A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
Marnix H. Medema Miaomiao Zhou Sacha A.F.T. van Hijum Jolein Gloerich Hans J.C.T Wessels Roland J. Siezen Marc Strous
BMC Genomics, 2010
https://doi.org/10.1186/1471-2164-11-299
Jolein Gloerich
Gloerich Jolein
ORCID: 0000-0001-5976-8426
Dickkopf-related protein 3 is a potential Aβ-associated protein in Alzheimer's Disease 10.1111/jnc.13216
Whole cell formaldehyde cross-linking simplifies purification of mitochondrial nucleoids and associated proteins involved in mitochondrial gene expression 10.1371/journal.pone.0116726
Peptide microarrays to probe for competition for binding sites in a protein interaction network 10.1016/j.jprot.2013.05.031
Analysis of 953 Human Proteins from a Mitochondrial HEK293 Fraction by Complexome Profiling 10.1371/journal.pone.0068340
The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium 10.1111/j.1462-2920.2012.02774.x
BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion 10.1089/ars.2011.4253
A comprehensive full factorial LC-MS/MS proteomics benchmark data set 10.1002/pmic.201100284
C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation 10.1093/nar/gkr1271
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase 10.1186/gb-2012-13-2-r12
Protein enrichment by capture-release based on strain-promoted cycloaddition of azide with bicyclononyne (BCN) 10.1016/j.bmc.2011.07.049
Surface-affinity profiling to identify host-pathogen interactions 10.1128/IAI.05572-11
Molecular mechanism of anaerobic ammonium oxidation 10.1038/nature10453
Pinpointing biomarkers in proteomic LC/MS data by moving-window discriminant analysis 10.1021/ac200334s
Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly 10.1002/9781118010518.ch43
Liquid chromatography - Mass spectrometry-based proteomics of Nitrosomonas 10.1016/B978-0-12-381294-0.00021-3
Improved parametric time warping for proteomics 10.1016/j.chemolab.2010.04.008
Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I 10.1016/j.cmet.2010.08.002
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis 10.1186/1471-2164-11-299
Nitrite-driven anaerobic methane oxidation by oxygenic bacteria 10.1038/nature08883
Automated measurement of permethylated serum N-glycans by MALDI-linear ion trap mass spectrometry 10.1016/j.carres.2009.06.010
Proteomic profiling and identification in peritoneal fluid of children treated by peritoneal dialysis 10.1093/ndt/gfn212
Hepatocystin Is not secreted in cyst fluid of hepatocystin mutant polycystic liver patients 10.1021/pr8000282
Proteomics approaches to study genetic and metabolic disorders 10.1021/pr060487w
Metabolism of phytol to phytanic acid in the mouse, and the role of PPARγ in its regulation 10.1194/jlr.M600050-JLR200
Bezafibrate induces FALDH in human fibroblasts; implications for Sjögren-Larsson syndrome 10.1016/j.ymgme.2006.05.009
Peroxisomal trans-2-enoyl-CoA reductase is involved in phytol degradation 10.1016/j.febslet.2006.03.011
Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis 10.1086/498880
A phytol-enriched diet induces changes in fatty acid metabolism in mice both via PPARα-dependent and -independent pathways 10.1194/jlr.M400337-JLR200
A novel HPLC-based method to diagnose peroxisomal D-bifunctional protein enoyl-CoA hydratase deficiency 10.1194/jlr.D200039-JLR200
Branched chain fatty acids induce nitric oxide-dependent apoptosis in vascular smooth muscle cells 10.1074/jbc.M204639200
Plasma C-Peptide and Risk of Developing Type 2 Diabetes in the General Population 10.3390/jcm9093001
Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters 10.1007/978-1-62703-122-6_2
Synthetic Biology in Streptomyces Bacteria 10.1016/b978-0-12-385075-1.00021-4
Computational approaches to natural product discovery 10.1038/nchembio.1884
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms 10.1038/nrmicro2478
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis 10.1371/journal.pcbi.1004016
Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism 10.1016/j.febslet.2011.06.014
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models 10.1371/journal.pone.0051511
The future of industrial antibiotic production: From random mutagenesis to synthetic biology 10.4161/bbug.2.4.16114
Metabolomics methods for the synthetic biology of secondary metabolism 10.1016/j.febslet.2012.02.008
Computational tools for the synthetic design of biochemical pathways 10.1038/nrmicro2717
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis 10.1186/1471-2164-11-299
Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus 10.1111/j.1751-7915.2010.00226.x
Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea 10.1111/j.1462-2920.2008.01724.x
Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters 10.1016/j.cell.2014.06.034
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products 10.1371/journal.pcbi.1003822
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters 10.1093/nar/gkv437
Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice 10.1016/j.copbio.2013.03.006
Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block 10.1021/sb500368w
