenges in benchmarking metagenomic profilers. 10.1038/s41592-021-01141-3

Taxonomic signatures of cause-specific mortality risk in human gut microbiome. 10.1038/s41467-021-22962-y

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. 10.1111/biom.13481

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition. 10.1128/msystems.01329-20

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 10.1038/nbt.1823

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. 10.4056/aigs.1443528

Origins of the genetic code: The escaped triplet theory 10.1146/annurev.biochem.74.082803.133119

Defining the human microbiome 10.1111/j.1753-4887.2012.00493.x

Dietary prebiotics and bioactive milk fractions improve NREM sleep, enhance REM sleep rebound and attenuate the stress-induced decrease in diurnal temperature and gut microbial alpha diversity 10.3389/fnbeh.2016.00240

Meta-analyses of human gut microbes associated with obesity and IBD 10.1016/j.febslet.2014.09.039

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations 10.1128/mBio.01526-14

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment 10.1145/1646468.1646481

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill 10.1038/ismej.2013.254

Meeting report for the 1st skin microbiota workshop, boulder, co October 15-16 2012 10.1186/1944-3277-9-13

Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk 10.1017/S0007114516004165

Host remodeling of the gut microbiome and metabolic changes during pregnancy 10.1016/j.cell.2012.07.008

A distinct immunogenic region of glutamic acid decarboxylase 65 is naturally processed and presented by human islet cells to cytotoxic CD8 T cells 10.1111/cei.12436

Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities 10.1128/AEM.01996-06

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation 10.1073/pnas.0902366106

A population of Pax7-expressing muscle progenitor cells show differential responses to muscle injury dependent on developmental stage and injury extent 10.3389/fnagi.2015.00161

Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch 10.1016/j.jmb.2013.02.023

Authors' reply to Mawer and Wilcox and Mullish and Williams 10.1136/bmj.h6132

The bacterial microbiota in the oral mucosa of rural Amerindians 10.1099/mic.0.043174-0

Selection, history and chemistry: The three faces of the genetic code 10.1016/S0968-0004(99)01392-4

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species 10.1007/s00442-015-3507-z

Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems 10.1890/10-0426.1

Specification of sensory neurons occurs through diverse developmental programs functioning in the brain and spinal cord 10.1002/dvdy.24184

Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses 10.1186/s40168-016-0153-6

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges 10.1101/gr.085464.108

Tfap2 transcription factors in zebrafish neural crest development and ectodermal evolution 10.1002/jez.b.21189

Direct sequencing of the human microbiome readily reveals community differences 10.1186/gb-2010-11-5-210

Human gut microbiome viewed across age and geography 10.1038/nature11053

Sources of bacteria in outdoor air across cities in the midwestern United States 10.1128/AEM.05498-11

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity 10.3389/fmicb.2014.00298

Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice 10.1053/j.gastro.2013.01.047

Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment 10.1111/1462-2920.12539

How delivery mode and feeding can shape the bacterial community in the infant gut 10.1503/cmaj.130147

Moving pictures of the human microbiome 10.1186/gb-2011-12-5-r50

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010 10.4056/sigs.1333437

The impact of the gut microbiota on human health: An integrative view 10.1016/j.cell.2012.01.035

Forensic identification using skin bacterial communities 10.1073/pnas.1000162107

Which is more important for classifying microbial communities: Who's there or what they can do? 10.1038/ismej.2014.157

Comparison of fecal collection methods for microbiota studies in Bangladesh 10.1128/AEM.00361-17

Using the gut microbiota as a novel tool for examining colobine primate GI health 10.1016/j.gecco.2016.06.004

Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113

The ecology of the phyllosphere: Geographic and phylogenetic variability in the distribution of bacteria on tree leaves 10.1111/j.1462-2920.2010.02258.x

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins 10.1073/pnas.1000071108

Metabolie syndrome and altered gut microbiota in mice lacking toll-like receptor 5 10.1126/science.1179721

A Microbiome Foundation for the Study of Crohn's Disease 10.1016/j.chom.2017.02.012

Comparison of collection methods for fecal samples for discovery metabolomics in epidemiologic studies 10.1158/1055-9965.EPI-16-0409

Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories 10.1261/rna.2183806

Bacterial phylogeny structures soil resistomes across habitats 10.1038/nature13377

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences 10.1038/ismej.2011.208

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes 10.1111/1462-2920.13684

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice 10.1016/j.chom.2012.07.004

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers 10.1093/nar/gkn491

Evolution of mammals and their gut microbes 10.1126/science.1155725

Vertebrate genome evolution: A slow shuffle or a big bang? 10.1002/(SICI)1521-1878(199908)21:8<697::AID-BIES9>3.0.CO;2-X

Biogeography and habitat modelling of high-alpine bacteria 10.1038/ncomms1055

Vertebrate hosts as Islands: Dynamics of selection, immigration, loss, persistence, and potential function of bacteria on salamander skin 10.3389/fmicb.2016.00333

MIxS-BE: A MIxS extension defining a minimum information standard for sequence data from the built environment 10.1038/ismej.2013.176

Finding specific RNA motifs: Function in a zeptomole world? 10.1261/rna.2138803

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis 10.1016/j.biocon.2015.04.007

Convergence of gut microbiomes in myrmecophagous mammals 10.1111/mec.12501

Changes through time: Integrating microorganisms into the study of succession 10.1016/j.resmic.2010.06.002

Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples 10.1128/AEM.04137-13

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns 10.1038/nmeth.1499

The molecular basis of nuclear genetic code change in ciliates 10.1016/S0960-9822(01)00028-8

Using QIIME to analyze 16s rRNA gene sequences from microbial communities 10.1002/9780471729259.mc01e05s27

Culturing: Looking it up in our gut 10.1038/nmicrobiol.2016.169

Human oral, gut, and plaque microbiota in patients with atherosclerosis 10.1073/pnas.1011383107

Microbial eukaryotes in the human microbiome: Ecology, evolution, and future directions 10.3389/fmicb.2011.00153

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks 10.1038/nmicrobiol.2016.177

Xenobiotics and the human gut microbiome: Metatranscriptomics reveal the active players 10.1016/j.cmet.2013.02.013

Experimental and analytical tools for studying the human microbiome 10.1038/nrg3129

Cohabiting family members share microbiota with one another and with their dogs 10.7554/eLife.00458

The gut microbiota in human energy homeostasis and obesity 10.1016/j.tem.2015.07.002

EMPeror: A tool for visualizing high-throughput microbial community data 10.1186/2047-217X-2-16

Is the genetic code really a frozen accident? New evidence from in vitro selection 10.1111/j.1749-6632.1999.tb08915.x

PyCogent: A toolkit for making sense from sequence 10.1186/gb-2007-8-8-r171

Microbes do not follow the elevational diversity patterns of plants and animals 10.1890/10-1170.1

QIIME allows analysis of high-throughput community sequencing data 10.1038/nmeth.f.303

UniFrac: A new phylogenetic method for comparing microbial communities 10.1128/AEM.71.12.8228-8235.2005

Soil bacterial and fungal communities across a pH gradient in an arable soil 10.1038/ismej.2010.58

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity 10.1111/mec.12846

Subsistence strategies in traditional societies distinguish gut microbiomes 10.1038/ncomms7505

Faecal transplants 10.1136/bmj.h5149

TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata 10.1093/bioinformatics/btr517

From molecules to dynamic biological communities 10.1007/s10539-013-9364-4

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species 10.1007/s00248-017-1041-8

Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separation 10.1016/j.surg.2016.10.033

Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1 10.1371/journal.pone.0050636

The human microbiome: Eliminating the biomedical/environmental dichotomy in microbial ecology 10.1111/j.1462-2920.2006.01222_3.x

Gut microbes and the brain: Paradigm shift in neuroscience 10.1523/JNEUROSCI.3299-14.2014

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat 10.1016/j.chom.2009.08.003

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish 10.1016/j.chom.2012.08.003

A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins 10.1074/mcp.M800384-MCP200

Context and the human microbiome 10.1186/s40168-015-0117-2

Seasonal variation of postmortem microbial communities 10.1007/s12024-015-9667-7

Diversity of rickettsiales in the microbiome of the lone star tick, amblyomma americanum 10.1128/AEM.02987-13

The under-recognized dominance of Verrucomicrobia in soil bacterial communities 10.1016/j.soilbio.2011.03.012

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains 10.1371/journal.pbio.1001920

Diversity, distribution and sources of bacteria in residential kitchens 10.1111/1462-2920.12036

Gut microbiomes of Malawian twin pairs discordant for kwashiorkor 10.1126/science.1229000

Composition of human skin microbiota affects attractiveness to malaria mosquitoes 10.1371/journal.pone.0028991

Finding the Missing Links among Metabolites, Microbes, and the Host 10.1016/j.immuni.2014.05.015

Do proteins predate DNA? 10.1126/science.286.5440.690

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing 10.1038/nmeth.2276

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex 10.1038/nmeth.1184

PyNAST: A flexible tool for aligning sequences to a template alignment 10.1093/bioinformatics/btp636

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits 10.1021/acssynbio.5b00133

Bacterial colonization and succession in a newly opened hospital 10.1126/scitranslmed.aah6500

High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity 10.1053/j.gastro.2009.08.042

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease 10.1016/j.surg.2016.05.005

Development of the human gastrointestinal microbiota and insights from high-throughput sequencing 10.1053/j.gastro.2011.02.011

Alterations in the gut microbiota associated with HIV-1 infection 10.1016/j.chom.2013.08.006

Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness 10.1097/MCC.0000000000000321

Diversity, structure and convergent evolution of the global sponge microbiome 10.1038/ncomms11870

New insight into the diversity of life's building blocks: Evenness, not variance 10.1089/ast.2011.2280

Bacteria from diverse habitats colonize and compete in the mouse gut 10.1016/j.cell.2014.09.008

Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs) 10.1371/journal.pone.0054703

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives 10.1093/nar/gkq066

Mosquito microbiome dynamics, a background for prevalence and seasonality of West Nile virus 10.3389/fmicb.2017.00526

Evolutionary rates vary among rRNA structural elements 10.1093/nar/gkm101

Simple, recurring RNA binding sites for L-arginine 10.1261/rna.1979410

Rewiring the keyboard: Evolvability of the genetic code 10.1038/35047500

Widespread colonization of the lung by Tropheryma whipplei in HIV infection 10.1164/rccm.201211-2145OC

Artificial Selection: Finding Function amongst Randomized Sequences 10.1002/9783527619504.ch47

Effects of field conditions on fecal microbiota 10.1016/j.mimet.2016.09.017

Dietary effects on human gut microbiome diversity 10.1017/S0007114514004127

An Elegan(t) Screen for Drug-Microbe Interactions 10.1016/j.chom.2017.04.014

The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome 10.1186/2047-217X-1-7

Variation in the microbiota of Ixodes ticks with regard to geography, species, and sex 10.1128/AEM.01562-15

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas) 10.1038/ismej.2015.168

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection 10.1186/s40168-015-0070-0

Using QIIME to analyze 16S rrna gene sequences from microbial communities 10.1002/0471250953.bi1007s36

Sharing and archiving nucleic acid structure mapping data 10.1261/rna.2753211

Advancing analytical algorithms and pipelines for billions of microbial sequences 10.1016/j.copbio.2011.11.028

Obesity alters gut microbial ecology 10.1073/pnas.0504978102

Why microbiome treatments could pay off soon 10.1038/scientificamerican0315-S5

Pathological rate matrices: From primates to pathogens 10.1186/1471-2105-9-550

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats 10.1371/journal.pone.0125889

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes 10.1111/j.1462-2920.2010.02277.x

Advancing the microbiome research community 10.1016/j.cell.2014.09.022

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences 10.7717/peerj.545

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States 10.1126/science.1243768

Interleukin-1β (IL-1β) promotes susceptibility of toll-like receptor 5 (TLR5) deficient mice to colitis 10.1136/gut.2011.240556

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis 10.1093/bib/bbr009

Characterizing microbial communities through space and time 10.1016/j.copbio.2011.11.017

Collecting fecal samples for microbiome analyses in epidemiology studies 10.1158/1055-9965.EPI-15-0951

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle 10.1152/ajpregu.00387.2012

DNA extraction for streamlined metagenomics of diverse environmental samples 10.2144/000114559

Fecal microbiome in epidemiologic studies-response 10.1158/1055-9965.EPI-16-0161

Bacterial communities of disease vectors sampled across time, space, and species 10.1038/ismej.2009.111

The hospital microbiome project: Meeting report for the 1st hospital microbiome project workshop on sampling design and building science measurements, chicago, usa, june 7th-8th 2012 10.4056/sigs.3717348

Short-term temporal variability in airborne bacterial and fungal populations 10.1128/AEM.01467-07

Linking long-term dietary patterns with gut microbial enterotypes 10.1126/science.1208344

Evidence for a persistent microbial seed bank throughout the global ocean 10.1073/pnas.1217767110

Metagenomic covariation along densely sampled environmental gradients in the Red Sea 10.1038/ismej.2016.99

How biologists conceptualize genes: An empirical study 10.1016/j.shpsc.2004.09.005

Worlds within worlds: Evolution of the vertebrate gut microbiota 10.1038/nrmicro1978

Ribosomal RNA, the lens into life 10.1261/rna.050799.115

Sequencing our way towards understanding global eukaryotic biodiversity 10.1016/j.tree.2011.11.010

Stress response, gut microbial diversity and sexual signals correlate with social interactions 10.1098/rsbl.2016.0352

Size, constant sequences, and optimal selection 10.1261/rna.2161305

Rethinking enterotypes 10.1016/j.chom.2014.09.013

tRNA creation by hairpin duplication 10.1007/s00239-004-0315-1

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease 10.1016/j.cell.2016.11.018

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample 10.1073/pnas.1000080107

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision 10.1038/ismej.2015.235

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (plethodon cinereus) 10.1038/ismej.2013.200

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water 10.1016/j.watres.2014.11.003

RNA-amino acid binding: A stereochemical era for the genetic code 10.1007/s00239-009-9270-1

Short pyrosequencing reads suffice for accurate microbial community analysis 10.1093/nar/gkm541

Heritable components of the human fecal microbiome are associated with visceral fat 10.1186/s13059-016-1052-7

Genetic Determinants of the Gut Microbiome in UK Twins 10.1016/j.chom.2016.04.017

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) 10.1186/1471-2180-13-114

Succession of microbial consortia in the developing infant gut microbiome 10.1073/pnas.1000081107

Dynamics of the human gut microbiome in inflammatory bowel disease 10.1038/nmicrobiol.2017.4

The founding charter of the Genomic Observatories Network 10.1186/2047-217X-3-2

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses 10.1038/ismej.2008.127

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans 10.1126/science.1198719

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples 10.1111/j.1574-6968.2010.01965.x

RNA structure prediction from evolutionary patterns of nucleotide composition 10.1093/nar/gkn987

Genetic and environmental control of host-gut microbiota interactions 10.1101/gr.194118.115

Analysis of membrane proteins from human chronic myelogenous leukemia cells: Comparison of extraction methods for multidimensional LC-MS/MS 10.1021/pr050313z

Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code 10.1007/s00239-004-0314-2

Comparison of methods for estimating the nucleotide substitution matrix 10.1186/1471-2105-9-511

From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal 10.1261/rna.881308

Tools for the microbiome: Nano and beyond 10.1021/acsnano.5b07826

Database-Driven Grid Computing and Distributed Web Applications: A Comparison 10.1002/9780470191637.ch11

Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data 10.1016/J.ENG.2017.01.020

Estimate of the abundance of cardiomyopathic mutations in the β-myosin gene 10.1016/j.ijcard.2008.12.199

Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA 10.1261/rna.2220210

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation 10.1016/j.tim.2011.07.006

Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis 10.1111/j.1365-294X.2012.05552.x

Keemei: Cloud-based validation of tabular bioinformatics file formats in Google Sheets 10.1186/s13742-016-0133-6

Vertebrate decomposition is accelerated by soil microbes 10.1128/AEM.00957-14

Satellite remote sensing data can be used to model marine microbial metabolite turnover 10.1038/ismej.2014.107

Diversity, stability and resilience of the human gut microbiota 10.1038/nature11550

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau 10.1111/j.1462-2920.2012.02799.x

Bacterial communities associated with the lichen symbiosis 10.1128/AEM.02257-10

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood 10.1101/gr.140608.112

Guilt by association: The arginine case revisited 10.1017/S1355838200000145

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest 10.1038/ismej.2014.36

Global patterns in bacterial diversity 10.1073/pnas.0611525104

Fast find: A novel computational approach to analyzing combinatorial motifs 10.1186/1471-2105-7-1

Predictive modeling of gingivitis severity and susceptibility via oral microbiota 10.1038/ismej.2014.32

Conceptualizing a Genomics Software Institute (GSI) 10.4056/sigs.2485911

Tracking down the sources of experimental contamination in microbiome studies 10.1186/s13059-014-0564-2

Replenishing our defensive microbes 10.1002/bies.201300018

Insights from Characterizing Extinct Human Gut Microbiomes 10.1371/journal.pone.0051146

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome 10.1371/journal.pbio.1001377

Unlocking the potential of metagenomics through replicated experimental design 10.1038/nbt.2235

Tiny microbes, enormous impacts: What matters in gut microbiome studies? 10.1186/s13059-016-1086-x

ConStrains identifies microbial strains in metagenomic datasets 10.1038/nbt.3319

Microbial community assembly and metabolic function during mammalian corpse decomposition 10.1126/science.aad2646

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome 10.1002/mds.26942

PH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils 10.1016/j.soilbio.2014.03.014

Fat and vitamin intakes during pregnancy have stronger relations with a proinflammatory maternal microbiota than does carbohydrate intake 10.1186/s40168-016-0200-3

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents 10.1038/ismej.2012.81

Microbiology of death 10.1016/j.cub.2016.03.042

A meta-analysis of changes in bacterial and archaeal communities with time 10.1038/ismej.2013.54

PrimerProspector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers 10.1093/bioinformatics/btr087

SnapShot: The Human Microbiome 10.1016/j.cell.2014.07.019

Microbial Skin Inhabitants: Friends Forever 10.1016/j.cell.2016.04.035

The microbiome explored: Recent insights and future challenges 10.1038/nrmicro2973

Supervised classification of microbiota mitigates mislabeling errors 10.1038/ismej.2010.148

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics 10.1021/ac035229m

Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease 10.1109/BigData.2016.7840731

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms 10.1038/ismej.2012.8

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate 10.1007/s00248-017-0938-6

Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei 10.1128/AEM.00447-09

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study 10.1097/PSY.0000000000000512

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys 10.1038/ismej.2011.186

Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences 10.1038/ismej.2011.187

The Earth Microbiome project: Successes and aspirations 10.1186/s12915-014-0069-1

Microbial biogeography of public restroom surfaces 10.1371/journal.pone.0028132

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer 10.1038/nm.4039

Mathematical approaches for describing microbial populations: Practice and theory for extrapolation of rich environments 10.1002/9781118409855.ch4

Meeting report of the RNA ontology consortium January 8-9, 2011 10.4056/sigs.1724282

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life 10.3945/ajcn.115.115451

Prevalence and genetic diversity of Blastocystis in family units living in the United States 10.1016/j.meegid.2016.08.018

Ancient human oral plaque preserves a wealth of biological data 10.1038/ng.2930

Examining the global distribution of dominant archaeal populations in soil 10.1038/ismej.2010.171

A lightweight, scalable grid computing framework for parallel bioinformatics applications 10.1109/HPCS.2005.7

Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness 10.1371/journal.pone.0096375

Activating and inhibiting connections in biological network dynamics 10.1186/1745-6150-3-49

Microbiota at multiple body sites during pregnancy in a rural tanzanian population and effects of Moringa-supplemented probiotic yogurt 10.1128/AEM.00780-15

Temporal variability is a personalized feature of the human microbiome 10.1186/s13059-014-0531-y

Can Your Microbiome Tell You What to Eat? 10.1016/j.cmet.2015.11.009

Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon 10.1371/journal.pone.0073140

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics 10.1186/1471-2148-8-327

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments 10.1038/ismej.2010.167

MotifCluster: An interactive online tool for clustering and visualizing sequences using shared motifs 10.1186/gb-2008-9-8-r128

Longitudinal analysis of microbial interaction between humans and the indoor environment 10.1126/science.1254529

The influence of sex, handedness, and washing on the diversity of hand surface bacteria 10.1073/pnas.0807920105

Human genetics shape the gut microbiome 10.1016/j.cell.2014.09.053

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity 10.1128/mBio.01371-14

Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape 10.1371/journal.pone.0173811

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system 10.7554/eLife.01104.001

Gut microbiota from twins discordant for obesity modulate metabolism in mice 10.1126/science.1241214

Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil 10.1016/j.soilbio.2010.02.003

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags 10.1186/1471-2180-10-206

The 'rare biosphere': A reality check 10.1038/nmeth0909-636

Variable responses of human and non-human primate gut microbiomes to a Western diet 10.1186/s40168-015-0120-7

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences 10.1038/nbt.2676

Global patterns in the biogeography of bacterial taxa 10.1111/j.1462-2920.2010.02315.x

RNASTAR: An RNA structural alignment repository that provides insight into the evolution of natural and artificial RNAs 10.1261/rna.032052.111

Spatial and temporal variability of the human microbiota 10.1111/j.1469-0691.2012.03861.x

Cross-biome comparison of microbial association networks 10.3389/fmicb.2015.01200

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice 10.1016/j.cmet.2012.12.007

Mass spectrometry based molecular 3D-cartography of plant metabolites 10.3389/fpls.2017.00429

Comparison of Collection Methods for Fecal Samples in Microbiome Studies 10.1093/aje/kww177

Translating the human microbiome 10.1038/nbt.2543

Specialized metabolites from the microbiome in health and disease 10.1016/j.cmet.2014.10.016

The treatment-naive microbiome in new-onset Crohn's disease 10.1016/j.chom.2014.02.005

Molecular cartography of the human skin surface in 3D 10.1073/pnas.1424409112

Reports of the death of the gene are greatly exaggerated 10.1007/s10539-006-9039-5

Antibiotic discovery is a walk in the park 10.1073/pnas.1618221114

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota 10.1038/ismej.2015.64

Natural and artificial RNAs occupy the same restricted region of sequence space 10.1261/rna.1923210

Stable tRNA-based phylogenies using only 76 nucleotides 10.1261/rna.726010

The microbiome quality control project: Baseline study design and future directions 10.1186/s13059-015-0841-8

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis 10.1371/journal.ppat.0040020

Normalization and microbial differential abundance strategies depend upon data characteristics 10.1186/s40168-017-0237-y

Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere 10.1371/journal.pone.0073079

TaskSpaces: A Software Framework for Parallel Bioinformatics on Computational Grids 10.1002/0471756504.ch26

Anal gas evacuation and colonic microbiota in patients with flatulence: Effect of diet 10.1136/gutjnl-2012-303013

Unique strain of Rickettsia parkeri associated with the hard tick Dermacentor parumapertus Neumann in the western United States 10.1128/AEM.03463-16

A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease 10.1371/journal.pone.0080702

Bringing the Dynamic Microbiome to Life with Animations 10.1016/j.chom.2016.12.009

The Human Microbiome Project 10.1038/nature06244

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota 10.1073/pnas.1306070110

Multilevel research strategies and biological systems 10.1086/677889

Microbiota and host nutrition across plant and animal kingdoms 10.1016/j.chom.2015.04.009

What is the value of a food and drug administration investigational new drug application for fecal microbiota transplantation to treat clostridium difficile infection? 10.1016/j.cgh.2013.10.009

Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns 10.1099/mic.0.2007/011833-0

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations 10.1038/ismej.2011.129

Our microbial selves: What ecology can teach us 10.1038/embor.2011.137

Postprandial remodeling of the gut microbiota in Burmese pythons 10.1038/ismej.2010.71

Parallel evolution of the genetic code in arthropod mitochondrial genomes 10.1371/journal.pbio.0040127

Origin of microbial biomineralization and magnetotaxis during the Archean 10.1073/pnas.1614654114

UCHIME improves sensitivity and speed of chimera detection 10.1093/bioinformatics/btr381

Parallel mapping of antibiotic resistance alleles in Escherichia coli 10.1371/journal.pone.0146916

Individual diet has sex-dependent effects on vertebrate gut microbiota 10.1038/ncomms5500

Conducting a microbiome study 10.1016/j.cell.2014.06.037

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake 10.1101/gr.107987.110

Boulder ALignment editor (ALE): A web-based RNA alignment tool 10.1093/bioinformatics/btr258

Insights and inferences about integron evolution from genomic data 10.1186/1471-2164-9-261

CodonExplorer: An interactive online database for the analysis of codon usage and sequence composition 10.1007/978-1-59745-251-9_10

Bioinformatics Assessment of β-Myosin Mutations Reveals Myosin's High Sensitivity to Mutations 10.1016/j.tcm.2008.04.001

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea 10.1038/ismej.2011.139

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites 10.1016/j.jaci.2012.03.010

Responses of gut microbiota to diet composition and weight loss in lean and obese mice 10.1038/oby.2011.111

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil 10.1128/AEM.00358-07

The RNA structure alignment ontology 10.1261/rna.1601409

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch) 10.1111/ele.12301

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project 10.4056/sigs.1433550

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota 10.1016/j.chom.2015.08.005

The genomic standards consortium: Bringing standards to life for microbial ecology 10.1038/ismej.2011.39

The long-term stability of the human gut microbiota 10.1126/science.1237439

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins 10.1126/scitranslmed.3002701

Carcass mass has little influence on the structure of gravesoil microbial communities 10.1007/s00414-015-1206-2

Supervised classification of human microbiota 10.1111/j.1574-6976.2010.00251.x

A core gut microbiome in obese and lean twins 10.1038/nature07540

Defining seasonal marine microbial community dynamics 10.1038/ismej.2011.107

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons 10.1101/gr.112730.110

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks 10.1016/j.mimet.2015.03.021

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions 10.1038/nmeth0910-668b

Euphorbia plant latex is inhabited by diverse microbial communities 10.3732/ajb.1500223

Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data 10.1038/ismej.2009.97

Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy 10.7554/eLife.11405.001

An ancient origin of magnetotactic bacteria 10.1073/pnas.1707301114

Global biogeography of highly diverse protistan communities in soil 10.1038/ismej.2012.147

Evolution of Symbiotic Bacteria in the Distal Human Intestine 10.1371/journal.pbio.0050156

Advancing our understanding of the human microbiome using QIIME 10.1016/B978-0-12-407863-5.00019-8

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae 10.7554/eLife.24214

BayesFold: Rational 2° folds that combine thermodynamic, covariation; and chemical data for aligned RNA sequences 10.1261/rna.5168504

The amphibian skin-associated microbiome across species, space and life history stages 10.1111/mec.12510

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer 10.1038/ismej.2012.26

Meta-analyses of studies of the human microbiota 10.1101/gr.151803.112

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice 10.1073/pnas.1600324113

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids 10.1093/nar/gki886

Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings 10.1016/j.antiviral.2013.12.004

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data 10.3233/AO-2011-0082

Microbiota restoration: Natural and supplemented recovery of human microbial communities 10.1038/nrmicro2473

Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids 10.1016/j.febslet.2005.05.038

Multiple pattern matching: A Markov chain approach 10.1007/s00285-007-0109-3

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities 10.1371/journal.pone.0047879

Microbiome Tools for Forensic Science 10.1016/j.tibtech.2017.03.006

Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli 10.1002/bit.26217

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys 10.1038/ismej.2011.82

Lake microbial communities are resilient after a whole-ecosystem disturbance 10.1038/ismej.2012.56

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta) 10.1002/ajp.22555

Bacterial community structures are unique and resilient in full-scale bioenergy systems 10.1073/pnas.1015676108

Structural basis for diversity in the SAM clan of riboswitches 10.1073/pnas.1312918111

Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow Nests 10.1007/s00248-013-0338-5

Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850

The Ecology of Microbial Communities Associated with Macrocystis pyrifera 10.1371/journal.pone.0067480

Does protein structure influence trypsin miscleavage? 10.1109/MEMB.2005.1436461

HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats 10.1371/journal.pone.0105684

Toward effective probiotics for autism and other neurodevelopmental disorders 10.1016/j.cell.2013.11.035

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns 10.1073/pnas.1002601107

Species divergence and the measurement of microbial diversity 10.1111/j.1574-6976.2008.00111.x

Microbial endocrinology: The interplay between the microbiota and the endocrine system 10.1093/femsre/fuu010

Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newborn 10.1073/pnas.1012458107

Bayesian community-wide culture-independent microbial source tracking 10.1038/nmeth.1650

MICROBIOME. A unified initiative to harness Earth's microbiomes. 10.1126/science.aac8480

How mitochondria redefine the code 10.1007/s002390010220

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets 10.1371/journal.pcbi.1002863

Walls talk: Microbial biogeography of homes spanning urbanization 10.1126/sciadv.1501061

CodonExplorer: An online tool for analyzing codon usage and sequence composition, scaling from genes to genomes 10.1093/bioinformatics/btp141

Biphasic assembly of the murine intestinal microbiota during early development 10.1038/ismej.2013.15

SitePainter: A tool for exploring biogeographical patterns 10.1093/bioinformatics/btr685

Bacterial community variation in human body habitats across space and time 10.1126/science.1177486

Human immunodeficiency virus nef signature sequences are associated with pulmonary hypertension 10.1089/aid.2011.0021

The unifrac significance test is sensitive to tree topology 10.1186/s12859-015-0640-y

Host-associated and free-living phage communities differ profoundly in phylogenetic composition 10.1371/journal.pone.0016900

Human-associated microbial signatures: Examining their predictive value 10.1016/j.chom.2011.09.003

Key challenges in proteomics and proteoinformatics 10.1109/MEMB.2005.1436456

The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice 10.1126/scitranslmed.3000322

