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Scopus Author ID: 35345083400
ResearcherID: D-4978-2009

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Works (50 of 52)

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High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities

Nature Protocols
2024-03 | Journal article
DOI: 10.1038/s41596-023-00926-4
Contributors: Patrick Müller; Jacobo de la Cuesta-Zuluaga; Michael Kuhn; Maral Baghai Arassi; Tim Treis; Sonja Blasche; Michael Zimmermann; Peer Bork; Kiran Raosaheb Patil; Athanasios Typas et al.
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Crossref

Computational exploration of the global microbiome for antibiotic discovery

2023-08-31 | Preprint
DOI: 10.1101/2023.08.31.555663
Contributors: Célio Dias Santos-Júnior; Marcelo Der Torossian Torres; Yiqian Duan; Álvaro Rodríguez del Río; Thomas S.B. Schmidt; Hui Chong; Anthony Fullam; Kuhn Michael; Chengkai Zhu; Amy Houseman et al.
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Crossref

Emergence of community behaviors in the gut microbiota upon drug treatment

2023-06-14 | Preprint
DOI: 10.1101/2023.06.13.544832
Contributors: Sarela Garcia-Santamarina; Michael Kuhn; Saravanan Devendran; Lisa Maier; Marja Driessen; André Mateus; Eleonora Mastrorilli; Ana Rita Brochado; Mikhail M. Savitski; Kiran R. Patil et al.
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Crossref

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Nucleic Acids Research
2023-01-06 | Journal article
DOI: 10.1093/nar/gkac1078
Contributors: Anthony Fullam; Ivica Letunic; Thomas S B Schmidt; Quinten R Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn; Martin Larralde; Oleksandr M Maistrenko; Lukas Malfertheiner et al.
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Crossref

Unravelling the collateral damage of antibiotics on gut bacteria

Nature
2021-11-04 | Journal article
DOI: 10.1038/s41586-021-03986-2
Contributors: Lisa Maier; Camille V. Goemans; Jakob Wirbel; Michael Kuhn; Claudia Eberl; Mihaela Pruteanu; Patrick Müller; Sarela Garcia-Santamarina; Elisabetta Cacace; Boyao Zhang et al.
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Crossref

Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum

PLOS ONE
2021-07-09 | Journal article
DOI: 10.1371/journal.pone.0254429
Contributors: Yuanyue Li; Qi Wu; Michael Kuhn; Joanna Zukowska-Kasprzyk; Marco L. Hennrich; Panagiotis L. Kastritis; Francis J. O’Reilly; Prasad Phapale; Martin Beck; Anne-Claude Gavin et al.
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Crossref

Dispersal strategies shape persistence and evolution of human gut bacteria.

Cell host & microbe
2021-06-09 | Journal article
DOI: 10.1016/j.chom.2021.05.008
PMID: 34111423
PMC: PMC8288446
Contributors: Michael Kuhn
Source: Self-asserted source
Michael Kuhn

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals.

Cell
2019-04-25 | Journal article
DOI: 10.1016/j.cell.2019.03.015
PMID: 31031010
PMC: PMC6988111
Contributors: Michael Kuhn
Source: Self-asserted source
Michael Kuhn

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

2019-03-11 | Other
DOI: 10.1101/573790
Contributors: Yuanyue Li; Michael Kuhn; Anne-Claude Gavin; Peer Bork
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Crossref

Extensive impact of non-antibiotic drugs on human gut bacteria.

Nature
2018-03-19 | Journal article
DOI: 10.1038/nature25979
PMID: 29555994
PMC: PMC6108420
Contributors: Michael Kuhn
Source: Self-asserted source
Michael Kuhn

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

Nature Microbiology
2018-03-19 | Journal article
DOI: 10.1038/s41564-018-0123-9
Contributors: Melanie Tramontano; Sergej Andrejev; Mihaela Pruteanu; Martina Klünemann; Michael Kuhn; Marco Galardini; Paula Jouhten; Aleksej Zelezniak; Georg Zeller; Peer Bork et al.
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Crossref

