Review: Opportunities and barriers for omics-based biomarker discovery in steatotic liver diseases.

Thiele M, Villesen IF, Niu L, Johansen S, Sulek K, Nishijima S, Van Espen L, Keller M, Israelsen M, Suvitaival T, de Zawadzki A, Juel HB, Brol MJ, Stinson SE, Huang Y, Alvarez Silva MC, Kuhn M, Anastasiadou E, Leeming DJ, Karsdal M, Matthijnssens J, Arumugam M, Dalgaard LT, Legido-Quigley C, Mann M, Trebicka J, Bork P, Jensen LJ, Hansen T, Krag A, MicrobLiver and GALAXY consortia, GALAXY consortium, MicrobLiver consortium

Journal of hepatology, 2024

doi:10.1016/j.jhep.2024.03.035.

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

Mücke MM, Hernández-Tejero M, Gu W, Kuhn M, Janz M, Keller MI, Fullam A, Altepeter L, Mücke VT, Finkelmeier F, Schwarzkopf KM, Cremonese C, Hunyady PM, Heilani MW, Uschner FE, Schierwagen R, Brol MJ, Fischer J, Klein S, Peiffer KH, Hogardt M, Shoaie S, Coenraad MJ, Bojunga J, Arroyo V, Zeuzem S, Kempf VAJ, Welsch C, Laleman W, Bork P, Fernandez J, Trebicka J, MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium

Alimentary Pharmacology and Therapeutics, 2024

doi:10.1111/apt.17899.

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

Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L

Nature protocols, 2023

doi:10.1038/s41596-023-00926-4.

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P

Nucleic acids research, 2023

doi:10.1093/nar/gkad943.

Computational exploration of the global microbiome for antibiotic discovery.

Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez del Río Á, Schmidt TS, Chong H, Fullam A, Michael K, Zhu C, Houseman A, Somborski J, Vines A, Zhao X, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP

bioRxiv, 2023

doi:10.1101/2023.08.31.555663.

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

Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P

Molecular systems biology, 2023

doi:10.15252/msb.202311525.

Sphingolipids are depleted in alcohol-related liver fibrosis.

Thiele M, Suvitaival T, Trošt K, Kim M, de Zawadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Moitinho-Silva L, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Quigley CL, Krag A, MicrobLiver, GALAXY Consortia

Gastroenterology, 2023

doi:10.1053/j.gastro.2023.02.023.

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

Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR

Nucleic acids research, 2022

doi:10.1093/nar/gkac1078.

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

Ferretti P, Wirbel J,Maistrenko OM, Van Rossum T, Alves R, Fullam A, Akanni W, Schudoma C, Schwarz A, Thielemann R, Thomas L, Kandels S, Hercog R, Telzerow A, Letunic I, Kuhn M, Zeller G, Schmidt SBT, Bork P

bioRxiv, 2022

doi:10.1101/2022.02.16.480740.

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

Li Y, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P

PloS one, 2021

doi:10.1371/journal.pone.0254429.

Combinatorial, additive and dose-dependent drug-microbiome associations.

Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft NB, Pedersen HK, Hansen TH, MetaCardis Consortium*, Gøtze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P

Nature, 2021

doi:10.1038/s41586-021-04177-9.

A previously undescribed highly prevalent phage identified in a Danish enteric virome catalog.

Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J

mSystems, 2021

doi:10.1128/mSystems.00382-21.

Unravelling the collateral damage of antibiotics on gut bacteria.

Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A

Nature, 2021

doi:10.1038/s41586-021-03986-2.

Dispersal strategies shape persistence and evolution of human gut bacteria.

Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P

Cell host & microbe, 2021

doi:10.1016/j.chom.2021.05.008.

Association of the liver and plasma lipidomes with the histological stage of alcohol-related liver disease.

Thiele M, Suvitaival T, Trošt K, Kim M, de Zewadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Silva LM, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Quigley CL, Krag A, on behalf of the MicrobLiver and GALAXY Consortia

medRxiv, 2021

doi:10.1101/2021.07.13.21260429.

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

Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium, Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisneswky J, Clément K, Bäckhed F

Nature communications, 2020

doi:10.1038/s41467-020-19589-w.

Dissecting the collateral damage of antibiotics on gut microbes.

Maier L, Goemans CV, Pruteanu M, Wirbel J, Kuhn M, Cacace E, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KP, Zeller G, Bork P, Typas A

bioRxiv, 2020

doi:10.1101/2020.01.09.893560.

Basic phenotypes of endocytic system recognized by independent phenotypes analysis of a high-throughput genomic screen.