Toward a predictive understanding of earth’s microbiomes to address 21st century challenges 10.1128/mBio.00714-16

A preliminary survey of lichen associated eukaryotes using pyrosequencing 10.1017/S0024282911000648

The convergence of carbohydrate active gene repertoires in human gut microbes 10.1073/pnas.0807339105

Analysis of the gut microbiota in the old order amish and its relation to the metabolic syndrome 10.1371/journal.pone.0043052

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011 10.4056/sigs.2134923

Using the nucleotide substitution rate matrix to detect horizontal gene transfer 10.1186/1471-2105-7-476

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat 10.1038/ismej.2012.79

Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity 10.1098/rspb.2016.1553

Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale 10.1128/AEM.00335-09

Precision medicine in alcoholic and nonalcoholic fatty liver disease via modulating the gut microbiota 10.1152/ajpgi.00245.2016

The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework 10.3390/ijms10114723

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts 10.1101/gr.138198.112

The intestinal metabolome: An intersection between microbiota and host 10.1053/j.gastro.2014.03.001

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins 10.1073/pnas.1002355107

Genomic standards consortium projects 10.4056/sigs.5559680

UniFrac: An effective distance metric for microbial community comparison 10.1038/ismej.2010.133

Let researchers try new paths 10.1038/538451a

Host-bacterial coevolution and the search for new drug targets 10.1016/j.cbpa.2008.01.015

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients 10.1038/ismej.2011.159

Technology and techniques for microbial ecology via DNA sequencing 10.1513/AnnalsATS.201306-160MG

The Western English Channel contains a persistent microbial seed bank 10.1038/ismej.2011.162

DivergentSet, a tool for picking non-redundant sequences from large sequence collections 10.1074/mcp.T600022-MCP200

The Genomic Standards Consortium 10.1371/journal.pbio.1001088

UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context 10.1186/1471-2105-7-371

Life through a microbial lens 10.1007/s11016-009-9288-4

Why microbiome treatments could pay off soon 10.1038/518S5a

The Microbiome and Human Biology. 10.1146/annurev-genom-083115-022438

Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort". 10.1128/msystems.00023-17

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. 10.1186/s40168-017-0269-3

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. 10.1128/msystems.00195-16

Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. 10.1158/1940-6207.capr-17-0010

Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-Oxide. 10.1165/rcmb.2017-0086oc

Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes". 10.1128/msphere.00296-17

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Oral probiotic versus placebo and the maternal microbiome during pregnancy: A randomized controlled trial 10.1016/j.ajog.2019.11.064

Using microbiome tools for estimating the postmortem interval 10.1016/B978-0-12-815379-6.00012-X

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. 10.1128/mbio.02901-19

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue 10.1111/1556-4029.13949

Fructose stimulated de novo lipogenesis is promoted by inflammation 10.1038/s42255-020-0261-2

The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences 10.1016/j.chom.2020.06.022

The emergence of microbiome centres 10.1038/s41564-019-0644-x

Expanding the scope and scale of microbiome research 10.1186/s13059-019-1804-2

Are microbiome studies ready for hypothesis-driven research? 10.1016/j.mib.2018.07.002

Molecular and microbial microenvironments in chronically diseased lungs associated with cystic fibrosis 10.1128/mSystems.00375-19

Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice 10.1113/JP277336

Gut microbiome in serious mental illnesses: A systematic review and critical evaluation 10.1016/j.schres.2019.08.026

Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India 10.1128/mSphere.00731-20

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes 10.1038/s41396-018-0175-0

Major shifts in gut microbiota during development and its relationship to growth in ostriches 10.1111/mec.15087

Voices in methods development 10.1038/s41592-019-0585-6

Engineering the microbiome for animal health and conservation 10.1177/1535370219830075

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces 10.1186/s40168-019-0666-x

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity 10.1186/s13059-019-1831-z

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020

The microbiome and its potential for pharmacology 10.1007/164_2019_317

Age- And sex-dependent patterns of gut microbial diversity in human adults 10.1128/mSystems.00261-19

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice 10.1016/j.cell.2019.05.004

Reply to Sun et al., “Identifying composition novelty in microbiome studies: Improvement of prediction accuracy” 10.1128/mBio.01234-19

Effects of the microalgae Chlamydomonas on gastrointestinal health 10.1016/j.jff.2019.103738

Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media 10.1093/gigascience/giaa156

Association of Loneliness and Wisdom With Gut Microbial Diversity and Composition: An Exploratory Study 10.3389/fpsyt.2021.648475

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics 10.1038/s41587-020-0660-7

Comparison of oral collection methods for studies of microbiota 10.1158/1055-9965.EPI-18-0312

Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00901-19

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome 10.1371/journal.pone.0229001

Redbiom: A rapid sample discovery and feature characterization system 10.1128/mSystems.00215-19

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort 10.1128/mBio.01751-18

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks 10.1371/journal.pcbi.1007007

Reply to Moossavi and Azad, “quantifying and interpreting the association between early-life gut microbiota composition and childhood obesity” 10.1128/MBIO.00047-19

Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus 10.1038/s41396-018-0214-x

Quantifying and understanding well-to-well contamination in microbiome research 10.1128/mSystems.00186-19

Preserving microbial diversity. 10.1126/science.aau8816

Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis. 10.4049/jimmunol.1800614

GABA-modulating bacteria of the human gut microbiota 10.1038/s41564-018-0307-3

Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude 10.1145/3311790.3399614

Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing 10.1021/acs.est.0c07952

Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice 10.3389/fpsyt.2020.00518

Publisher Correction: The gut-liver axis and the intersection with the microbiome. 10.1038/s41575-018-0031-8

Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis 10.1016/j.eurpsy.2018.05.011

The microbiome and human cancer 10.1126/science.abc4552

Best practices for analysing microbiomes 10.1038/s41579-018-0029-9

Consent insufficient for data release−Response 10.1126/science.aax7509

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans 10.1016/j.cell.2020.09.009

Microbial biogeography and ecology of the mouth and implications for periodontal diseases 10.1111/prd.12268

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota 10.1038/s41467-018-05284-4

Erratum to: The sponge microbiome project. 10.1093/gigascience/giy145

Guiding longitudinal sampling in IBD cohorts 10.1136/gutjnl-2017-315352

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease 10.1038/s41467-019-09455-9

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3

High-throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county 10.1128/MSYSTEMS.00045-21

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians 10.1016/j.cgh.2018.09.017

Coordinating and assisting research at the SARS-CoV-2/ microbiome nexus 10.1128/MSYSTEMS.00999-20

Expanding magnetic organelle biogenesis in the domain Bacteria 10.1186/s40168-020-00931-9

Toward unrestricted use of public genomic data 10.1126/science.aaw1280

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection 10.1186/s40168-021-01026-9

Single-cell transcriptomics reveal a correlation between genome architecture and gene family evolution in ciliates 10.1128/mBio.02524-19

Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease 10.1073/pnas.2017129117

Ground beef microbiome changes with antimicrobial decontamination interventions and product storage 10.1371/journal.pone.0217947

Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a “Two Hit” Stressor Model 10.3389/fphys.2020.524833

Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) 10.1177/0022034519881978

SARS-CoV-2 Screening among Symptom-Free Healthcare Workers 10.1017/ice.2021.81

Links between gut microbiome composition and fatty liver disease in a large population sample 10.1080/19490976.2021.1888673

Docent: Transforming personal intuitions to scientific hypotheses through content learning and process training 10.1145/3231644.3231646

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity 10.1093/ibd/izaa262

Home chemical and microbial transitions across urbanization 10.1038/s41564-019-0593-4

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome 10.1038/s41598-019-49823-5

Evaluating metagenomic prediction of the metaproteome in a 4.5-year study of a patient with Crohn’s disease 10.1128/MSYSTEMS.00337-18

SHOGUN: A modular, accurate and scalable framework for microbiome quantification 10.1093/bioinformatics/btaa277

CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection 10.1073/pnas.2003656117

Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets 10.1128/MSYSTEMS.01216-20

Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study 10.1111/cts.12785

Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment 10.1093/sleep/zsz113

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024

Reduced independence in daily living is associated with the gut microbiome in people with HIV and HCV 10.1128/mSystems.00528-20

Host variables confound gut microbiota studies of human disease 10.1038/s41586-020-2881-9

High-Resolution longitudinal dynamics of the cystic fibrosis sputum microbiome and metabolome through antibiotic therapy 10.1128/mSystems.00292-20

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing 10.1038/s41592-020-01041-y

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes 10.1186/s40168-020-00857-2

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities 10.1016/j.cels.2019.09.004

Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria 10.1128/mSystems.00083-18

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6

Disease-modifying therapies alter gut microbial composition in MS 10.1212/NXI.0000000000000517

Current Concepts, Opportunities, and Challenges of Gut Microbiome-Based Personalized Medicine in Nonalcoholic Fatty Liver Disease 10.1016/j.cmet.2020.11.010

Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi 10.1002/ajp.22989

Large-scale replicated field study of maize rhizosphere identifies heritable microbes 10.1073/pnas.1800918115

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models. 10.1038/s41591-018-0219-z

Three-dimensional culture of oral progenitor cells: Effects on small extracellular vesicles production and proliferative function 10.1111/jop.12981

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017 10.1186/s40168-018-0596-z

Human skin, oral, and gut microbiomes predict chronological age 10.1128/mSystems.00630-19

Identifying and predicting novelty in microbiome studies 10.1128/mBio.02099-18

Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry 10.1053/j.gastro.2020.09.038

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media 10.1038/s41597-019-0331-z

High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity 10.1128/mSystems.00166-18

Species-level functional profiling of metagenomes and metatranscriptomes 10.1038/s41592-018-0176-y

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases 10.1038/s41586-019-1237-9

Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes 10.1056/NEJMoa2003697

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 10.1038/s41467-020-16366-7

Is there convergence of gut microbes in blood-feeding vertebrates? 10.1098/rstb.2018.0249

The genetic basis for adaptation of modeldesigned syntrophic co-cultures 10.1371/journal.pcbi.1006213

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information 10.1101/gr.260380.119

Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes 10.1128/AEM.00369-19

Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908

ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7

Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0

Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study 10.1002/ijc.33473

Microbe-metabolite associations linked to the rebounding murine gut microbiome postcolonization with vancomycin-resistant enterococcus faecium 10.1128/mSystems.00452-20

A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children 10.1128/mSystems.00293-19

Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the Apc^Min^/+ mouse model 10.1002/ijc.33477

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data 10.1002/cpbi.100

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9

Striped UniFrac: enabling microbiome analysis at unprecedented scale 10.1038/s41592-018-0187-8

Role of the microbiome in human development 10.1136/gutjnl-2018-317503

Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9

The gut microbiome, aging, and longevity: A systematic review 10.3390/nu12123759

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media 10.1038/s41597-019-0051-4

Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome 10.3389/fphys.2021.663950

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations 10.1016/j.tim.2018.11.003

A distinct microbiome signature in posttreatment lyme disease patients 10.1128/mBio.02310-20

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1186/s40168-020-00960-4

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004

Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis 10.1177/1352458520924594

Exposure to toxic metals triggers unique responses from the rat gut microbiota 10.1038/s41598-018-24931-w

Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9

Farm-like indoor microbiota in non-farm homes protects children from asthma development 10.1038/s41591-019-0469-4

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/gr.265645.120

Creating a 3D microbial and chemical snapshot of a human habitat. 10.1038/s41598-018-21541-4

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. 10.1371/journal.pntd.0006344

Microbiome and metagenome analyses of a closed habitat during human occupation 10.1128/mSystems.00367-20

Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations 10.1371/journal.pone.0224757

Temporal, environmental, and biological drivers of the mucosal microbiome in a Wild Marine Fish, Scomber japonicus 10.1128/MSPHERE.00401-20

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month 10.1186/s40168-019-0645-2

Altered Gut Microbiota and Host Metabolite Profiles in Women with Human Immunodeficiency Virus 10.1093/cid/ciz1117

Multiple-disease detection and classification across cohorts via microbiome search 10.1128/mSystems.00150-20

Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. 10.1186/s13059-020-01970-z

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection 10.1084/jem.20192276

Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk 10.1016/j.bbi.2020.10.003

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary 10.2144/btn-2018-0192

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States 10.1016/j.cell.2021.03.052

Regional variation limits applications of healthy gut microbiome reference ranges and disease models 10.1038/s41591-018-0164-x

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus 10.1186/s12866-018-1341-2

Learning representations of microbe–metabolite interactions 10.1038/s41592-019-0616-3

Establishing microbial composition measurement standards with reference frames 10.1038/s41467-019-10656-5

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny 10.1186/s13059-019-1807-z

American Gut: An open platform for citizen science microbiome research 10.1128/MSYSTEMS.00031-18

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities 10.2144/BTN-2020-0153

Author Correction: Inflammation-induced IgA⁺ cells dismantle anti-liver cancer immunity. 10.1038/s41586-018-0304-y

Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing 10.1016/j.envint.2020.105604

Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations 10.1053/j.gastro.2019.11.305

Calour: an Interactive, Microbe-Centric Analysis Tool 10.1128/MSYSTEMS.00269-18

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects 10.1016/j.schres.2018.09.014

Challenges in the construction of knowledge bases for human microbiome-disease associations 10.1186/s40168-019-0742-2

Evaluating organism-wide changes in the metabolome and microbiome following a single dose of antibiotic 10.1128/MSYSTEMS.00340-20

Links between environment, diet, and the hunter-gatherer microbiome 10.1080/19490976.2018.1494103

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism 10.1038/s41467-018-05336-9

The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment 10.3389/fmicb.2020.02015

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4

Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1

A novel sparse compositional technique reveals microbial perturbations 10.1128/MSYSTEMS.00016-19

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study 10.1038/s41598-020-59016-0

Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load 10.1128/MSYSTEMS.01182-20

Associations of the fecal microbial proteome composition and proneness to diet-induced obesity 10.1074/mcp.RA119.001623

Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics 10.1093/gbe/evy133

Early-life gut dysbiosis linked to juvenile mortality in ostriches 10.1186/s40168-020-00925-7

Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures 10.1016/j.cell.2020.07.040

Species abundance information improves sequence taxonomy classification accuracy 10.1038/s41467-019-12669-6

Organ-level protein networks as a reference for the host effects of the microbiome 10.1101/gr.256875.119

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893) 10.1038/nbt0718-660d

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota 10.1038/s41597-020-00656-2

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1128/mSystems.00635-19

Animal Models for Microbiome Research and Drug Discovery 10.1016/j.ddmod.2019.09.001

FXR Regulates Intestinal Cancer Stem Cell Proliferation 10.1016/j.cell.2019.01.036

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months 10.1093/ajcn/nqaa011

Intermittent hypoxia and hypercapnia reproducibly change the gut microbiome and metabolome across rodent model systems 10.1128/mSystems.00058-19

Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 10.1186/s40168-020-00951-5

Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals 10.1161/JAHA.120.016641

Longitudinal survey of microbiome associated with particulate matter in a megacity 10.1186/s13059-020-01964-x

Early-career scientists shaping the world 10.1128/mSystems.00196-19

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z

The gut-liver axis and the intersection with the microbiome 10.1038/s41575-018-0011-z