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers 10.1093/nar/gkt449
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences 10.1093/nar/gkr466
The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways 10.1093/gbe/evq013
MS/MS networking guided analysis of molecule and gene cluster families 10.1073/pnas.1303471110
Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast 10.1093/molbev/mst025
Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii 10.1128/jb.02132-12
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity 10.1093/nar/gkr323
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation 10.1128/mmbr.00037-08
Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum. 10.1186/s12864-015-2154-4
Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66 10.1021/acschembio.5b00801
Computational strategies for genome-based natural product discovery and engineering in fungi 10.1016/j.fgb.2016.01.006
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters 10.1093/nar/gkw960
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides 10.1038/nmicrobiol.2016.197
Editorial: Synthetic biology and bioinformatics 10.1039/c6np90031c
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters 10.1093/nar/gkx305
Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus 10.1186/s12864-017-3966-1
Mining prokaryotes for antimicrobial compounds: from diversity to function 10.1093/femsre/fux014
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters 10.1093/bib/bbx146
Standardization for natural product synthetic biology 10.1039/c6np00030d
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways 10.1039/c6np00035e
Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin 10.1128/genomea.00453-17
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria 10.1093/bioinformatics/btx400
Collaborating with Undergraduates To Contribute to Biochemistry Community Resources 10.1021/acs.biochem.7b00872
Road MAPs to engineer host microbiomes. 10.1016/j.mib.2017.11.023
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. 10.1111/1462-2920.13927
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. 10.1073/pnas.1705567114
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. 10.1093/nar/gkx319
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. 10.1016/j.fgb.2016.01.012
Exploration and exploitation of the environment for novel specialized metabolites. 10.1016/j.copbio.2018.01.017
Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology 10.1128/mSystems.00182-17
Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics. 10.1016/j.chembiol.2018.02.008
HEx: A heterologous expression platform for the discovery of fungal natural products. 10.1126/sciadv.aar5459
luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria. 10.1128/msystems.00208-17
A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. 10.1021/jacs.7b13292
Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium. 10.3389/fmicb.2018.01158
Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. 10.1038/s41396-018-0186-x
Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH. 10.1007/978-1-4939-7874-8_15
A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences 10.1186/s40793-018-0318-y
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters 10.1093/nar/gky1060
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1101/463620
Mining bacterial genomes to reveal secret synergy 10.1074/jbc.H118.006669
Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters 10.1038/s42003-019-0333-6
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping 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
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline 10.1093/nar/gkz310
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459
BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs 10.1101/gr.243477.118
Genome Mining Approaches to Bacterial Natural Product Discovery 10.1016/b978-0-12-409547-2.14627-x
Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines 10.1039/C9NP00021F
PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters 10.1101/083535
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools 10.3390/metabo9070144
Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L. 10.3389/fpls.2019.00846
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome 10.1126/science.aaw9285
MIBiG 2.0: a repository for biosynthetic gene clusters of known function 10.1093/nar/gkz882
A metabolic pathway for bile acid dehydroxylation by the gut microbiome 10.1101/758557
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines 10.1101/669291
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery 10.1021/acscentsci.9b00806
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology 10.1038/s41564-019-0588-1
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia 10.1101/856955
Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae 10.1111/nph.16338
Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat 10.1098/rspb.2019.2527
Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota 10.1101/2020.03.06.976126
