Michael Kuhn

发表

Drug Target Identification Using Side-Effect Similarity

P. Bork, L. Jensen, A. Gavin, 2008, Science.

A side effect resource to capture phenotypic effects of drugs

P. Bork, L. Jensen, M. Campillos, 2010, Molecular systems biology.

STRING 8—a global view on proteins and their functional interactions in 630 organisms

Christian von Mering, Peer Bork, Jean Muller, 2008, Nucleic Acids Res..

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

Katarzyna H. Kaminska, P. Bork, G. Zeller, 2013, Molecular systems biology.

Systematic identification of proteins that elicit drug side effects

P. Bork, L. Jensen, A. Gavin, 2013, Molecular systems biology.

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

P. Bork, L. Jensen, A. Gavin, 2010, Molecular systems biology.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

P. Bork, G. Zeller, Michael Kuhn, 2018, Nature Microbiology.

Year : 2013 STRING v 9 . 1 : protein-protein interaction networks , with increased coverage and integration

Alexander C. J. Roth, P. Bork, L. Jensen, 2017 .

Conservation of expression regulation throughout the animal kingdom

A. Beyer, Michael Kuhn, 2014, bioRxiv.

Large‐scale prediction of drug–target relationships

P. Bork, L. Jensen, M. Campillos, 2008, FEBS letters.

Strand‐loop‐strand motifs: Prediction of hairpins and diverging turns in proteins

Jens Meiler, David Baker, Michael Kuhn, 2004, Proteins.

The current understanding of protein – lipid recognition comes from the study of a limited number of lipids , principally

P. Bork, L. Jensen, A. Gavin, 2010 .

Dissecting the collateral damage of antibiotics on gut microbes

Exene Erin Anderson, P. Bork, G. Zeller, 2020, bioRxiv.

A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

P. Bork, M. Arumugam, T. Nielsen, 2021, mSystems.

The STRING database in 2017

Damian Szklarczyk, Peer Bork, Michael Kuhn, 2017 .

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

P. Bork, S. Sunagawa, D. Mende, 2022, Nucleic Acids Res..

Reflect: augmented browsing for the life scientist

Michael Kuhn, Lars Juhl Jensen, Evangelos Pafilis, 2009, Nature Biotechnology.

Consistency across multi-omics layers in a drug-perturbed gut microbial community

Thomas S. B. Schmidt, Philipp E. Geyer, P. Bork, 2023, bioRxiv.

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

Davide Heller, Damian Szklarczyk, Christian von Mering, 2014, Nucleic Acids Res..

eggNOG v4.0: nested orthology inference across 3686 organisms

Damian Szklarczyk, Christian von Mering, Peer Bork, 2013, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Peer Bork, 2011, Nucleic Acids Res..

Extensive impact of non-antibiotic drugs on human gut bacteria

Peer Bork, Kiran Raosaheb Patil, Michael Kuhn, 2018, Nature.

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

Damian Szklarczyk, Christian von Mering, John H. Morris, 2016, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Peer Bork, 2015, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2012, Nucleic Acids Res..

STITCH: interaction networks of chemicals and proteins

Christian von Mering, Peer Bork, Lars Juhl Jensen, 2007, Nucleic Acids Res..

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

Davide Heller, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2010, Nucleic Acids Res..

STITCH 4: integration of protein–chemical interactions with user data

Damian Szklarczyk, Christian von Mering, Thomas Blicher, 2013, Nucleic Acids Res..

The UCSC Genome Browser database: 2017 update

D. Karolchik, R. M. Kuhn, R. Baertsch, 2016, Nucleic Acids Res..

Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome

Anthony A. Hyman, Michael Kuhn, Andreas Beyer, 2014, PLoS Comput. Biol..

Drug-Induced Regulation of Target Expression

Peer Bork, Lars Juhl Jensen, Michael Kuhn, 2010, PLoS Comput. Biol..

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

P. Bork, A. Gavin, Michael Kuhn, 2021, PloS one.

The SIDER database of drugs and side effects

Peer Bork, Ivica Letunic, Lars Juhl Jensen, 2015, Nucleic Acids Res..