A gut bacterial amyloid promotes a-synuclein aggregation and motor impairment in mice 10.7554/eLife.53111

Leveling up citizen science 10.1038/s41587-020-0694-x

Evaluating the information content of shallow shotgun metagenomics 10.1128/mSystems.00069-18

Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study 10.1016/j.envres.2021.111084

Depression in individuals coinfected with HIV and HCV is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00465-20

Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota 10.1038/s41396-020-00855-0

Microbial ecology of atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota 10.1128/AEM.00411-20

Handwashing and detergent treatment greatly reduce SARS-CoV-2 viral load on halloween candy handled by COVID-19 patients 10.1128/mSystems.01074-20

Author Correction: Farm-like indoor microbiota in non-farm homes protects children from asthma development. 10.1038/s41591-019-0546-8

The Effects of Captivity on the Mammalian Gut Microbiome. 10.1093/icb/icx090

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0218-196a

Leukotriene B₄-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. 10.1080/2162402x.2017.1361593

Genetic influences on the human oral microbiome. 10.1186/s12864-017-4008-8

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. 10.1126/science.aan4834

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. 10.1073/pnas.1711235114

Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection. 10.1021/acs.analchem.7b02423

The sponge microbiome project. 10.1093/gigascience/gix077

Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants. 10.1093/icb/icx088

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. 10.1038/nbt.3981

Impacts of the Human Gut Microbiome on Therapeutics. 10.1146/annurev-pharmtox-042017-031849

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. 10.1128/msystems.00093-17

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. 10.1038/nature24485

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. 10.1128/mbio.01343-17

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. 10.1371/journal.pone.0184336

A communal catalogue reveals Earth's multiscale microbial diversity. 10.1038/nature24621

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. 10.1016/j.chom.2017.10.001

Evaluating the impact of domestication and captivity on the horse gut microbiome. 10.1038/s41598-017-15375-9

Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/nature25028

Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes. 10.1128/msystems.00092-17

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. 10.1111/1365-2656.12781

Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). 10.1128/mbio.01836-17

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. 10.1128/msystems.00188-17

Expanding our Understanding of the Role of the Microbiome in Health and Disease. 10.1016/j.arcmed.2018.02.002

Bacterial density rather than diversity correlates with hatching success across different avian species. 10.1093/femsec/fiy022

Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. 10.1073/pnas.1712337115

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. 10.3390/genes9020104

Improving saliva shotgun metagenomics by chemical host DNA depletion. 10.1186/s40168-018-0426-3

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. 10.1128/msystems.00218-17

Bacterial community changes in an industrial algae production system. 10.1016/j.algal.2017.09.010

Earth Microbiome Project and Global Systems Biology. 10.1128/msystems.00217-17

Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. 10.1093/femsec/fiy063

Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space. 10.1089/bfm.2018.29072.rjk

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. 10.1128/msystems.00021-18

Gut microbiota utilize immunoglobulin A for mucosal colonization. 10.1126/science.aaq0926

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. 10.1186/s40168-018-0470-z

Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. 10.1016/j.cels.2018.04.010

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome. 10.1128/msystems.00020-18

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. 10.3389/fmicb.2018.02559

Microbiota as in farm homes protect children from asthma 10.1183/13993003.congress-2018.oa337

Diet and the Gut Microbiome in 10–18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19) 10.1093/cdn/nzz040.or01-08-19

Neighborhoods to Nucleotides—Advances and Gaps for an Obesity Disparities Systems Epidemiology Model 10.1007/s40471-019-00221-5

Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054

Visualizing 'omic feature rankings and log-ratios using Qurro. 10.1093/nargab/lqaa023

A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis. 10.1016/j.cmet.2020.06.005

Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort. 10.1158/1055-9965.epi-20-0824

Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos. 10.1093/ajcn/nqab001

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. 10.21203/rs.3.rs-56028/v1

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 10.1101/2021.02.06.21251159

The early evolution of the genetic code. 10.1016/s0092-8674(00)80866-1

Measuring adaptation within the genetic code. 10.1016/s0968-0004(99)01531-5

Early fixation of an optimal genetic code. 10.1093/oxfordjournals.molbev.a026331

An amphioxus Krox gene: insights into vertebrate hindbrain evolution. 10.1007/s004270000092

Identification of conserved C2H2 zinc-finger gene families in the Bilateria. 10.1186/gb-2001-2-5-research0016

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. 10.1186/gb-2001-2-4-research0010

Analyzing partially randomized nucleic acid pools: straight dope on doping. 10.1093/nar/gng030

Do universal codon-usage patterns minimize the effects of mutation and translation error? 10.1186/gb-2005-6-11-r91

Information, probability, and the abundance of the simplest RNA active sites. 10.2741/3137

Systems biology: Understanding function from genes to networks 10.2174/157016409788680974

The mind-body-microbial continuum. 10.31887/dcns.2011.13.1/agonzalez

Analytic Strategies for Understanding Host-Associated Microbial Communities: Faster and cheaper DNA sequencing technologies combined with open-access analytic software packages are opening new vistas 10.1128/microbe.6.389.1

Human microbiome science: Vision for the future, Bethesda, MD, July 24 to 26, 2013 10.1186/2049-2618-2-16

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0718-660a

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. 10.7554/elife.01104

Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy. 10.7554/elife.11405

Roman Borisov

Borisov Roman

ORCID: 0000-0002-8203-7055

Silylation with the Generation of a Fixed Charge for the Analysis of Alcohols by MALDI and SALDI Mass Spectrometry 10.1134/S1061934818140149

The complex Eu(phen)L3 · 5CH 2Cl 2 (HL is 1,3-bis(1,3-dimethyl-1 H-pyrazol-4-yl)propane-1,3-dione): Synthesis, crystal structure, and luminescent properties 10.1007/s11172-011-0238-0

Eugenol derivatives of higher chlorocyclophosphazenes and related epoxy oligomers 10.1134/S1560090413050060

Yttrium(III) and lanthanum(III) tris(1,3-bis(1,3-dimethyl-1H-pyrazol-4-yl)propane-1,3-dionato)(1,10-phenanthroline): Synthesis and study by mass spectrometry, X-ray diffraction analysis, and ⁸⁹Y and ¹³⁹La NMR spectroscopy 10.1134/S1070328415040089

Specific electron ionization-induced fragmentation of secondary alcohol methoxyacetates 10.1255/ejms.391

Features of the First and Second Order Electrospray Ionization Mass Spectra for Salt-Like Products Derived from Monools and Diols Using Combined Reagents Based on ω-Bromoacyl Chlorides and Nitrogen Bases 10.1134/S1061934817140052

Transformations of tetrahydro-pyrido[4,3-d]pyrimidines [b]-condensed with isoxazole, thiazole, thiadiazole, and triazole units under the action of activated alkynes 10.1007/s10593-009-0217-7

Combination of planar chromatography with matrix-assisted laser desorption/ionization mass spectrometry for the analysis of biologically active compounds 10.1134/S1061934815140038

Determination of Composition of Poly(ethylene-co-propylene) Glycoles at Molecular Level by MALDI Mass Spectrometry Following Preliminary Derivatization 10.1080/1023666X.2012.725269

A new approach to construction of isoindolo[1,2-a]isoquinoline alkaloids Nuevamine, Jamtine, and Hirsutine via IMDAF reaction 10.1016/j.tet.2009.02.024

The first synthesis of 8,10a-epoxypyrido[2,1-a]iso-indolo-7-carboxylic acids 10.1007/s10593-008-0130-5

Electron ionization mass spectra of alkylated sulfabenzamides 10.1002/rcm.4918

Derivatization of synthetic polymers in mass spectrometric studies 10.1134/S1061934810140017

Preparation of films based on β-diketophosphazene and different amines and study their properties 10.1016/j.matchemphys.2018.11.008

A “soft” ionization mass spectrometric study of organic sulfides as sulfonium salts 10.1134/S1061934816140070

Monomeric and dimeric magnesium mono-BHT complexes as effective ROP catalysts 10.1016/j.catcom.2016.09.018

Study of synthetic aliphatic copolyamides by time-of-flight matrix assisted laser desorption/ionization mass spectrometry 10.1007/s11172-007-0209-7

Epoxy oligomers based on eugenol cyclotriphosphazene derivatives 10.1134/S0965545X08060035

Synthesis of hexakis(hydroxyaryloxy)cyclotriphosphazene based on bisphenol A 10.1016/j.mencom.2014.04.009

Laser Mass Spectrometry Analysis of the Formation of Phosphazene-Containing Epoxy Oligomers 10.1134/S1560090418030065

Preliminary Derivatization during Investigation of Polymers with Labile Bonds via Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry1 10.1134/S156009041210003X

Compositions and structures of oligosiloxanes forming during the partial acidolysis of PhSi(OMe)3 10.1134/S1560090415010078

Single-stage synthesis of phosphazene-containing epoxy oligomers 10.1134/S1560090414040113

A New Post-Chromatographic Derivatization Approach to the Identification of Alcohols and Phenols in Complex Mixtures by a Combination of Planar Chromatography and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry 10.1134/S106193481813004X

A concise approach toward tetrazolyl-substituted benzazocines via a novel isocyanide-based multicomponent reaction 10.1055/s-0033-1340861

Preliminary silylation for structure determination of oligomeric silsesquioxanes by matrix-assisted laser desorption/ ionisation mass spectrometry 10.1255/ejms.946

A gas chromatography/mass spectrometry study of the conversion of alicyclic alcohols on membrane-type catalysts using a pulse microreactor implanted into a gas chromatograph injector 10.1134/S1061934816130037

Synthesis of the new framework phosphates and their catalytic activity in ethanol conversion into hydrocarbons 10.1016/j.cattod.2012.02.029

Removal of trichloroethylene from water in the catalytic membrane reactor 10.1016/j.cattod.2016.02.023

New synthetic approach to substituted isoindolo[2,1-a]quinoline carboxylic acids via intramolecular Diels-Alder reaction of 4-(N-furyl-2)-4- arylaminobutenes-1 with maleic anhydride 10.1016/j.tet.2005.02.017

Aryloxy Alkyl Magnesium versus Dialkyl Magnesium in the Lanthanidocene-Catalyzed Coordinative Chain Transfer Polymerization of Ethylene 10.1021/acs.organomet.9b00243

Derivatization by forming schiff bases in the study of synthetic polymers bearing amino groups by MALDI mass spectrometry 10.1134/S1061934812130126

Methacrylate composites containing maleic derivatives of cyclotriphosphazene 10.1134/S156009041306002X

Oligomeric Hydroxyaryloxyphosphase Based on Resorcinol 10.1134/S1560090419030023

Synthesis, molecular docking, and biological activity of 2-vinyl chromones: Toward selective butyrylcholinesterase inhibitors for potential Alzheimer's disease therapeutics 10.1016/j.bmc.2018.08.010

Ring opening in 1,2,3,4-tetrahydrochromeno[3,2-c]pyridines under the action of electron-deficient alkynes 10.1016/j.mencom.2017.11.035

A MALDI mass spectrometry investigation of the compositions of the products of the partial acidolysis of MeSi(OMe)3 10.1134/S1560090414010035

Chromatographic-mass spectrometric analysis of fischer-tropsch synthesis products 10.1023/A:1015754120136

Halogenated hydroxy-aryloxy phosphazenes and epoxy oligomers based on them 10.1134/S1070427213100200

Derivatization aids in the determination of end groups in poly(alkylene glycol)s by matrix-assisted laser desorption/ionization mass spectrometry 10.1002/rcm.4251

Effect of the Method of Synthesizing a Nickel-Containing Catalyst on Lignin Conversion in Liquid-Phase Hydrodepolymerization 10.1134/S0965544119010055

Chemoselectivity of [4+2] cycloaddition in n-maleyl-and n-allyl-2,6-difurylpiperidin-4-ones 10.1007/s10593-012-1057-4

Simple approach to derivatization of alcohols and phenols for the analysis by matrix(surface)-assisted laser desorption/ionization time-of-flight mass spectrometry 10.1002/rcm.7008

α,ω-N,N-Dimethylaminoalkylamines as possible derivatization agents for the analysis of small carbonyl compounds by low energy mass spectrometry 10.1255/ejms.1422

Microwave Discharge in Liquid Hydrocarbons: Study of a Liquid Hydrocarbon after Exciting the Discharge 10.1134/S0018143918040100

Oligomeric hydroxy-aryloxy phosphazene based on cyclic chlorophosphazenes 10.1134/S1070427213120161

Novel Reactive Matrices for the Analysis of Alcohols by Matrix-Assisted Laser Desorption/Ioization Mass Spectrometry 10.1134/S1061934818140113

Synthesis and modification of oligo(aryloxycyclotriphosphazenes) based on 4,4′-dihydroxydiphenyl-2,2-propane 10.1134/S1560090411060078

Unique para-effect in electron ionization mass spectra of bis(perfluoroacyl) derivatives of bifunctional aminobenzenes 10.1002/rcm.4661

Stereospecific ion-molecule reactions in the trans-decahydro-4-hydroxyquinoline series upon chemical ionization 10.1255/ejms.482

Chemical ionization mass spectrometric determination of the configuration of decahydroquinolin-4-ols 10.1023/A:1021389510415

Concise approach toward tetrazolo[1,5-a ][1,4]benzodiazepines via a novel multicomponent isocyanide-based condensation 10.1021/ol101590w

Stereochemistry of the [3+2] cycloaddition of acrylonitrile to the N-oxide of 5-methyl-4,5-dihydro-3H-spiro[benz-2-azepine-3,1′-cyclohexane] 10.1023/A:1013853728211

Substituted and fused spiro[benzo-2-azepine-3,1′-cyclohexanes] 10.1007/s11172-005-0022-0

A general strategy for the synthesis of oxoisoindolo[2,1-a]quinoline derivatives: The first efficient synthesis of 5,6,6a,11-tetrahydro-11-oxoisoindolo[2,1-a]quinoline-10-carboxylic acids 10.1016/S0040-4039(03)00705-6

Combination of graphite-assisted laser desorption/ionization (GALDI) mass spectrometry with thin layer chromatography 10.1134/S1061934814140032

Matrix effect in matrix-assisted laser desorption/ionization mass spectra of derivatized oligomeric polyols 10.1002/rcm.6449

Synthesis of oligoorganosilsesquioxanes via acidohydrolytic polycondensation 10.1134/S1560090413070014

A novel trityl/acridine derivatization agent for analysis of thiols by (matrix-assisted)(nanowire-assisted)laser desorption/ionization and electrospray ionization mass spectrometry 10.1039/c7ay01965c

A novel synthesis of pyrrolo[1,2-d][1,4]diazocines from tetrahydropyrrolo[1,2-a] pyrazines using activated alkynes in pyrazine ring expansion 10.1016/j.tet.2010.04.104

Methods of step extraction of rocks of high-carbon formations for the study of the component distribution of bitumen and variability of their basic geochemical parameters 10.18599/grs.2019.2.172-182

Composite glycerol/graphite/aromatic acid matrices for thin-layer chromatography/matrix-assisted laser desorption/ionization mass spectrometry of heterocyclic compounds 10.1016/j.chroma.2016.09.075