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Nucleic acids research
2016-10-18 | Journal article
DOI: 10.1093/nar/gkw937
PMID: 27924014
PMC: PMC5210637
Contributors: Michael Kuhn
Source: Self-asserted source
Michael Kuhn

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

2016-01 | Journal article
DOI: 10.1093/nar/gkv1248
PMID: 26582926
Contributors: Huerta-Cepas J; Szklarczyk D; Forslund K; Cook H; Heller D; Walter MC; Rattei T; Mende DR; Sunagawa S; Kuhn M et al.
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

2016-01 | Journal article
DOI: 10.1093/nar/gkv1277
PMID: 26590256
Contributors: Szklarczyk D; Santos A; von Mering C; Jensen LJ; Bork P; Kuhn M
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

The SIDER database of drugs and side effects.

2016-01 | Journal article
DOI: 10.1093/nar/gkv1075
PMID: 26481350
Contributors: Kuhn M; Letunic I; Jensen LJ; Bork P
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

STRING v10: protein-protein interaction networks, integrated over the tree of life.

2015-01 | Journal article
DOI: 10.1093/nar/gku1003
PMID: 25352553
PMC: PMC4383874
Contributors: Szklarczyk D; Franceschini A; Wyder S; Forslund K; Heller D; Huerta-Cepas J; Simonovic M; Roth A; Santos A; Tsafou KP et al.
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

Development of a Kinetic Assay for Late Endosome Movement

Journal of Biomolecular Screening
2014 | Journal article
DOI: 10.1177/1087057114524278
WOSUID:

WOS:000340235600008
Contributors: Esner, M.; Meyenhofer, F.; Kuhn, M.; Thomas, M.; Kalaidzidis, Y.; Bickle, M.
Source: Self-asserted source
Michael Kuhn via ResearcherID

Conservation of expression regulation throughout the animal kingdom

2014-07-18 | Report
DOI: 10.1101/007252
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Crossref

Coiled-coil proteins facilitated the functional expansion of the centrosome.

PLoS computational biology
2014-06-05 | Journal article
DOI: 10.1371/journal.pcbi.1003657
PMID: 24901223
PMC: PMC4046923
Contributors: Michael Kuhn
Source: Self-asserted source
Michael Kuhn

eggNOG v4.0: nested orthology inference across 3686 organisms.

2014-01 | Journal article
DOI: 10.1093/nar/gkt1253
PMID: 24297252
PMC: PMC3964997
Contributors: Powell S; Forslund K; Szklarczyk D; Trachana K; Roth A; Huerta-Cepas J; Gabaldón T; Rattei T; Creevey C; Kuhn M et al.
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

STITCH 4: integration of protein-chemical interactions with user data.

2014-01 | Journal article
DOI: 10.1093/nar/gkt1207
PMID: 24293645
PMC: PMC3964996
Contributors: Kuhn M; Szklarczyk D; Pletscher-Frankild S; Blicher TH; von Mering C; Jensen LJ; Bork P
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.

2013 | Journal article
DOI: 10.1038/msb.2013.20
PMID: 23632384
PMC: PMC3658274
Contributors: Iskar M; Zeller G; Blattmann P; Campillos M; Kuhn M; Kaminska KH; Runz H; Gavin AC; Pepperkok R; van Noort V et al.
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

Systematic identification of proteins that elicit drug side effects.

2013 | Journal article
DOI: 10.1038/msb.2013.10
PMID: 23632385
PMC: PMC3693830
Contributors: Kuhn M; Al Banchaabouchi M; Campillos M; Jensen LJ; Gross C; Gavin AC; Bork P
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.

2013-01 | Journal article
DOI: 10.1093/nar/gks1094
PMID: 23203871
PMC: PMC3531103
Contributors: Franceschini A; Szklarczyk D; Frankild S; Kuhn M; Simonovic M; Roth A; Lin J; Minguez P; Bork P; von Mering C et al.
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Nucleic Acids Research
2012 | Journal article
EID: 2-s2.0-84861203603
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

STITCH 3: Zooming in on protein-chemical interactions

Nucleic Acids Research
2012 | Journal article
EID: 2-s2.0-84861508376
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

2012-01 | Journal article
DOI: 10.1093/nar/gkr1060
PMID: 22096231
PMC: PMC3245133
Contributors: Powell S; Szklarczyk D; Trachana K; Roth A; Kuhn M; Muller J; Arnold R; Rattei T; Letunic I; Doerks T et al.
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

STITCH 3: zooming in on protein-chemical interactions.