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery 10.1101/2020.03.14.992123
Linking genomics and metabolomics to chart specialized metabolic diversity 10.1039/D0CS00162G
Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota 10.1099/mgen.0.000373
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining 10.1093/nar/gkaa374
Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products 10.1101/2020.05.19.104752
Ecology and genomics of Actinobacteria: new concepts for natural product discovery 10.1038/s41579-020-0379-y
The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms 10.1038/s42003-020-0993-2
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters 10.1101/2020.08.17.240838
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia 10.1074/jbc.RA120.013528
Microbial natural product databases: moving forward in the multi-omics era 10.1039/D0NP00053A
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms 10.1038/s42003-020-01228-1
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery 10.1128/mSystems.00267-20
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms 10.1038/s42003-020-01271-y
BiG-FAM: the biosynthetic gene cluster families database 10.1093/nar/gkaa812
Coevolution-based prediction of protein–protein interactions in polyketide biosynthetic assembly lines 10.1093/bioinformatics/btaa595
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes 10.1093/nar/gkaa978
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order 10.1038/s41598-020-77723-6
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes 10.1101/2020.12.14.422671
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides 10.1371/journal.pbio.3001026
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters 10.1093/gigascience/giaa154
The year 2020 in natural product bioinformatics: an overview of the latest tools and databases 10.1039/D0NP00090F
Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis 10.1101/2021.02.11.430889
A systematic analysis of metabolic pathways in the human gut microbiota 10.1101/2021.02.25.432841
Omics-based strategies to discover novel classes of RiPP natural products 10.1016/j.copbio.2020.12.008
Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria 10.1038/s41467-021-21163-x
The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range 10.3389/fbioe.2021.623701
Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques 10.1101/2021.01.20.427441
Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes 10.3389/fmicb.2020.574053
A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo 10.21203/rs.3.rs-126949/v1
A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters 10.1016/j.chembiol.2020.11.009
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters 10.1101/2020.11.08.370601
antiSMASH 6.0: improving cluster detection and comparison capabilities 10.1093/nar/gkab335
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota 10.1093/nar/gkab353
Mining genomes to illuminate the specialized chemistry of life 10.1038/s41576-021-00363-7
Dominant drivers of the human plasma metabolome 10.21203/rs.3.rs-688716/v1
A global survey of specialized metabolic diversity encoded in bacterial genomes 10.1101/2021.08.11.455920
cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters 10.1093/bioadv/vbab016
Marc Strous
Strous Marc
ORCID: 0000-0001-9600-3828
Environmental Breviatea harbour mutualistic Arcobacter epibionts 10.1038/nature18297
Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly 10.1002/9781118010518.ch43
Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture 10.1111/1462-2920.12552
The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms 10.1007/s002530051340
Ultrastructure of the denitrifying methanotroph "Candidatus methylomirabilis oxyfera," a novel polygon-shaped bacterium 10.1128/JB.05816-11
Co-localization of particulate methane monooxygenase and cd1 nitrite reductase in the denitrifying methanotroph 'Candidatus Methylomirabilis oxyfera' 10.1111/j.1574-6968.2012.02615.x
New concepts of microbial treatment processes for the nitrogen removal in wastewater 10.1016/S0168-6445(03)00039-1
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software 10.1038/nmeth.4458
Use of highly alkaline conditions to improve cost-effectiveness of algal biotechnology 10.1007/s00253-015-7208-7
Denitrification and aerobic respiration, hybrid electron transport chains and co-evolution 10.1016/j.bbabio.2012.10.002
Anammox organisms: Enrichment, cultivation, and environmental analysis 10.1016/S0076-6879(05)97003-1
Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa 10.1038/ismej.2013.135
Candidatus 'Brocadia fulgida': An autofluorescent anaerobic ammonium oxidizing bacterium 10.1111/j.1574-6941.2007.00408.x
Ammonium removal from concentrated waste streams with the anaerobic ammonium oxidation (anammox) process in different reactor configurations 10.1016/S0043-1354(97)00055-9
An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by 31P NMR 10.1007/s00253-009-2309-9
Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat 10.3389/fmicb.2014.00231