Catalytic activity of phenyl substituted cyclopentadienyl neodymium complexes in the ethylene oligomerization process 10.1016/j.jorganchem.2016.06.003

Epoxy oligomers modified with epoxyphosphazenes 10.1134/S1560090416050018

Regio-isomeric effects in tandem mass spectra of sulfonium cations generated from thiacyclane based sulfonium salts under soft ionization conditions 10.1177/1469066717723909

Determination of the molecular-mass characteristics of polyethylene oligomers with terminal iodine atoms by MALDI mass spectrometry after derivatization 10.1134/S1061934813140049

Investigation of the complex antibiotic INA-5812 10.1134/S1068162016060078

Suitable in-situ derivatization of alcohols by reaction with basic amines in Direct Analysis in Real Time mass spectrometry 10.1016/j.talanta.2019.03.037

Post-chromatographic fixed-charge derivatization for the analysis of hydroxyl-containing compounds by a combination of thin-layer chromatography and matrix-assisted laser desorption/ionization mass spectrometry 10.1016/j.chroma.2018.05.025

Tris(2,6-dimethoxyphenyl)methyl carbenium ion as a charge derivatization agent for the analysis of primary amines by MALDI mass spectrometry 10.1134/S106193481614015X

Monolithic thin-layer chromatography plates with covalently bonded matrix for hyphenation with matrix-assisted laser desorption/ionization 10.1002/jssc.201800679

Interaction of 4,5,7-trimethyl-4,5,6,7-tetrahydropyrrolo[3,2-c]pyridines with acetic and trifluoroacetic anhydrides 10.1007/s10593-005-0197-1

The first synthesis of 6-(phenylethynyl)-substituted tetrahydroazocino[5,4-b]indoles 10.1007/s10593-016-1831-9

Soft-ionization mass spectrometric observation of isomeric effects occurring in the synthesis of bis-sulfonium salts from thiacyclanes/xylylene dibromides and collision induced dissociation of bis-sulfonium cations 10.1016/j.ijms.2018.07.003

New Approaches to the Application of DART Mass Spectrometry Coupled with Planar Chromatography for the Analysis of Mixtures of Organic Compounds 10.1134/S106193481714009X

Spectral and thermochemical properties of the [Na(H 2O) 4] [EuL 4]·0.775CH 2Cl 2 complex, HL = 1,3-bis(1,3-dimethyl-1H-pyrazol-4-yl)-1,3-propanedione 10.1134/S1070363211100239

Investigation of 1,1′-disubstituted 4,4′-bipyridinium salts by various mass spectrometry techniques 10.1134/S1061934813140037

Synthesis of oligomeric epoxycyclotriphosphazenes and their properties as reactive flame-retardants for epoxy resins 10.1080/10426507.2016.1274752

A novel cascade Kröhnke condensation-an intramolecular nucleophilic cyclization approach toward annulated chromenes 10.1016/j.tetlet.2010.02.102

Intramolecular Diels - Alder reaction of 4-(N-furfuryl)aminobut-1-enes. New approach to the synthesis of 6,8a-epoxyoctahydroisoquinoline (3-aza-11-oxatricyclo[6.2.1.0 ^1,6]undec-9-ene) derivatives 10.1023/B:RUCB.0000037856.61928.c4

Geochemical technique of organic matter research in deposits enrich in kerogene (the Bazhenov Formation, West Siberia) 10.3103/S0145875215050075

Modification of dipeptides by alkyl chloroformate-alkanol mixtures for analysis by gas chromatography/mass spectrometry with electron and chemical ionization and collisional activation: Differentiation of isomers 10.1007/s11172-006-0584-5

Synthesis of resorcinol-based phosphazene-containing epoxy oligomers 10.3390/polym11040614

Wagner-Meerwein Skeletal Rearrangement of 3-Spiroannulated 6,8a-Epoxy- and 6,8a;7,8-Diepoxyisoquinolines (3-Aza-11-oxatricyclo[6.2.1.0 ^1,6]undec-9-enes). Isolation and Identification of 5-Aza-2-oxatricyclo[6.2.1.0^3,9]undec-3-enes 10.1021/jo0353684

The first example of tetrahydrothieno[3,2-d]azocines synthesis 10.1016/j.tet.2008.08.034

Synthesis of tetrazolodiazepines by a five-centered four-component azide Ugi reaction. Scope and limitations 10.1007/s11172-012-0214-3

Stereospecific ion-molecule reactions of anabolic-type steroid tertiary alcohols with proton-donating cations 10.1255/ejms.578

Characterization of low-molecular weight iodine-terminated polyethylenes by gas chromatography/mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with the use of derivatization 10.1255/ejms.1223

Tryptamine: a Reactive Matrix for MALDI Mass Spectrometry 10.1134/S106193481713010X

2-Alkyl-4-oxohexahydropyrimido[4,5-d]- and -[5,4-d]azocines 10.1007/s10593-011-0744-x

Determination of the configuration of piperidin-4-ol silyl ethers by mass spectrometry with chemical ionization 10.1007/s11172-006-0474-x

First efficient one-pot synthesis of tetrahydropyrrolo[2,3-d]azocines and tetrahydroazocino[4,5-b]indoles 10.2174/1570178053400090

A simple and easy approach to the derivatization of alcohols for study by soft ionization mass spectrometry methods 10.1134/S106193481513002X

The Characteristics of the Organic Matter of the Upper Devonian Domanik-Type Deposits in the Northern and Central Regions of the Volga-Ural Basin According to Saturated Biomarkers Composition 10.1134/S0016702918080104

Improvement of MWCO determination by using branched PEGs and MALDI method 10.1016/j.seppur.2018.09.043

Oligo- and polysiloxanephosphazenes based on eugenol cyclotriphosphazene derivatives 10.1134/S1560090411020059

Formation of volatile copper carbonyl during the preparation of copper nanoparticles in the copper acetate hydrate-polyacrylonitrile heterogeneous system under IR radiation 10.1134/S0036023610050153

Reactions of 4,5-dihydro-5-methyl-3H-spiro[benz-2-azepine-3-cyclohexane] N-oxide with some nucleophilic reagents 10.1023/A:1017515318197

First example of a new multicomponent reaction of a tetrahydropyridine ring expansion 10.1007/s10593-012-1044-9

Reactive matrices for matrix-assisted laser desorption/ionization mass spectrometry of primary amines 10.1255/ejms.1353

Novel approach to synthesis of [c]-condensed decahydroisoindolo[2,1-a]quinolines 10.1007/s10593-005-0145-0

Mass Spectrometry in Petroleum Chemistry (Petroleomics) (Review) 10.1134/S0965544119100025

Homobivalent Lamellarin-Like Schiff Bases: In Vitro Evaluation of Their Cancer Cell Cytotoxicity and Multitargeting Anti-Alzheimer’s Disease Potential 10.3390/molecules26020359

Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. 10.1080/10408347.2021.1873100

New suitable deprotonating matrices for the analysis of carboxylic acids and some acidic compounds by matrix-assisted laser desorption/ionization mass spectrometry in negative ion mode. 10.1002/rcm.8954

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. 10.1038/s41587-020-0700-3

A simple, inexpensive, non-enzymatic microwave-assisted method for determining bisphenol-A in urine in the form of trimethylsilyl derivative by GC/MS with single quadrupole. 10.1016/j.jpba.2020.113417

Suitable analysis of α-amino acids by a direct combination of thin-layer chromatography and matrix-assisted laser desorption/ionization mass spectrometry in conjunction with post-chromatographic fixed-charge derivatization. 10.1016/j.chroma.2020.461335

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS 10.1101/2020.01.13.905091

Synthesis of Bisphenol A Based Phosphazene-Containing Epoxy Resin with Reduced Viscosity. 10.3390/polym11121914

An approach to analysis of primary amines by a combination of thin-layer chromatography and matrix-assisted laser desorption ionization mass spectrometry in conjunction with post-chromatographic derivatization. 10.1002/jssc.201900644

Larisa Kulikova

Kulikova Larisa / Kulikova L. N.

ORCID: 0000-0001-5111-8111

Recent Advances in Phthalan and Coumaran Chemistry 10.1002/open.201800184

Synthesis, molecular docking, and biological activity of 2-vinyl chromones: Toward selective butyrylcholinesterase inhibitors for potential Alzheimer's disease therapeutics 10.1016/j.bmc.2018.08.010

8H-Chromeno[2',3':4,5]imidazo[2,1-a]isoquinoline 10.1107/S1600536810006744

Investigation on the antiplatelet activity of pyrrolo[3,2-c]pyridine-containing compounds. 10.1211/002235702676

Synthesis of 4-amino-substituted tetrahydropyrimido[4,5-d]azocines 10.1007/s10593-013-1361-7

The reaction of tetrahydrochromeno[3,4-c]pyridines with activated alkynes. the first synthesis of tetrahydrochromeno[4,3-d]azocines 10.1016/j.tetlet.2011.06.012

Ring opening in 1,2,3,4-tetrahydrochromeno[3,2-c]pyridines under the action of electron-deficient alkynes 10.1016/j.mencom.2017.11.035

Transformations of tetrahydro-pyrido[4,3-d]pyrimidines [b]-condensed with isoxazole, thiazole, thiadiazole, and triazole units under the action of activated alkynes 10.1007/s10593-009-0217-7

Cleavage of some annulated tetrahydropyridines under the action of dimethyl acetylene dicarboxylate in protic solvents. New practical route to substituted pyrroles and indoles 10.1023/B:MODI.0000006760.30731.46

Conversion of 2-ethyl- 3, 3, 5, 5-tetramethyl- and 2-ethyl- 1, 3, 3, 5, 5-pentamethyl-1, 2, 4, 5-tetra- hydro-3H-benz-2-azepines by the action of ethyl propiolate 10.1007/s10593-010-0414-4

Chapter 2 Synthesis of Heteroannulated Azocine Derivatives 10.1016/S0065-2725(07)00002-5

Tandem enlargement of the tetrahydropyridine ring in 1-aryl-tetrahydroisoquinolines using activated alkynes-a new and effective synthesis of benzoazocines 10.1016/j.tetlet.2006.04.151

The first synthesis and X-ray crystal structure of tetrahydropyrrolo[2,3-d]azocines 10.1016/S0040-4039(02)01520-4

The first synthesis of tetrahydrobenzo[b]pyrrolo[2,1-f][1,6]naphthyridine by the Michael addition of butyn-2-one to 1-(2-methoxycarbonylvinyl) tetrahydrobenzo[b][1,6]naphthyridine 10.1007/s11172-010-0208-y

Synthesis of azecino[5,4-b]indoles and indolo[3,2-e][2]benzazonines via tandem transformation of hydrogenated indoloquinolizines and indolizines 10.1007/s11172-012-0167-6

The first synthesis of 6-(phenylethynyl)-substituted tetrahydroazocino[5,4-b]indoles 10.1007/s10593-016-1831-9

Transformations of nitro-substituted dihydroisoindoles in reactions with activated alkynes 10.1007/s10593-010-0558-2

The chemistry of the tandem reaction of 1-aryltetrahydrobenzothieno[2,3-c] pyridines with activated alkynes 10.1007/s10593-010-0513-2

Transformations of tetrahydropyrido[4′,3′:4,5]thieno[2,3-d] pyrimidin-4(3H)-ones in the presence of alkynes bearing electron-withdrawing substituents 10.1007/s11172-012-0052-3

2-Alkyl-4-oxohexahydropyrimido[4,5-d]- and -[5,4-d]azocines 10.1007/s10593-011-0744-x

New Approaches to the Application of DART Mass Spectrometry Coupled with Planar Chromatography for the Analysis of Mixtures of Organic Compounds 10.1134/S106193481714009X

Transformation of 2-ethyl-1-m-fluoro-phenyl-β-carboline by the action of dimethyl acetylenedicarboxylate in the presence of indoles. New method of synthesis of bisindolylarylmethanes 10.1007/s10593-010-0617-8

First efficient one-pot synthesis of tetrahydropyrrolo[2,3-d]azocines and tetrahydroazocino[4,5-b]indoles 10.2174/1570178053400090

A novel cascade Kröhnke condensation-an intramolecular nucleophilic cyclization approach toward annulated chromenes 10.1016/j.tetlet.2010.02.102

Tetrahydropyridine (THP) ring expansion under the action of activated terminal alkynes. The first synthesis and X-ray crystal structure of tetrahydropyrimido[4,5-d]azocines 10.1016/j.tetlet.2005.11.136

Reaction of 1-substituted tetrahydro-β-carbolines with activated alkynes - A new original approach to the synthesis of tetrahydroazocino[5,4-b] indoles 10.1007/s10593-007-0093-y

Transformations of tetrahydro-1,4-benzoxazepines and tetrahydro-1,4- benzothiazepines under the action of alkynes. First example of the synthesis of tetrahydro-1,4-benzothiazonine-6-carboxylate 10.1007/s10593-013-1251-z

First example of a new multicomponent reaction of a tetrahydropyridine ring expansion 10.1007/s10593-012-1044-9

Tandem cleavage of hydrogenated β- and γ-carbolines - New practical synthesis of tetrahydroazocino[4,5-b]indoles and tetrahydroazocino[5, 4-b]indoles showing acetylcholinesterase inhibitory activity 10.1002/ejoc.200400107

1-R-2-[(1E,3E)-4-Aminobuta-1,3-dien-1-yl]-1H-benzimidazoles. Synthesis and some transformations 10.1007/s11172-010-0198-9

Interaction of 4-hydroxymethyl- 2-(3,4-dimethoxybenzyl)isoindoline with methyl propiolate 10.1007/s10593-009-0261-3

A novel synthesis of pyrrolo[1,2-d][1,4]diazocines from tetrahydropyrrolo[1,2-a] pyrazines using activated alkynes in pyrazine ring expansion 10.1016/j.tet.2010.04.104

A novel alkyne-induced recyclization of 4-hydroxymethyl or 4-formyl-1H-2,3-dihydroisoindoles-an effective pathway to substituted isobenzofurans 10.1016/j.tetlet.2009.06.036

Transformations of 2-trifluoroacetyl-4,5,6,7-tetrahydro-1H-pyrrolo[3,2-c] pyridines by the action of ethyl propynoate. A novel synthesis of 2-trifluoroacetyl-4,7,8,9-tetrahydro-1H-pyrrolo[2,3-d]azocines 10.1134/S1070428006120165

Derivatization by forming schiff bases in the study of synthetic polymers bearing amino groups by MALDI mass spectrometry 10.1134/S1061934812130126

Tandem cleavage of 2,3,5-trimethyl 7-trifluoroacetyl-1,2,3,4-tetrahydro- pyrrolo[1,2-c]pyrimidine by activated alkynes, caused by Michael addition of a tertiary nitrogen atom to a triple bond 10.1007/s10593-007-0144-4

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Scouting around 1,2,3,4‐Tetrahydrochromeno[3,2‐ c ]pyridin‐10‐ones for Single‐ and Multitarget Ligands Directed towards Relevant Alzheimer's Targets 10.1002/cmdc.202000468