STRING 7—recent developments in the integration and prediction of protein interactions

Christian von Mering, Peer Bork, Berend Snel, 2006, Nucleic Acids Res..

Dispersal strategies shape persistence and evolution of human gut bacteria

P. Bork, Pamela Ferretti, H. Nielsen, 2021, Cell host & microbe.

C. difficile is overdiagnosed in adults and a commensal in infants

Wasiu A. Akanni, P. Bork, Pamela Ferretti, 2022, bioRxiv.

STITCH 3: zooming in on protein–chemical interactions

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2011, Nucleic Acids Res..

SuperTarget and Matador: resources for exploring drug-target relationships

Robert B. Russell, Philip E. Bourne, Reinhard Schneider, 2007, Nucleic Acids Res..

Reflect: A practical approach to web semantics

Michael Kuhn, Lars Juhl Jensen, Venkata P. Satagopam, 2010, J. Web Semant..

Reflect: augmented browsing for the life scientist

Seán I O'Donoghue, Michael Kuhn, Heiko Horn, 2009, Nature Biotechnology.

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

Luis Pedro Coelho, P. Bork, F. Bäckhed, 2020, Nature Communications.

Prediction of human population responses to toxic compounds by a collaborative competition

Karsten M. Borgwardt, Ana L. Teixeira, Eleni G. Christodoulou, 2015, Nature Biotechnology.

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

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2009, Nucleic Acids Res..

Unravelling the collateral damage of antibiotics on gut bacteria

Exene Erin Anderson, P. Bork, G. Zeller, 2021, Nature.

eggNOG: automated construction and annotation of orthologous groups of genes

Christian von Mering, Peer Bork, Jean Muller, 2007, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Peer Bork, 2009, Nucleic Acids Res..

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

Xing-Ming Zhao, Peer Bork, Georg Zeller, 2011, PLoS Comput. Biol..

Combinatorial, additive and dose-dependent drug–microbiome associations

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2021, Nature.

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2020, Nature.

1 Reflect – Augmented Browsing for the Life Scientist

L. Jensen, H. Horn, N. P. Brown, 2009 .

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

Peer Bork, Michael Kuhn, Yuanyue Li, 2019, bioRxiv.

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

P. Bork, R. Aebersold, Michael Kuhn, 2019, Cell.

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2020, Nature.

Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

Luis Pedro Coelho, P. Bork, F. Bäckhed, 2020, Nature Communications.

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants

Wasiu A. Akanni, P. Bork, Pamela Ferretti, 2022, bioRxiv.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

Akira R. Kinjo, Kiyoko F. Aoki-Kinoshita, Kiyoshi Asai, 2010, J. Biomed. Semant..

The UCSC Genome Browser database: 2017 update

David Haussler, Brian J. Raney, David Gibson, 2016, Nucleic Acids Res..

Emergence of community behaviors in the gut microbiota upon drug treatment

Ana Rita Brochado, P. Bork, Michael Kuhn, 2023, bioRxiv.

STRING and STITCH: known and predicted interactions between proteins and chemicals

Christian von Mering, Peer Bork, Lars Juhl Jensen, 2008 .

Repository of the Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association

Karen, Lajos, P. Bork, 2023 .

Consistency across multi‐omics layers in a drug‐perturbed gut microbial community

Philipp E. Geyer, P. Bork, R. Hercog, 2023, Molecular systems biology.

Drug Target Identification Using Side-Effect Similarity

P. Bork, L. Jensen, A. Gavin, 2008, Science.

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

Reinhard Schneider, Georgios A. Pavlopoulos, Sean D. Hooper, 2009, Bioinform..

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

Shahriyar Mahdi Robbani, T. Nielsen, Michael Kuhn, 2024, bioRxiv.

Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.

Michael Kuhn, R. Schierwagen, F. Uschner, 2024, Alimentary pharmacology & therapeutics.

Supplementary Information for a Systematic Screen for Protein-lipid Interactions in Saccharomyces Cerevisiae Supplementary Materials and Methods Supplementary Figures S1 -s10 Supplementary Movies (description) Supplementary References

P. Bork, A. Gavin, V. Rybin, 2022 .