Paperbase

Kelly Weldon

Weldon Kelly

ORCID: 0000-0003-1064-8153

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure 10.1101/804401

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

Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure 10.1002/rcm.8725

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

Targeted Neuronal Activation of the Gastrointestinal Tract Shapes the Environment of the Gut in Mice 10.1101/2021.04.12.439539

Reference data-set driven metabolomics 10.21203/rs.3.rs-654519/v1

Austin Swafford

Swafford Austin

ORCID: 0000-0001-5655-8300

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

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

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

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1101/2020.05.12.20073577

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

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures 10.1101/2021.04.04.438427

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

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. 10.1128/msystems.01216-20

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

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

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/v2

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

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

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV. 10.1128/msystems.00528-20

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets 10.1101/2020.10.06.327080

Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. 10.1128/msystems.00465-20

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

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

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy. 10.1128/msystems.00292-20

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

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs. 10.1128/msystems.00635-19

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

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age. 10.1128/msystems.00630-19

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

In vivo evaluation of the CB₁ allosteric modulator LDK1258 reveals CB₁-receptor independent behavioral effects. 10.1016/j.pbb.2019.172840

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

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

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0252-6

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0209-9

Light-Induced Stress as a Primary Evolutionary Driver of Eye Origins 10.20944/preprints201904.0107.v2

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. 10.1128/msystems.00261-19

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data 10.1101/591016

Age and sex-dependent patterns of gut microbial diversity in human adults 10.1101/544270

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science 10.7287/peerj.preprints.27295v2

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. 10.1128/msystems.00166-18

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

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

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/msystems.00031-18

American Gut: an Open Platform for Citizen-Science Microbiome Research 10.1101/277970

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

Inhibition of DYRK1A and GSK3B induces human β-cell proliferation. 10.1038/ncomms9372

Detection and correction of artefacts in estimation of rare copy number variants and analysis of rare deletions in type 1 diabetes. 10.1093/hmg/ddu581

An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes. 10.2337/db10-0446

Thermal ablation of tumor cells with antibody-functionalized single-walled carbon nanotubes. 10.1073/pnas.0803557105

Julia Gauglitz

Gauglitz Julia / Julia M. Vraspir

ORCID: 0000-0003-3146-2489

Amphiphilic siderophore production by oil-associating microbes 10.1039/c4mt00047a

Microbial Tailoring of Acyl Peptidic Siderophores 10.1021/bi500266x

A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill 10.1016/j.jinorgbio.2011.10.013

Optical Signatures of Dissolved Organic Matter Transformation in the Global Ocean 10.3389/fmars.2015.00118

Amino acid variability in the peptide composition of a suite of amphiphilic peptide siderophores from an open ocean Vibrio species 10.1007/s00775-013-0995-3

Identification of new members within suites of amphiphilic marine siderophores 10.1007/s10534-010-9378-1

Chemistry of Marine Ligands and Siderophores 10.1146/annurev.marine.010908.163712

Both Incubation Temperature and Posthatching Temperature Affect Swimming Performance and Morphology of Wood Frog Tadpoles ( Rana sylvatica ) 10.1086/498182

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages 10.1101/347716

Untargeted Mass Spectrometry-Based Metabolomics Approach Unveils Molecular Changes in Raw and Processed Foods and Beverages 10.1016/j.foodchem.2019.125290

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds 10.1101/824888

A UHPLC-HRMS based metabolomics and chemoinformatics approach to chemically distinguish ‘super foods’ from a variety of plant-based foods 10.1016/j.foodchem.2019.126071

Active nitrogen fixation by Crocosphaera expands their niche despite the presence of ammonium – A case study 10.1038/s41598-019-51378-4

Quantifying Oxygen Management and Temperature and Light Dependencies of Nitrogen Fixation by Crocosphaera watsonii 10.1128/msphere.00531-19

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales 10.1016/j.ddmod.2019.08.012

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree 10.1101/2020.05.04.077636

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

Anupriya Tripathi

Tripathi Anupriya

ORCID: 0000-0001-8912-9684

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

Links between gut microbiome composition and fatty liver disease in a large population sample 10.1101/2020.07.30.20164962

The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361

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

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21