Carbon isotope-labelling experiments indicate that ladderane lipids of anammox bacteria are synthesized by a previously undescribed, novel pathway 10.1111/j.1574-6968.2008.01483.x
Challenging protein purification from anammox bacteria 10.1016/j.ijbiomac.2006.02.018
Full-scale granular sludge Anammox process 10.2166/wst.2007.238
Kinetics, diffusional limitation and microscale distribution of chemistry and organisms in a CANON reactor 10.1016/j.femsec.2004.09.003
Deciphering the evolution and metabolism of an anammox bacterium from a community genome 10.1038/nature04647
A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis 10.1186/1745-6150-4-8
Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations 10.1038/ismej.2016.197
Combined structural and chemical analysis of the anammoxosome: A membrane-bounded intracytoplasmic compartment in anammox bacteria 10.1016/j.jsb.2007.05.005
Erratum to "Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam". [Water Research 41 (2007) 18] (DOI:10.1016/j.watres.2007.03.044) 10.1016/j.watres.2007.11.001
The anammoxosome: An intracytoplasmic compartment in anammox bacteria 10.1016/j.femsle.2004.01.044
Robust, high-productivity phototrophic carbon capture at high pH and alkalinity using natural microbial communities 10.1186/s13068-017-0769-1
Aerobic and anaerobic ammonia oxidizing bacteria - Competitors or natural partners? 10.1016/S0168-6496(01)00208-2
Impact of temperature on ladderane lipid distribution in anammox bacteria 10.1128/AEM.01796-09
Missing lithotroph identified as new planctomycete 10.1038/22749
Archaeal nitrification in the ocean 10.1073/pnas.0600756103
Ladderane phospholipids in anammox bacteria comprise phosphocholine and phosphoethanolamine headgroups 10.1111/j.1574-6968.2006.00233.x
Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria 10.1128/AEM.70.6.3785-3788.2004
A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones 10.1111/j.1462-2920.2008.01640.x
Comparative proteomics of three species of ammonia-oxidizing bacteria 10.3389/fmicb.2018.00938
The anammox case - A new experimental manifesto for microbiological eco-physiology 10.1023/A:1020590413079
Anaerobic ammonia oxidation in the presence of nitrogen oxides (NOx) by two different lithotrophs 10.1128/AEM.68.11.5351-5357.2002
Close relationship of RNase P RNA in Gemmata and anammox planctomycete bacteria 10.1111/j.1574-6968.2006.00597.x
Factors influencing the density of aerobic granular sludge 10.1007/s00253-012-4459-4
Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp 10.3389/fmicb.2017.01461
FACIL: Fast and accurate genetic code inference and logo 10.1093/bioinformatics/btr316
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly 10.1093/bioinformatics/btp377
Metagenome from a Spirulina digesting biogas reactor: Analysis via binning of contigs and classification of short reads 10.1186/s12866-015-0615-1
Metabolic specialization of denitrifiers in permeable sediments controls N2O emissions 10.1111/1462-2920.14385
Microbial nitrate respiration - Genes, enzymes and environmental distribution 10.1016/j.jbiotec.2010.12.025
Optimizing membrane protein overexpression in the Escherichia coli strain Lemo21(DE3) 10.1016/j.jmb.2012.07.019
Candidatus "Anammoxoglobus propionicus" a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria 10.1016/j.syapm.2006.03.004
1994-2004: 10 Years of research on the anaerobic oxidation of ammonium 10.1042/BST0330119
Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria 10.1007/s00253-003-1422-4
Intracellular localization of membrane-bound ATPases in the compartmentalized anammox bacterium 'Candidatus Kuenenia stuttgartiensis' 10.1111/j.1365-2958.2010.07242.x
Biofilm-based photobioreactors: Their design and improving productivity through efficient supply of dissolved inorganic carbon 10.1093/femsle/fnx218
Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea 10.1111/j.1462-2920.2008.01724.x
Anaerobic ammonium-oxidizing bacteria in marine environments: Widespread occurrence but low diversity 10.1111/j.1462-2920.2007.01266.x
Haloalkaline Bioconversions for Methane Production from Microalgae Grown on Sunlight 10.1016/j.tibtech.2016.02.008
Erratum: Archaeal nitrification in the ocean (Proceedings of the National Academy of Sciences of the United States of America (2006) 103, 33, (12317-12322) DOI: 10.1073/pnas.0600756103)) 10.1073/pnas.0701630104
Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': Kinetic and transcriptional analysis 10.1111/j.1462-2920.2011.02682.x
Completely autotrophic nitrogen removal over nitrite in one single reactor 10.1016/S0043-1354(01)00476-6
A new soluble 10 kDa monoheme cytochrome c-552 from the anammox bacterium Candidatus "Kuenenia stuttgartiensis" 10.1016/j.femsle.2005.09.007
Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum 10.1128/AEM.00067-09
Erratum to Predicting microbial nitrogen pathways from basic principles [Environ Microbiol, 13, (2013) 1477-1487] 10.1111/1462-2920.12354
The occurrence of hopanoids in planctomycetes: Implications for the sedimentary biomarker record 10.1016/j.orggeochem.2004.01.013