2012-01 | Journal article
DOI: 10.1093/nar/gkr1011
PMID: 22075997
PMC: PMC3245073
Contributors: Kuhn M; Szklarczyk D; Franceschini A; von Mering C; Jensen LJ; Bork P
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

Prediction of drug combinations by integrating molecular and pharmacological data

PLoS Computational Biology
2011 | Journal article
EID: 2-s2.0-84855272311
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored

Nucleic Acids Research
2011 | Journal article
EID: 2-s2.0-78651324347
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Prediction of drug combinations by integrating molecular and pharmacological data.

2011-12 | Journal article
DOI: 10.1371/journal.pcbi.1002323
PMID: 22219721
PMC: PMC3248384
Contributors: Zhao XM; Iskar M; Zeller G; Kuhn M; van Noort V; Bork P
Source: Self-asserted source
Michael Kuhn via Europe PubMed Central

A side effect resource to capture phenotypic effects of drugs

Molecular Systems Biology
2010 | Journal article
EID: 2-s2.0-76149120425
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

A systematic screen for proteing-lipid interactions in Saccharomyces cerevisiae

Molecular Systems Biology
2010 | Journal article
EID: 2-s2.0-78649853031
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Drug-induced regulation of target expression

PLoS Computational Biology
2010 | Journal article
EID: 2-s2.0-78049449443
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Live coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009

PLoS Computational Biology
2010 | Journal article
EID: 2-s2.0-76749122393
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Live coverage of scientific conferences using web technologies

PLoS Computational Biology
2010 | Journal article
EID: 2-s2.0-76749162367
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Reflect: A practical approach to web semantics

Journal of Web Semantics
2010 | Journal article
EID: 2-s2.0-77955228152
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

eggNOG v2.0: Extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

Nucleic Acids Research
2009 | Journal article
EID: 2-s2.0-75549085495
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Microblogging the ISMB: A new approach to conference reporting

PLoS Computational Biology
2009 | Journal article
EID: 2-s2.0-59149092679
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

OnTheFly: A tool for automated document-based text annotation, data linking and network generation

Bioinformatics
2009 | Journal article
EID: 2-s2.0-63549085123
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Reflect: Augmented browsing for the life scientist

Nature Biotechnology
2009 | Journal article
EID: 2-s2.0-67149113481
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

STITCH 2: An interaction network database for small molecules and proteins

Nucleic Acids Research
2009 | Journal article
EID: 2-s2.0-75549087827
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

STRING 8 - A global view on proteins and their functional interactions in 630 organisms

Nucleic Acids Research
2009 | Journal article
EID: 2-s2.0-58149193234
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Drug target identification using side-effect similarity

Science
2008 | Journal article
EID: 2-s2.0-47249146126
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

eggNOG: Automated construction and annotation of orthologous groups of genes

Nucleic Acids Research
2008 | Journal article
EID: 2-s2.0-38549177928
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Large-scale prediction of drug-target relationships

FEBS Letters
2008 | Journal article
EID: 2-s2.0-41149096945
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

STITCH: Interaction networks of chemicals and proteins

Nucleic Acids Research
2008 | Journal article
EID: 2-s2.0-38549130733
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

SuperTarget and Matador: Resources for exploring drug-target relationships

Nucleic Acids Research
2008 | Journal article
EID: 2-s2.0-38549182474
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

STRING 7 - Recent developments in the integration and prediction of protein interactions

Nucleic Acids Research
2007 | Journal article
EID: 2-s2.0-33846086800
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier

Automated alignment and pattern recognition of single-molecule force spectroscopy data

Journal of Microscopy
2005 | Journal article
EID: 2-s2.0-18444364820
Source: Self-asserted source
Michael Kuhn via Scopus - Elsevier
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