Kirill Veselkov

Veselkov Kirill

ORCID: 0000-0002-1164-0359

https://www.imperial.ac.uk/people/kirill.veselkov04

ChemDistiller: an engine for metabolite annotation in mass spectrometry 10.1093/bioinformatics/bty080

Bi-clustering of metabolic data using matrix factorization tools 10.1016/j.ymeth.2018.02.004

Exosomal microRNAs derived from colorectal cancer-associated fibroblasts: role in driving cancer progression 10.18632/aging.101355

Translational utility of a hierarchical classification strategy in biomolecular data analytics 10.1038/s41598-017-14092-7

A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy 10.1038/s41598-017-08150-3

Faster, More Reproducible DESI-MS for Biological Tissue Imaging 10.1007/s13361-017-1714-z

Metabolic Profiling in Patients with Pneumonia on Intensive Care 10.1016/j.ebiom.2017.03.034

Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer 10.1039/c6sc03738k

Epithelial ovarian carcinoma diagnosis by desorption electrospray ionization mass spectrometry imaging 10.1038/srep39219

A novel methodology for in vivo endoscopic phenotyping of colorectal cancer based on real-time analysis of the mucosal lipidome: a prospective observational study of the iKnife 10.1007/s00464-016-5121-5

Imaging of Esophageal Lymph Node Metastases by Desorption Electrospray Ionization Mass Spectrometry. 10.1158/0008-5472.can-16-0699

Investigation of the Impact of Desorption Electrospray Ionization Sprayer Geometry on Its Performance in Imaging of Biological Tissue 10.1021/acs.analchem.6b00345

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments 10.1016/j.csbj.2016.02.005

Multivariate metabotyping of plasma predicts survival in patients with decompensated cirrhosis 10.1016/j.jhep.2016.01.003

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry 10.1186/s13742-015-0059-4

Spatially resolved metabolic phenotyping of breast cancer by desorption electrospray ionization mass spectrometry. 10.1158/0008-5472.can-14-2258

Mass Spectrometric Analysis of Exhaled Breath for the Identification of Volatile Organic Compound Biomarkers in Esophageal and Gastric Adenocarcinoma. 10.1097/sla.0000000000001101

Metabolic, Immune, and Gut Microbial Signals Mount a Systems Response to Leishmania major Infection 10.1021/pr5008202

XMS: Cross-Platform Normalization Method for Multimodal Mass Spectrometric Tissue Profiling 10.1007/s13361-014-0997-6

Characterization and Identification of Clinically Relevant Microorganisms Using Rapid Evaporative Ionization Mass Spectrometry 10.1021/ac501075f

Rapid diagnosis and staging of colorectal cancer via high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy of intact tissue biopsies. 10.1097/sla.0b013e31829d5c45

Discrimination of lymph node metastases using desorption electrospray ionisation-mass spectrometry imaging 10.1039/c3cc48927b

Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer 10.1073/pnas.1310524111

Intraoperative Tissue Identification Using Rapid Evaporative Ionization Mass Spectrometry 10.1126/scitranslmed.3005623

Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry 10.1039/c3cc42015a

1H NMR study on the short- and long-term impact of two training programs of sprint running on the metabolic fingerprint of human serum. 10.1021/pr300846x

UPLC-MS metabolic profiling of second trimester amniotic fluid and maternal urine and comparison with NMR spectral profiling for the identification of pregnancy disorder biomarkers 10.1039/c2mb05424h

Untargeted Metabolome Quantitative Trait Locus Mapping Associates Variation in Urine Glycerate to Mutant Glycerate Kinase 10.1021/pr200566t

Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery 10.1021/ac201065j

A Metabolic Entropy Approach for Measurements of Systemic Metabolic Disruptions in Patho-Physiological States 10.1021/pr1000576

Urinary Metabolic Phenotyping Differentiates Children with Autism from Their Unaffected Siblings and Age-Matched Controls 10.1021/pr901188e

Cluster Analysis Statistical Spectroscopy Using Nuclear Magnetic Resonance Generated Metabolic Data Sets from Perturbed Biological Systems 10.1021/ac901240j

Panorganismal Metabolic Response Modeling of an Experimental Echinostoma caproni Infection in the Mouse 10.1021/pr900185s

Recursive Segment-Wise Peak Alignment of Biological H-1 NMR Spectra for Improved Metabolic Biomarker Recovery 10.1021/ac8011544

Human metabolic phenotype diversity and its association with diet and blood pressure 10.1038/nature06882

Species variation in the fecal metabolome gives insight into differential gastrointestinal function 10.1021/pr070340k

Structural basis for the binding affinity of a homologous series of synthetic phenoxazone drugs with DNA: NMR and molecular mechanics analysis 10.1080/07391102.2007.10507132

Metabolic Biomarkers of Ageing in C57BL/6J Wild-Type and Flavin-Containing Monooxygenase 5 (FMO5)-Knockout Mice 10.3389/fmolb.2018.00028

Exploiting and assessing multi-source data for supervised biomedical named entity recognition 10.1093/bioinformatics/bty152

BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology 10.1038/s41598-018-22499-z

Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level 10.1186/s40246-018-0142-x

A Unified Conceptual Framework for Metabolic Phenotyping in Diagnosis and Prognosis 10.1016/j.tips.2019.08.004

Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop 10.1097/MPA.0000000000001412

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data 10.1038/s41587-020-0700-3

De Novo Lipogenesis Alters the Phospholipidome of Esophageal Adenocarcinoma 10.1158/0008-5472.CAN-19-4035

Colorectal Peritoneal Metastases: A Systematic Review of Current and Emerging Trends in Clinical and Translational Research 10.1155/2019/5180895

Spatially resolved profiling of colorectal cancer lipid biochemistry via DESI imaging mass spectrometry to reveal morphology-dependent alterations in fatty acid metabolism 10.1200/JCO.2016.34.15_suppl.e15104

Repeatability and reproducibility of desorption electrospray ionization-mass spectrometry (DESI-MS) for the imaging analysis of human cancer tissue: a gateway for clinical applications 10.1039/c4ay01770f

Network Mapping of Molecular Biomarkers Influencing Radiation Response in Rectal Cancer 10.1016/j.clcc.2019.01.004

Network-driven analytics of published tissue-based biomarkers to predict response to neoadjuvant therapy in rectal cancer 10.1158/1538-7445.AM2017-839

Response to Comment on "Optimized Preprocessing of Ultra-Performance Liquid Chromatography/Mass Spectrometry Urinary Metabolic Profiles for Improved Information Recovery" 10.1021/ac202516e

Mass Spectrometry Imaging (MSI) of Microbiome-Metabolome Interactions in Colorectal Cancer 10.1016/S0016-5085(16)30202-5

PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY OF PLASMA IN PATIENTS WITH CIRRHOSIS CORRELATES WITH ARTERIAL AMMONIA BUT NOT GRADE OF HEPATIC ENCEPHALOPATHY 10.1136/gutjnl-2012-302514c.45

Metabolic maturation in the first 2 years of life in resource-constrained settings and its association with postnatal growths 10.1126/sciadv.aay5969

METABOLIC PROFILING OF PLASMA BY NMR SPECTROSCOPY ACCURATELY PREDICTS OUTCOME IN PATIENTS WITH DECOMPENSATED CIRRHOSIS AND ACUTE ON CHRONIC LIVER FAILURE 10.1136/gutjnl-2012-302514c.46

Metabolic characterization of colorectal cancer cells harbouring different KRAS mutations in codon 12, 13, 61 and 146 using human SW48 isogenic cell lines 10.1007/s11306-020-01674-2

HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods 10.1038/s41598-019-45349-y

Statistical Tools for Molecular Covariance Spectroscopy 10.1016/B978-0-12-409547-2.12113-4

Multivariate Data Analysis Methods for NMR-based Metabolic Phenotyping in Pharmaceutical and Clinical Research 10.1002/9780470034590.emrstm1407

The age of data analytics: converting biomedical data into actionable insights 10.1016/j.ymeth.2018.10.017

Network machine learning maps phytochemically rich "Hyperfoods" to fight COVID-19 10.1186/s40246-020-00297-x

Standardized nomenclature and open science in Human Genomics 10.1186/s40246-021-00312-9

Predicting anticancer hyperfoods with graph convolutional networks 10.1186/s40246-021-00333-4

Phytochemically rich dietary components and the risk of colorectal cancer: A systematic review and meta-analysis of observational studies 10.5306/wjco.v12.i6.482

Virus-induced Volatile Organic Compounds are Detectable in Exhaled Breath During Pulmonary Infection. 10.1164/rccm.202103-0660OC

Wout Bittremieux

Bittremieux Wout

ORCID: 0000-0002-3105-1359

http://www.bittremieux.be/

https://scholar.google.com/citations?user=fBl8-IwAAAAJ

https://github.com/bittremieux

https://www.uantwerpen.be/en/staff/wout-bittremieux/

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania 10.1101/2021.09.14.460245

A learned embedding for efficient joint analysis of millions of mass spectra 10.1101/483263

jqcML: An Open-Source Java API for Mass Spectrometry Quality Control Data in the qcML Format 10.1021/pr401274z

A Primer to Frequent Itemset Mining for Bioinformatics 10.1093/bib/bbt074

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments 10.1074/mcp.M113.035907

Machine Learning Applications in Proteomics Research: How the Past Can Boost the Future 10.1002/pmic.201300289

Efficient Reduction of Candidate Matches in Peptide Spectrum Library Searching Using the Top k Most Intense Peaks 10.1021/pr401269z

iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring 10.1021/acs.jproteome.5b00127

Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics 10.1021/acs.jproteome.6b00028

On the Feasibility of Mining CD8+ T-Cell Receptor Patterns Underlying Immunogenic Peptide Recognition 10.1007/s00251-017-1023-5

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph 10.1109/TCBB.2016.2576440

Computational Quality Control Tools for Mass Spectrometry Proteomics 10.1002/pmic.201600159

Designing Biomedical Proteomics Experiments: State-of-the-Art and Future Perspectives 10.1586/14789450.2016.1172967

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing 10.1021/acs.jproteome.8b00359

The Human Proteome Organization–Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry 10.1021/acs.analchem.6b04310

TCRex: A Webtool for the Prediction of T-Cell Receptor Sequence Epitope Specificity 10.1101/373472

Quality Control in Mass Spectrometry-Based Proteomics 10.1002/mas.21544

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work 10.1021/acs.jproteome.7b00370

Grasping Frequent Subgraph Mining for Bioinformatics Applications 10.1186/s13040-018-0181-9

A Community Proposal to Integrate Proteomics Activities in ELIXIR [Version 1; Referees: 2 Approved] 10.12688/f1000research.11751.1

Proceedings of the EuBIC Developer's Meeting 2018 10.1016/j.jprot.2018.05.015

MESSAR: Automated Recommendation of Metabolite Substructures from Tandem Mass Spectra 10.1101/134189

Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units 10.1101/627497

Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis 10.3390/metabo9030054

2018 YPIC Challenge: A case study in characterizing an unknown protein sample 10.7287/peerj.preprints.27802v1

2018 YPIC Challenge: A case study in characterizing an unknown protein sample 10.7287/peerj.preprints.27802

On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognition 10.1101/118539

Fast open modification spectral library searching through approximate nearest neighbor indexing 10.1101/326173

spectrum_utils: A Python package for mass spectrometry data processing and visualization 10.1101/725036

2018 YPIC Challenge: A case study in characterizing an unknown protein sample 10.7287/peerj.preprints.27802v2

Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units 10.1021/acs.jproteome.9b00291

2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample 10.1021/acs.jproteome.9b00384

spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization 10.1021/acs.analchem.9b04884

MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra 10.1371/journal.pone.0226770

Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service 10.1101/2020.05.09.086066

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

Current challenges for epitope-agnostic TCR interaction prediction and a new perspective derived from image classification 10.1101/2019.12.18.880146

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Large-scale tandem mass spectrum clustering using fast nearest neighbor searching 10.1101/2021.02.05.429957

Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2 10.1021/acs.jproteome.0c00929

Sharing biological data: why, when, and how 10.1002/1873-3468.14067

The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and research 10.1002/rcm.9087

ppx: Programmatic access to proteomics data repositories 10.1101/2021.05.29.446304

Large‐scale tandem mass spectrum clustering using fast nearest neighbor searching 10.1002/rcm.9153

Reference data-set driven metabolomics 10.21203/rs.3.rs-654519/v1

ppx: Programmatic Access to Proteomics Data Repositories 10.1021/acs.jproteome.1c00454

Physicochemical and Pharmacokinetic Properties Determining Drug Detection in Skin 10.1101/2021.08.17.456720

Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors 10.1101/2021.09.03.458897

Brooke Anderson

Anderson Brooke

ORCID: 0000-0002-9919-1390

Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host 10.1021/acssynbio.0c00431

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. 10.1038/s41587-020-0700-3

Targeted metabolomics of Physaria fendleri, an industrial crop producing hydroxy fatty acids. 10.1093/pcp/pcu011

Justin van der Hooft

van der Hooft Justin / Justin J.J. van der Hooft

ORCID: 0000-0002-9340-5511

Structural elucidation of low abundant metabolites in complex sample matrices 10.1007/s11306-013-0519-8

Non-smoky GLYCOSYLTRANSFERASE1 prevents the release of smoky aroma from tomato fruit 10.1105/tpc.113.114231

Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea 10.1021/ac400861a

Substructure-based annotation of high-resolution multistage MSn spectral trees 10.1002/rcm.6364

Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts 10.1021/jf300297y

Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake 10.1021/ac3017339

Spectral trees as a robust annotation tool in LC-MS based metabolomics 10.1007/s11306-011-0363-7

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees 10.1021/ac2034216

Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi 10.1002/jsfa.5522

A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR 10.1002/mrc.2833

Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell 10.1063/1.3530735

Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation 10.1021/ac102546x

Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae) 10.1016/j.bse.2009.05.003

Topic modeling for untargeted substructure exploration in metabolomics 10.1073/pnas.1608041113

Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089

Did a plant-herbivore arms race drive chemical diversity in Euphorbia? 10.1101/323014

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa. 10.5702/massspectrometry.S0033

Interactions of blacktea polyphenols with human gut microbiota: implications for gut and cardiovascular health 10.3945/ajcn.113.058263

Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes 10.1111/tpj.13527

Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines 10.3389/fbioe.2015.00026

Rapid and sustained systemic circulation of conjugated gut microbiol catabolites after single-dose black tea extract consumption 10.1021/pr5001253

In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine 10.1021/ac403875b

Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose 10.1007/s11306-018-1438-5

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1101/463620

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1101/491506

Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics 10.1021/acs.analchem.8b05112

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages 10.1101/347716

Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings https://doi.org/10.1016/j.mam.2017.11.002

Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy 10.1007/978-3-319-28275-6_6-2

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry 10.1093/bioinformatics/btx582

A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats https://doi.org/10.1016/j.freeradbiomed.2016.08.001

The food metabolome: a window over dietary exposure 10.3945/ajcn.113.076133

Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols 10.3945/ajcn.113.058958

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics 10.1021/acs.analchem.7b01391

A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes 10.18174/FAIRdata2018.16286

Implementations of the chemical structural and compositional similarity metric in R and Python 10.1101/546150

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1111/tpj.14292

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters 10.1186/s13104-019-4222-3

The Metabolomics Society—Current State of the Membership and Future Directions 10.3390/metabo9050089

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1039/C8FD00235E

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459

Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli 10.3389/fmicb.2019.00252

Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l. 10.3389/fpls.2019.00846

Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools 10.3390/metabo9070144

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics 10.3390/metabo9100219

MIBiG 2.0: a repository for biosynthetic gene clusters of known function 10.1093/nar/gkz882

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/j.foodchem.2019.125290

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery 10.1021/acscentsci.9b00806

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow 10.1016/j.phytochem.2020.112292

Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication 10.1126/sciadv.aax6328

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree 10.1101/2020.05.04.077636

Linking genomics and metabolomics to chart specialized metabolic diversity 10.1039/D0CS00162G

Reproducible molecular networking of untargeted mass spectrometry data using GNPS 10.1038/s41596-020-0317-5

Decomposing metabolite set activity levels with PALS 10.1101/2020.06.07.138974

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1101/2020.06.12.148205

Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking 10.1021/acs.orglett.0c02153

matchms - processing and similarity evaluation of mass spectrometry data 10.1101/2020.08.06.239244

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1101/2020.08.11.245928

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters 10.1101/2020.08.17.240838

matchms - processing and similarity evaluation of mass spectrometry data. 10.21105/joss.02411

ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7

Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6

Rapid Development of Improved Data-dependent Acquisition Strategies 10.1101/2020.09.11.293092

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361

BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes 10.1101/2020.12.14.422671

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters 10.1093/gigascience/giaa154

Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs 10.1371/journal.ppat.1008932

Comparative Metabologenomics Analysis of Polar Actinomycetes 10.3390/md19020103

Ranking Metabolite Sets by Their Activity Levels 10.3390/metabo11020103

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1371/journal.pcbi.1008724

Rapid Development of Improved Data-Dependent Acquisition Strategies 10.1021/acs.analchem.0c03895

MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons 10.1101/2021.04.18.440324

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1371/journal.pcbi.1008920

Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview 10.3390/metabo11070445

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21

Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery 10.1128/mSystems.00726-21

Biswapriya Misra

Misra Biswapriya / Biswapriya B. Misra / Misra B B

ORCID: 0000-0003-2589-6539

Email: bbmisraccb@gmail.com

https://bbmisraccb.wixsite.com/bbmisraccb

https://scholar.google.com/citations?user=s-OkiKkAAAAJ&hl=en

https://www.researchgate.net/profile/Biswapriya_Misra

Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery 10.1101/2021.09.12.459579

Untargeted metabolomics in primary murine bone marrow stromal cells reveals distinct profile throughout osteoblast differentiation 10.1007/s11306-021-01829-9

The Chemical Exposome of Human Aging 10.3389/fgene.2020.574936

A workflow in single cell-Type metabolomics: From data pre-processing and statistical analysis to biological insights 10.1002/9781119509967.ch6

State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing 10.3389/fgene.2020.610798

Perspectives on Multi-Omics and Omics Applications in Biomedical Research: an Interview with Dr. Biswapriya B. Misra 10.17145/jab.20.011

Immunolocalization of santalol in sandalwood 10.1080/10412905.2014.910709

Plant single-cell and single-cell-type metabolomics 10.1016/j.tplants.2014.05.005

Culture of East Indian sandalwood tree somatic embryos in air-lift bioreactors for production of santalols, phenolics and arabinogalactan proteins 10.1093/aobpla/plt025

Purification and characterization of a betanidin glucosyltransferase from Amaranthus tricolor L catalyzing non-specific biotransformation of flavonoids 10.1016/j.plantsci.2013.07.003

Developmental variations in sesquiterpenoid biosynthesis in East Indian sandalwood tree (Santalum album L.) 10.1007/s00468-013-0858-0

Biological Activities of East Indian Sandalwood Tree, Santalum album 10.7287/PEERJ.PREPRINTS.96

An Updated Snapshot of Recent Advances in Transcriptomics and Genomics of Phytomedicinals 10.14304/surya.jpr.v2n2.1

Volatile profiling from heartwood of East Indian sandalwood tree 10.1016/j.jopr.2013.04.030

Is a plant’s ploidy status reflected in its metabolome? 10.14304/surya.jpr.v3n4.1

The guard cell metabolome: functions in stomatal movement and global food security 10.3389/fpls.2015.00334

The Plant Subcellular Metabolome: Current State and Advances 10.14304/surya.jpr.v3n6.7

Advances in understanding CO2 responsive plant metabolomes in the era of climate change 10.1007/s11306-015-0825-4

Molecular Evolution and Functional Divergence of Chitinase Gene Family in Hevea brasiliensis Genome 10.15200/winn.144125.54243

Updates in Metabolomics Tools and Resources: 2014-2015 10.1002/elps.201500417

When plants brace for the emerging pathogens 10.1016/j.pmpp.2015.03.004

Metabolomic Responses of Guard Cells and Mesophyll Cells to Bicarbonate 10.1371/journal.pone.0144206

Plant Volatilome Resources 10.2174/2213235x04666160317000919

Ten ‘Personal’ Reasons why I am skeptical about Open Access (OA): Thoughts of an Individual Researcher 10.15200/winn.145789.92186

The Black-Box of Plant Apoplast Lipidomes 10.3389/fpls.2016.00323

Jasmonate-mediated stomatal closure under elevated CO2revealed by time-resolved metabolomics 10.1111/tpj.13296

Differential metabolomic responses of PAMP-triggered immunity and effector-triggered immunity in Arabidopsis suspension cells 10.1007/s11306-016-0984-y

Polyploidy and the proteome 10.1016/j.bbapap.2016.03.010

New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants 10.1016/j.jprot.2016.02.012

Evaluation of in vivo anti-hyperglycemic and antioxidant potentials of α-santalol and sandalwood oil 10.1016/j.phymed.2012.12.017

Draft genome sequence of the rubber tree Hevea brasiliensis 10.1186/1471-2164-14-75

Metabolomic Responses of Arabidopsis Suspension Cells to Bicarbonate under Light and Dark Conditions 10.1038/srep35778

Cataloging the Brassica napus seed metabolome 10.1080/23311932.2016.1254420

Quick tips to perform a metabolomics study 10.7287/PEERJ.PREPRINTS.2002V1

Quick tips to perform a metabolomics study 10.7287/PEERJ.PREPRINTS.2002

Sentinel of Science award certificate from Publons: Top Reviewer in Plant Science for Year 2015-2016 10.13140/RG.2.2.27584.12809

Experimental Design in Metabolomics 10.13140/RG.2.1.3823.2720

Data Analysis for MS-based Metabolomics 10.13140/RG.2.1.3561.1281

Book Review:Plant Life of Southwestern Australia: Adaptations for Survival Philip Groom and Byron Lamont 2015. ISBN-13: 978-3-11-037016-4 eBook, open access. 268 pp. De Gruyter Open, Warsaw, Poland 10.13140/RG.2.1.2766.5047

Cataloging the Brassica napus seed metabolome 10.6084/M9.FIGSHARE.4229480

Cataloging the Brassica napus seed metabolome 10.6084/M9.FIGSHARE.4229480.V1

Immunolocalization of α-santalol in sandalwood 10.6084/M9.FIGSHARE.C.1958132

Comparative Metabolomics of Bacterial Flagellin 22 Responses in Plant Single Cell-Types Source: http://www.moleculardetective.org/2014_UF_Metabolomics_Workshop_Program.pdf 10.13140/RG.2.2.20769.20325

Time-Resolved Cell-type Specific Metabolomes Reveal Differential Metabolomic Responses to Elevated [CO2] in Guard Cells and Mesophyll Cells 10.13140/RG.2.1.2337.6880

Metabolomics of CO2 responses in Brassica napus guard cells revealed the signaling role of jasmonates 10.13140/RG.2.1.1813.4000

Differential Metabolomic responses to Elevated [CO2] in Guard Cells and Mesophyll Cells 10.13140/RG.2.1.1158.0408

Time-resolved Metabolomics Reveals Guard Cell Phytohormone Functions Under High and Low CO2 10.13140/RG.2.1.2476.9522

Review of emerging metabolomic tools and resources: 2015-2016 10.1002/elps.201700110

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems 10.1002/jobm.201700341

New tools and resources in metabolomics: 2016-2017 10.1002/elps.201700441

Updates on Resources, Software Tools, and Databases for Plant Proteomics in 2016-2017 10.1002/elps.201700401

Nonhuman primate breath volatile organic compounds associate with developmental programming and cardio-metabolic status 10.1088/1752-7163/aaba84

DIMEdb: an integrated database and web service for metabolite identification in direct infusion mass spectrometery 10.1101/291799

Optimized GC–MS metabolomics for the analysis of kidney tissue metabolites 10.1007/s11306-018-1373-5

High-resolution gas chromatography/mass spectrometry metabolomics of non-human primate serum 10.1002/rcm.8197

Standards for Reporting Metabolomics Data in Phytomedicine Research 10.31219/osf.io/amdt2

PROSPECTING OF PHENYLPROPANOIDS AND TERPENOIDS IN EAST INDIAN SANDALWOOD (SANTALUM ALBUM L.) 10.31237/osf.io/psw2r

High-throughput phenotyping by applying digital morphometrics and fluorescence induction curves in seeds to identifying variations: A case study of Annona (Annonaceae) species 10.1016/j.inpa.2018.07.001

Visual gene network analysis of aging-specific gene co-expression in human indicates overlaps with immuno-pathological regulations 10.1051/fopen/2018004

2392 10.1017/cts.2017.229

Integrated Omics: Tools, Advances, and Future Approaches. 10.1530/jme-18-0055

Whole genome sequence analyses of brain imaging measures in the Framingham Study. 10.1212/WNL.0000000000004820

PROSPECTING OF PHENYLPROPANOIDS AND TERPENOIDS IN EAST INDIAN SANDALWOOD (SANTALUM ALBUM L.) 10.17605/osf.io/psw2r

Standards for Reporting Metabolomics Data in Phytomedicine Research 10.17605/osf.io/amdt2

The guard cell ionome: Understanding the role of ions in guard cell functions 10.1016/j.pbiomolbio.2018.11.007

Tools and Resources for Metabolomics Research Community: A 2017-2018 update 10.1002/elps.201800428

Metabolic Reprogramming: Short-term Western Diet Exposure Induces Sustained Changes in Plasma Metabolites 10.1101/554980

Standards for Reporting Metabolomics Data in Phytomedicine Research 10.17605/osf.io/ydwh5

1H NMR metabolomic analysis of skin and blubber of bottlenose dolphins reveals a functional metabolic dichotomy 10.1016/j.cbd.2019.02.004

Analysis of serum changes in response to a high fat high cholesterol diet challenge reveals metabolic biomarkers of atherosclerosis 10.1371/journal.pone.0214487

Individualized metabolomics: Opportunities and challenges 10.1515/cclm-2019-0130

Challenges and Opportunities in Cancer Metabolomics 10.1002/pmic.201900042

Metabolomics Tools to Study Links Between Pollution and Human Health: an Exposomics Perspective 10.1007/s40726-019-00109-4

Comparison of a GC-Orbitrap-MS with Parallel GC-FID Capabilities for Metabolomics of Human Serum 10.1101/740795

Biological Activities of East Indian Sandalwood Tree, Santalum album 10.7287/peerj.preprints.96v1

Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer 10.7150/thno.35186

Chemodiversity of the Glucosinolate-Myrosinase System at the Single Cell Type Resolution 10.3389/fpls.2019.00618

Open-source software tools, databases, and resources for single-cell and single-cell-type metabolomics 10.1007/978-1-4939-9831-9_15

Metabolite Extraction and Derivatization of Plasma/ Serum Samples for High Resolution GC-MS- based Metabolomics dx.doi.org/10.17504/protocols.io.723hqgn

Metabolite Extraction and Derivatization of Plasma/ Serum Samples for High Resolution GC-MS- based Metabolomics v1 (protocols.io.723hqgn) 10.17504/protocols.io.723hqgn

Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics dx.doi.org/10.17504/protocols.io.8txhwpn

The chemical exposome of type 2 diabetes mellitus: Opportunities and challenges in the omics era 10.1016/j.dsx.2019.12.001

The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research 10.1177/1099800420903083

High Resolution GC-Orbitrap-MS Metabolomics Using Both Electron Ionization and Chemical Ionization for Analysis of Human Plasma 10.1021/acs.jproteome.9b00774

Software tools, databases and resources in metabolomics: updates from 2018 to 2019 10.1007/s11306-020-01657-3

Data normalization strategies in metabolomics: Current challenges, approaches, and tools 10.1177/1469066720918446

Short-term effects of the allelochemical umbelliferone on Triticum durum L. metabolism through GC–MS based untargeted metabolomics 10.1016/j.plantsci.2020.110548

Time-course analysis of Streptococcus sanguinis after manganese depletion reveals changes in glycolytic, nucleotide, and redox metabolites 10.1101/2020.08.30.274233

Phytotoxicity, Morphological, and Metabolic Effects of the Sesquiterpenoid Nerolidol on Arabidopsis thaliana Seedling Roots 10.3390/plants9101347

Solute Carrier Family 37 Member 2 (SLC37A2) Negatively Regulates Murine Macrophage Inflammation by Controlling Glycolysis 10.1016/j.isci.2020.101125

De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. 10.1073/pnas.1902766117

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS 10.1101/2020.01.13.905091

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Time-course analysis of Streptococcus sanguinis after manganese depletion reveals changes in glycolytic and nucleic acid metabolites 10.1007/s11306-021-01795-2

Loss of function of lysosomal acid lipase (LAL) profoundly impacts osteoblastogenesis and increases fracture risk in humans 10.1016/j.bone.2021.115946

New software tools, databases, and resources in metabolomics: updates from 2020 10.1007/s11306-021-01796-1

Advances in high resolution GC-MS technology: a focus on the application of GC-Orbitrap-MS in metabolomics and exposomics for FAIR practices 10.1039/D1AY00173F

Comparative phytochemical analysis and antibacterial efficacy of in vitro and in vivo extracts from East Indian sandalwood tree (Santalum album L.) 10.1111/lam.12005

Katherine Maloney

Maloney Katherine

ORCID: 0000-0003-3472-7593

Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau 10.1021/acs.jnatprod.9b01128

Synthesis of Deoxyradicinin, an Inhibitor of Xylella fastidiosa and Liberibacter crescens, a Culturable Surrogate for Candidatus Liberibacter asiaticus 10.1021/acs.jnatprod.9b01207

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

dinesh barupal

barupal dinesh

ORCID: 0000-0002-9954-8628

Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets. 10.1016/j.copbio.2018.01.010

Effects of exposure to water disinfection by-products in a swimming pool: A metabolome-wide association study. 10.1016/j.envint.2017.11.017

Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets. 10.1038/s41598-017-15231-w

Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia. 10.18632/oncotarget.18434

Identification of small molecules using accurate mass MS/MS search. 10.1002/mas.21535