Enrichment and characterization of marine anammox bacteria associated with global nitrogen gas production 10.1111/j.1462-2920.2008.01643.x
Propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria 10.1128/AEM.71.2.1066-1071.2005
Ladderane lipid distribution in four genera of anammox bacteria 10.1007/s00203-008-0364-8
A microbial consortium couples anaerobic methane oxidation to denitrification 10.1038/nature04617
The binning of metagenomic contigs for microbial physiology of mixed cultures 10.3389/fmicb.2012.00410
Methanotrophic symbionts provide carbon for photosynthesis in peat bogs 10.1038/nature03802
A mixed ladderane/n-alkyl glycerol diether membrane lipid in an anaerobic ammonium-oxidizing bacterium 10.1039/b409806d
Implementation of the anammox process for improved nitrogen removal 10.1081/ESE-120037873
Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria 10.1111/j.1462-2920.2008.01733.x
A multi-proxy study of anaerobic ammonium oxidation in marine sediments of the Gullmar Fjord, Sweden 10.1111/j.1758-2229.2010.00233.x
Activity and diversity of haloalkaliphilic methanogens in Central Asian soda lakes 10.1016/j.jbiotec.2012.04.003
Molecular mechanism of anaerobic ammonium oxidation 10.1038/nature10453
Role of extracellular carbonic anhydrase in dissolved inorganic carbon uptake in alkaliphilic phototrophic biofilm 10.3389/fmicb.2018.02490
Novel compartmentalisation in planctomycete bacteria 10.1017/S1431927604886963
Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: Biogas production, metagenome and metatranscriptome 10.3389/fmicb.2015.00597
Improved nitrogen removal by application of new nitrogen-cycle bacteria 10.1023/A:1015191724542
Nitrite-driven anaerobic methane oxidation by oxygenic bacteria 10.1038/nature08883
Microbiology and application of the anaerobic ammonium oxidation ('anammox') process 10.1016/S0958-1669(00)00211-1
Biochemistry and molecular biology of anammox bacteria biochemistry and molecular biology of anammox bacteria M.S.M. Jetten et al. 10.1080/10409230902722783
Anaerobic oxidation of methane and ammonium 10.1146/annurev.micro.58.030603.123605
The environmental controls that govern the end product of bacterial nitrate respiration 10.1126/science.1254070
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis 10.1186/1471-2164-11-299
Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., Two New Species of Anaerobic Ammonium Oxidizing Bacteria 10.1078/072320203770865837
Biomarkers for in situ detection of anaerobic ammonium-oxidizing (Anammox) bacteria 10.1128/AEM.71.4.1677-1684.2005
Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents 10.1038/ismej.2008.72
Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem 10.1038/ismej.2008.75
Assessing species biomass contributions in microbial communities via metaproteomics 10.1038/s41467-017-01544-x
Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria 10.1042/BST0330205
Designer microbiomes for environmental, energy and health biotechnology 10.1016/j.mib.2017.12.007
Cell division ring, a new cell division protein and vertical inheritance of a bacterial organelle in anammox planrtomycetes 10.1111/j.1365-2958.2009.06841.x
Mobility and persistence of methane in groundwater in a controlled-release field experiment 10.1038/ngeo2919
Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities 10.1073/pnas.1722325115
An improved medium for the anaerobic growth of Paracoccus denitrificans Pd1222 10.3389/fmicb.2014.00018
Predicting microbial nitrogen pathways from basic principles 10.1111/j.1462-2920.2011.02450.x
Enrichment of anammox from activated sludge and its application in the CANON process 10.1007/s00248-004-0186-4
Global impact and application of the anaerobic ammonium-oxidizing (anammox) bacteria 10.1042/BST0340174
Linking ultrastructure and function in four genera of anaerobic ammonium-oxidizing bacteria: Cell plan, glycogen storage, and localization of cytochrome c proteins 10.1128/JB.01449-07
Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge 10.1007/s00253-011-3361-9
Linearly concatenated cyclobutane lipids form a dense bacterial membrane 10.1038/nature01128
Anammox bacteria disguised as denitrifiers: Nitrate reduction to dinitrogen gas via nitrite and ammonium 10.1111/j.1462-2920.2006.01183.x
Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation 10.1016/S0723-2020(00)80050-8
Continuous cultivation and thermodynamic aspects of niche definition in the nitrogen cycle 10.1016/B978-0-12-381294-0.00002-X
Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations 10.1111/1462-2920.13895
Physiological role of the respiratory quinol oxidase in the anaerobic nitrite-reducing methanotroph 'candidatus methylomirabilis oxyfera' 10.1099/mic.0.045187-0
Structural identification of ladderane and other membrane lipids of planctomycetes capable of anaerobic ammonium oxidation (anammox) 10.1111/j.1742-4658.2005.04842.x
Anaerobic ammonium oxidation by anammox bacteria in the Black Sea 10.1038/nature01472
The anaerobic oxidation of ammonium 10.1016/S0168-6445(98)00023-0