Nikitina K, Segeletz S, Kuhn M, Kalaidzidis Y, Zerial M

2019

doi:10.1145/3365966.3365972.

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

Li Y, Kuhn M, Gavin AC, Bork P

Bioinformatics (Oxford, England), 2019

doi:10.1093/bioinformatics/btz736.

Disentangling genetic and environmental effects on the proteotypes of individuals.

Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P

Cell, 2019

doi:10.1016/j.cell.2019.03.015.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR

Nature microbiology, 2018

doi:10.1038/s41564-018-0123-9.

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

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A

Nature, 2018

doi:10.1038/nature25979.

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

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C

Nucleic acids research, 2016

doi:10.1093/nar/gkw937.

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

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P

Nucleic acids research, 2015

doi:10.1093/nar/gkv1248.

The SIDER database of drugs and side effects.

Kuhn M, Letunic I, Jensen LJ, Bork P

Nucleic acids research, 2015

doi:10.1093/nar/gkv1075.

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

Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M

Nucleic acids research, 2015

doi:10.1093/nar/gkv1277.

Conservation of expression regulation throughout the animal kingdom.

Kuhn M, Beyer A

bioRxivorg, 2015

doi:10.1101/007252.

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

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C

Nucleic acids research, 2014

doi:10.1093/nar/gku1003.

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

Kuhn M, Hyman AA, Beyer A

PLoS computational biology, 2014

doi:10.1371/journal.pcbi.1003657.

Development of a kinetic assay for late endosome movement.

Esner M, Meyenhofer F, Kuhn M, Thomas M, Kalaidzidis Y, Bickle M

Journal of Biomolecular Screening, 2014

doi:10.1177/1087057114524278.

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

Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P

Nucleic acids research, 2013

doi:10.1093/nar/gkt1207.

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

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P

Nucleic acids research, 2013

doi:10.1093/nar/gkt1253.

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

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ

Nucleic acids research, 2013

doi:10.1093/nar/gks1094.

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

Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P

Molecular systems biology, 2013

doi:10.1038/msb.2013.20.

Systematic identification of proteins that elicit drug side effects.

Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P

Molecular systems biology, 2013

doi:10.1038/msb.2013.10.

STITCH 3: zooming in on protein-chemical interactions

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P

Nucleic acids research, 2012

doi:10.1093/nar/gkr1011.

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

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P

Nucleic acids research, 2012

doi:10.1093/nar/gkr1060.

Prediction of drug combinations by integrating molecular and pharmacological data.

Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P

PLoS computational biology, 2011

doi:10.1371/journal.pcbi.1002323.

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

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C

Nucleic acids research, 2011

doi:10.1093/nar/gkq973.

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.

Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC

Molecular systems biology, 2010

doi:10.1038/msb.2010.87.

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

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T

Journal of biomedical semantics, 2010

doi:10.1186/2041-1480-1-8.

Drug-induced regulation of target expression.

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P

PLoS computational biology, 2010

doi:10.1371/journal.pcbi.1000925.

A side effect resource to capture phenotypic effects of drugs.

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P

Molecular systems biology, 2010

doi:10.1038/msb.2009.98.

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

Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P

Nucleic acids research, 2010

doi:10.1093/nar/gkp937.

Live coverage of scientific conferences using web technologies.

Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R

PLoS computational biology, 2009

doi:10.1371/journal.pcbi.1000563.

Live coverage of intelligent systems for molecular biology/European conference on computational biology (ISMB/ECCB) 2009.

Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R

PLoS computational biology, 2010

doi:10.1371/journal.pcbi.1000640.

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

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P

Nucleic acids research, 2010

doi:10.1093/nar/gkp951.

Reflect: a practical approach to web semantics.

O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ

Web semantics (Online), 2010

doi:10.1016/j.websem.2010.03.003.

Reflect: augmented browsing for the life scientist.

Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R

Nature biotechnology, 2009

doi:10.1038/nbt0609-508.

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

Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btp081.

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

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C

Nucleic acids research, 2009

doi:10.1093/nar/gkn760.

Microblogging the ISMB: a new approach to conference reporting.

Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S

PLoS computational biology, 2009

doi:10.1371/journal.pcbi.1000263.

Drug target identification using side-effect similarity.

Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P

Science , 2008

doi:10.1126/science.1158140.

Large-scale prediction of drug-target relationships.

Kuhn M, Campillos M, González P, Jensen LJ, Bork P

FEBS letters, 2008

doi:10.1016/j.febslet.2008.02.024.

SuperTarget and Matador: resources for exploring drug-target relationships

Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R

Nucleic acids research, 2007

doi:10.1093/nar/gkm862.