The impact of ambient air pollution on the human blood metabolome. 10.1016/j.envres.2017.03.042

compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets. 10.1021/acs.analchem.6b02394

Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. 10.1371/journal.pone.0171046

Dietary flavonoid intake and colorectal cancer risk in the European prospective investigation into cancer and nutrition (EPIC) cohort. 10.1002/ijc.30582

Environmental Tobacco Smoke Alters Metabolic Systems in Adult Rats. 10.1021/acs.chemrestox.6b00187

Prioritizing Chemicals for Risk Assessment Using Chemoinformatics: Examples from the IARC Monographs on Pesticides. 10.1289/ehp186

Systematic analysis of the polyphenol metabolome using the Phenol-Explorer database. 10.1002/mnfr.201500435

Alteration of amino acid and biogenic amine metabolism in hepatobiliary cancers: Findings from a prospective cohort study. 10.1002/ijc.29718

Polyphenol metabolome in human urine and its association with intake of polyphenol-rich foods across European countries. 10.3945/ajcn.114.101881

Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry. 10.3390/metabo5020192

MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets. 10.1093/bioinformatics/btu705

The blood exposome and its role in discovering causes of disease. 10.1289/ehp.1308015

Inactivation of metabolic genes causes short- and long-range dys-regulation in Escherichia coli metabolic network. 10.1371/journal.pone.0078360

Comparative metabolomics of estrogen receptor positive and estrogen receptor negative breast cancer: alterations in glutamine and beta-alanine metabolism. 10.1016/j.jprot.2013.10.002

Pharmacometabolomic signature of ataxia SCA1 mouse model and lithium effects. 10.1371/journal.pone.0070610

A new metabolomic workflow for early detection of Alzheimer's disease. 10.1016/j.chroma.2013.06.005

Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism. 10.1371/journal.pone.0046770

System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. 10.1074/mcp.m111.016733

MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity 10.1186/1471-2105-13-99

Metabolomics of human breast cancer: New approaches for tumor typing and biomarker discovery 10.1186/gm336

The volatile compound BinBase mass spectral database 10.1186/1471-2105-12-321

Extending biochemical databases by metabolomic surveys. 10.1074/jbc.r110.173617

Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry 10.1186/1472-6750-10-40

Human gut microbiome adopts an alternative state following small bowel transplantation 10.1073/pnas.0904847106

Extending biochemical databases by metabolomic surveys (Journal of Biological Chemistry (2011) 286, (23637-23643)) 10.1074/jbc.A110.173617

Comprehensive Circulatory Metabolomics in ME/CFS Reveals Disrupted Metabolism of Acyl Lipids and Steroids 10.3390/metabo10010034

Data Processing, Metabolomic Databases and Pathway Analysis 10.1002/9781444339956.ch12

Arginine reprogramming in ADPKD results in arginine-dependent cystogenesis 10.1152/ajprenal.00025.2018

A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium 10.3390/metabo9050101

Perspective: Dietary Biomarkers of Intake and Exposure - Exploration with Omics Approaches 10.1093/advances/nmz075

Metabolomic analysis of serum and myocardium in compensated heart failure after myocardial infarction 10.1016/j.lfs.2019.01.040

Generation and quality control of lipidomics data for the alzheimer’s disease neuroimaging initiative cohort 10.1038/sdata.2018.263

Metabolomics of photobiological hydrogen production induced by CCCP in Chlamydomonas reinhardtii 10.1016/j.ijhydene.2013.09.116

Sets of coregulated serum lipids are associated with Alzheimer's disease pathophysiology 10.1016/j.dadm.2019.07.002

Generating the blood exposome database using a comprehensive text mining and database fusion approach 10.1289/EHP4713

Systematic Error Removal Using Random Forest for Normalizing Large-Scale Untargeted Lipidomics Data 10.1021/acs.analchem.8b05592

Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics 10.1038/s41598-018-28477-9

A lipidome-wide association study of the lipoprotein insulin resistance index 10.1186/s12944-020-01321-8

A Pilot Study on the Effect of Prebiotic on Host-Microbial Co-metabolism in Peritoneal Dialysis Patients 10.1016/j.ekir.2020.05.023

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics 10.1021/acs.analchem.9b05765

Serum triglycerides in Alzheimer disease: Relation to neuroimaging and CSF biomarkers 10.1212/WNL.0000000000009436

Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease 10.1016/j.xcrm.2020.100138

Functional Microbiomics Reveals Alterations of the Gut Microbiome and Host Co-Metabolism in Patients With Alcoholic Hepatitis. 10.1002/hep4.1537

The circulating lipidome is largely defined by sex descriptors in the GOLDN, GeneBank and the ADNI studies 10.1101/731448

A comprehensive plasma metabolomics dataset for a cohort of mouse knockouts within the international mouse phenotyping consortium 10.1101/624437

Advisory Group recommendations on priorities for the IARC Monographs. 10.1016/s1470-2045(19)30246-3

Sets of Co-regulated Serum Lipids are Associated with Alzheimer Disease Pathophysiology 10.1101/550723

Prioritization of metabolic genes as novel therapeutic targets in estrogen-receptor negative breast tumors using multi-omics data and text mining 10.1101/515403

Serum triglycerides in Alzheimer’s disease: Relation to neuroimaging and CSF biomarkers 10.1101/441394

Prioritizing cancer hazard assessments for IARC Monographs using an integrated approach of database fusion and text mining 10.1016/j.envint.2021.106624

Yann GUITTON

GUITTON Yann

ORCID: 0000-0002-4479-0636

https://sites.google.com/site/rpackagemseasy/

http://workflow4metabolomics.org

http://laberca.org

https://www.pf-corsaire.org

https://www.rfmf.fr

Cytotoxicity, Fractionation and Dereplication of Extracts of the Dinoflagellate Vulcanodinium rugosum, a Producer of Pinnatoxin G 10.3390/md11093350

Isolation and functional characterization of a τ-cadinol synthase, a new sesquiterpene synthase from Lavandula angustifolia 10.1007/s11103-013-0131-3

Cytotoxicity and mycotoxin production of shellfish-derived Penicillium spp., a risk for shellfish consumers 10.1111/lam.12143

MSeasy: Unsupervised and untargeted GC-MS data processing 10.1093/bioinformatics/bts427

Essential oils from wild populations of algerian lavandula stoechas L.: Composition, chemical variability, and in vitro biological properties 10.1002/cbdv.201000301

Differential accumulation of volatile terpene and terpene synthase mRNAs during lavender (Lavandula angustifolia and L. x intermedia) inflorescence development 10.1111/j.1399-3054.2009.01315.x

Dereplication of Mammea neurophylla metabolites to isolate original 4-phenylcoumarins 10.1016/j.phytol.2014.11.011

Functional characterization of terpene synthases and chemotypic variation in three lavender species of section Stoechas 10.1111/ppl.12241

Impact of Marine-DerivedPenicilliumSpecies in the Discovery of New Potential Antitumor Drugs 10.1002/9783527681501.ch03

Serum-based metabolomics characterization of pigs treated with ractopamine 10.1007/s11306-017-1212-0

Successes and pitfalls in automated dereplication strategy using liquid chromatography coupled to mass spectrometry data: A CASMI 2016 experience 10.1016/j.phytol.2016.12.025

Successes and Pitfalls in Automated Dereplication Strategy Using Mass Spectrometry Data: a CASMI Experience 10.2174/2213235x04666160622074357

Synthesis and antiproliferative activity of ligerin and new fumagillin analogs against osteosarcoma 10.1016/j.ejmech.2014.04.012

Fungi isolated from Madagascar shrimps - investigation of the Aspergillus niger metabolism by combined LC-MS and NMR metabolomics studies 10.1016/j.aquaculture.2017.07.015

Time Dependency of Chemodiversity and Biosynthetic Pathways: An LC-MS Metabolomic Study of Marine-Sourced Penicillium 10.3390/md14050103

Automated Detection of Natural Halogenated Compounds from LC-MS Profiles–Application to the Isolation of Bioactive Chlorinated Compounds from Marine-Derived Fungi 10.1021/acs.analchem.6b02128

Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics 10.1016/j.copbio.2016.08.004

Genome size and plastid trnK-matK markers give new insights into the evolutionary history of the genus Lavandula L 10.1080/11263504.2015.1014006

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics 10.1007/s11306-017-1233-8

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics 10.1016/j.biocel.2017.07.002

Breast Milk Lipidome Is Associated with Early Growth Trajectory in Preterm Infants 10.3390/nu10020164

Breast Milk Lipidome Is Associated with Early Growth Trajectory in Preterm Infants 10.20944/preprints201712.0068.v1

Consequences of blunting the mevalonate pathway in cancer identified by a pluri-omics approach 10.1038/s41419-018-0761-0

Comprehensive Preterm Breast Milk Metabotype Associated with Optimal Infant Early Growth Pattern 10.3390/nu11030528

Ammonium Fluoride as Suitable Additive for HILIC-Based LC-HRMS Metabolomics 10.3390/metabo9120292

Correction: Alexandre-Gouabau et al. “Comprehensive Preterm Breast Milk Metabotype Associated with Optimal Infant Early Growth Pattern”, Nutrients, 2019, 11, 528 10.3390/nu12010162

Optimized characterization of short-, medium, and long-chain chlorinated paraffins in liquid chromatography-high resolution mass spectrometry 10.1016/j.chroma.2020.460927

Electrospray ionization and heterogeneous matrix effects in liquid chromatography/mass spectrometry based meta‐metabolomics: A biomarker or a suppressed ion? 10.1002/rcm.8977

A multidimensional H-1 NMR lipidomics workflow to address chemical food safety issues 10.1007/s11306-018-1360-x

Modeling the fragmentation patterns of triacylglycerides in mass spectrometry allows the quantification of the regioisomers with a minimal number of standards 10.1016/j.aca.2019.01.017

Rapid evaporative ionisation mass spectrometry and chemometrics for high-throughput screening of growth promoters in meat producing animals 10.1080/19440049.2017.1421778

Elucidation of non-intentionally added substances migrating from polyester-polyurethane lacquers using automated LC-HRMS data processing 10.1007/s00216-018-0968-z

HaloSeeker 1.0: A user-friendly software to highlight halogenated chemicals in nontargeted high-resolution mass spectrometry data sets 10.1021/acs.analchem.8b05103

Quantitative resistance to clubroot deconvoluted into QTL-specific metabolic modules 10.1093/jxb/erz265

Corrigendum to “Dye residues in aquaculture products: Targeted and metabolomics mass spectrometric approaches to track their abuse [Food Chem. 294 (2019) 355–367] 10.1016/j.foodchem.2019.125539

A European proposal for quality control and quality assurance of tandem mass spectral libraries Open Access 10.1186/s12302-020-00314-9

Workﬂow4Metabolomics: A collaborative research infrastructure for computational metabolomics 10.1093/bioinformatics/btu813

Simultaneous exploration of nutrients and pollutants in human milk and their impact on preterm infant growth: An integrative cross-platform approach 10.1016/j.envres.2019.109018

WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data 10.3390/metabo9090171

Dye residues in aquaculture products: Targeted and metabolomics mass spectrometric approaches to track their abuse 10.1016/j.foodchem.2019.05.056

W4M00004_GCMS-Algae 10.15454/1.4811272313071519E12

W4M00005_Ractopamine-Pig 10.15454/1.4811287270056958E12

Single-Step Extraction Coupled with Targeted HILIC-MS/MS Approach for Comprehensive Analysis of Human Plasma Lipidome and Polar Metabolome 10.3390/metabo10120495

Non-targeted screening methodology to characterise human internal chemical exposure: Application to halogenated compounds in human milk 10.1016/j.talanta.2020.121979

Lavender inflorescence A model to study regulation of terpenes synthesis 10.4161/PSB.5.6.11704

Combining MS/MS fragmentation, correlation and biochemical reaction networks to improve compound annotation in metabolome investigations of marine-derived Penicillium species 10.1055/S-0034-1394586

Marine halogenated compound analysis: from an R package to the isolation of new griseophenone derivatives 10.1055/S-0036-1596648

Automated MS/MS data annotation: CASMI experiences 10.1055/S-0036-1596289

A comparative study of terpene composition in different clades of the genus Lavandula 10.1080/23818107.2018.1500305

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data 10.1038/S41587-020-0700-3

Untargeted Lipidomic Profiling of Dry Blood Spots Using SFC-HRMS 10.3390/metabo11050305

Extending the Lipidome Coverage by Combining Different Mass Spectrometric Platforms: An Innovative Strategy to Answer Chemical Food Safety Issues 10.3390/foods10061218

Louis-Felix NOTHIAS

NOTHIAS Louis-Felix

ORCID: 0000-0001-6711-6719

https://dorresteinlab.ucsd.edu/

Jatrophane diterpenes as inhibitors of chikungunya virus replication: structure-activity relationship and discovery of a potent lead. 10.1021/np500271u

Antiviral Activity of Diterpene Esters on Chikungunya Virus and HIV Replication 10.1021/acs.jnatprod.5b00073

LC-MS2-Based dereplication of Euphorbia extracts with anti-Chikungunya virus activity 10.1016/j.fitote.2015.06.021

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation 10.1021/acs.jnatprod.7b00737

Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089

Did a plant-herbivore arms race drive chemical diversity in Euphorbia? 10.1101/323014

Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908

Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking 10.1038/s41598-019-39583-7

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools 10.3390/metabo9070144

Feature-based Molecular Networking in the GNPS Analysis Environment 10.1101/812404

ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules 10.1101/842740

Classes for the masses: Systematic classification of unknowns using fragmentation spectra 10.1101/2020.04.17.046672

Ion Identity Molecular Networking in the GNPS Environment 10.1101/2020.05.11.088948

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC 10.1038/s42256-020-00234-6

Publisher Correction: Database-independent molecular formula annotation using Gibbs sampling through ZODIAC 10.1038/s42256-020-00259-x

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Studying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale 10.1021/jasms.0c00240

The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra 10.1038/s41587-020-0740-8

Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21

Mabel Gonzalez

Gonzalez Mabel

ORCID: 0000-0003-4649-2963

Field but not lab paradigms support generalisation by predators of aposematic polymorphic prey: The Oophaga histrionica complex 10.1007/s10682-013-9635-1

Conspicuousness, color resemblance, and toxicity in geographically diverging mimicry: The pan-Amazonian frog Allobates femoralis 10.1111/evo.13170

Behavioral responses of Rhodnius prolixus to volatile organic compounds released in vitro by bacteria isolated from human facial skin. 10.1371/journal.pntd.0006423

Yeast Smell Like What They Eat: Analysis of Volatile Organic Compounds of Malassezia furfur in Growth Media Supplemented with Different Lipids 10.3390/molecules24030419

Volatilomics of Natural Products: Whispers from Nature 10.5772/intechopen.97228

Learning about microbial language: possible interactions mediated by microbial volatile organic compounds (VOCs) and relevance to understanding Malassezia spp. metabolism 10.1007/s11306-021-01786-3

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Empowering Latina scientists 10.1126/science.aaw6004

First characterization of toxic alkaloids and volatile organic compounds (VOCs) in the cryptic dendrobatid Silverstoneia punctiventris 10.1186/s12983-021-00420-1