Rapid recovery of cyanobacterial pigments in desiccated biological soil crusts following addition of 10.1371/journal.pone.0112372
Impacts of chemical gradients on microbial community structur 10.1038/ismej.2016.175
Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities 10.3389/fmicb.2015.01461
Erratum to "Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam" [Water Research 41 (2007) 18] (DOI:10.1016/j.watres.2007.03.044) 10.1016/j.watres.2009.09.051
Application, eco-physiology and biodiversity of anaerobic ammonium-oxidizing bacteria 10.1007/s11157-004-7247-5
Adaptation of a freshwater anammox population to high salinity wastewater 10.1016/j.jbiotec.2006.05.012
A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus 'Methylomirabilis oxyfera' 10.1042/BST0390243
Cell compartmentalisation in planctomycetes: Novel types of structural organisation for the bacterial cell 10.1007/s002030100280
Startup of reactors for anoxic ammonium oxidation: Experiences from the first full-scale anammox reactor in Rotterdam 10.1016/j.watres.2007.03.044
Sacha van Hijum
van Hijum Sacha
ORCID: 0000-0003-0741-2991
Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in L. lactis SK11. 10.3389/fmicb.2018.02418
Integrating glycomics and genomics uncovers SLC10A7 as essential factor for bone mineralization by regulating post-Golgi protein transport and glycosylation. 10.1093/hmg/ddy213
The Contribution of Genetic Variation of Streptococcus Pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease. 10.1093/cid/ciy417
Primary cilia-regulated transcriptome in the renal collecting duct. 10.1096/fj.201701228r
Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. 10.1186/s40168-017-0395-y
Correction for Quainoo et al., "Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis". 10.1128/CMR.00082-17
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. 10.1128/CMR.00016-17
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. 10.7717/peerj.3698
Gut microbiome in ADHD and its relation to neural reward anticipation. 10.1371/journal.pone.0183509
The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease 10.1101/169722
Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. 10.1186/s40168-017-0278-2
Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. 10.1164/rccm.201605-1042OC
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine 10.7287/peerj.preprints.2918
Draft Genome Sequences of 24 Lactococcus lactis Strains. 10.1128/genomeA.01737-16
Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains. 10.1128/genomeA.01739-16
Advances and perspectives in computational prediction of microbial gene essentiality. 10.1093/bfgp/elv063
Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data. 10.1038/srep42808
Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease. 10.1128/mBio.01984-16
Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis. 10.1371/journal.pone.0167944
Reply to Meisel et al. 10.1016/j.jid.2016.11.013
An In vitro Model for Bacterial Growth on Human Stratum Corneum. 10.2340/00015555-2401
Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin. 10.1016/j.jaci.2016.09.017
Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5. 10.1128/genomeA.01090-16
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). 10.1186/s40793-016-0172-8
Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats. 10.1111/1462-2920.13455
Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening. 10.1016/j.ijfoodmicro.2016.03.027
Nomadic Lifestyle of Lactobacillus plantarum Revealed by Comparative Genomics of 54 strains Isolated from Different Niches 10.1101/043117
Draft Genome Sequence of Lactobacillus plantarum SF2A35B. 10.1128/genomeA.01638-15
Resequencing of the Lactobacillus plantarum Strain WJL Genome. 10.1128/genomeA.01382-15
Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland. 10.1128/genomeA.01377-15
Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877. 10.1128/genomeA.01370-15
The post-vaccine microevolution of invasive Streptococcus pneumoniae. 10.1038/srep14952
Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice. 10.1093/carcin/bgv120
Microbial bioinformatics for food safety and production. 10.1093/bib/bbv034
Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. 10.1371/journal.pone.0127036
Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU. 10.3389/fmicb.2015.00422
CiVi: circular genome visualization with unique features to analyze sequence elements. 10.1093/bioinformatics/btv249
Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine. 10.1128/genomeA.00097-15
The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. 10.1186/2049-2618-2-44
Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology. 10.1186/1471-2164-15-1106
From microbial gene essentiality to novel antimicrobial drug targets. 10.1186/1471-2164-15-958
Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness. 10.1186/s12934-014-0148-6
Degenerate target sites mediate rapid primed CRISPR adaptation. 10.1073/pnas.1400071111
Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains. 10.1016/j.plasmid.2014.01.002
Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress. 10.1371/journal.pone.0085625
Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress. 10.1128/AEM.03434-13
Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract. 10.1002/biot.201200259
Multifactorial diversity sustains microbial community stability. 10.1038/ismej.2013.108
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. 10.1371/journal.pone.0063523
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. 10.1093/bfgp/elt008
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods. 10.1186/1471-2180-13-68
Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. 10.1371/journal.pone.0059239
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. 10.1186/1471-2334-13-110
Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer. 10.1016/j.bpg.2013.03.008
A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children. 10.1186/1471-2164-14-74
Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. 10.1128/genomeA.00119-12
Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes. 10.1186/1471-2164-14-7
Genome Analysis of Moraxella catarrhalis Strain RH4, a Human Respiratory Tract Pathogen. 10.1128/JB.01831-12
Microbiome dynamics of human epidermis following skin barrier disruption. 10.1186/gb-2012-13-11-r101
Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1. 10.1371/journal.pone.0045097
Application of state-of-art sequencing technologies to indigenous food fermentations. 10.1016/j.copbio.2012.08.004
ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. 10.1371/journal.pone.0043012
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? 10.1093/bib/bbs034
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. 10.1186/1471-2164-13-170
Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730). 10.1128/JB.00141-12
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. 10.1128/JB.06275-11
Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. 10.1099/mic.0.055434-0
Characterization of the global impact of low temperature gas plasma on vegetative microorganisms. 10.1002/pmic.201000637
FACIL: Fast and Accurate Genetic Code Inference and Logo. 10.1093/bioinformatics/btr316
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. 10.1111/j.1751-7915.2011.00247.x
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis. 10.1128/AEM.02283-10
Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. 10.1128/AEM.01122-10
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. 10.1093/bioinformatics/btq535
Genome (re-)annotation and open-source annotation pipelines. 10.1111/j.1751-7915.2010.00191.x
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. 10.1186/1471-2164-11-299
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen. 10.1128/JB.00121-10
Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. 10.1128/JB.00276-10
PanCGHweb: a web tool for genotype calling in pangenome CGH data. 10.1093/bioinformatics/btq103
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. 10.1128/MMBR.00037-08
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. 10.1093/bioinformatics/btp013
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. 10.1186/1471-2105-9-535
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. 10.1093/bioinformatics/btn588
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. 10.1186/1471-2164-9-495
Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons. 10.1128/AEM.00117-08
The relative value of operon predictions. 10.1093/bib/bbn019
Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons. 10.1186/1471-2105-9-93
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. 10.1093/bioinformatics/btl658
Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media. 10.1021/bp0602294
BAGEL: a web-based bacteriocin genome mining tool. 10.1093/nar/gkl237
Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae. 10.1074/jbc.m601661200
Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance. 10.1128/AAC.50.5.1753-1761.2006
SIMAGE: simulation of DNA-microarray gene expression data. 10.1186/1471-2105-7-205
Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria. 10.1128/MMBR.70.1.157-176.2006
Comparative and functional genomics of lactococci. 10.1016/j.femsre.2005.04.004
The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element. 10.1074/jbc.m502349200
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. 10.1093/nar/gki356
Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. 10.1128/JB.187.11.3752-3761.2005
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. 10.1186/1471-2164-6-77
Saturation and quantization reduction in microarray experiments using two scans at different sensitivities. 10.2202/1544-6115.1057
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. 10.1093/bioinformatics/bth206
PreP: gene expression data pre-processing. 10.1093/bioinformatics/btg318
Projector: automatic contig mapping for gap closure purposes. 10.1093/nar/gng144
UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. 10.1093/bioinformatics/btg203
Transcriptome analysis and related databases of Lactococcus lactis. 10.1023/a:1020691801251
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran