Publications of M. Kuhn

Publications of M. Kuhn

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2024 1 publication(s).
43.
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
2024 Jan 5; 52: D777-D783. PubMed: 37897342.
Abstract + PDF
2023 4 publication(s).
42.
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
2023 Jan 6; 51: D760-D766. PubMed: 36408900.
Abstract + PDF
41.
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
2023 Dec 13; [Epub ahead of print] PubMed: 38092943.
Abstract
40.
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
2023 Jun 26; 164(7): 1248-1260. PubMed: 36849086.
Abstract + PDF
39.
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
2023 Sep 12; 19(9): e11525. PubMed: 37485738.
Abstract + PDF
2021 5 publication(s).
38.
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
2021 Dec 8; 600(7889): 500-505. PubMed: 34880489.
Abstract + PDF
37.
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
2021 Jul 14; 29(7): 1167-1176.e9. PubMed: 34111423.
Abstract + PDF
36.
Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.
Li YY, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P
2021; 16(7): e0254429. PubMed: 34242379.
Abstract + PDF
35.
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
2021 Nov 13; 599(7883): 120-124. PubMed: 34646011.
Abstract + PDF
34.
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
2021 Oct 26; 6(5): e0038221. PubMed: 34665009.
Abstract + PDF
2020 1 publication(s).
33.
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li YY, Kuhn M, Gavin AC, Bork P
2020 Feb 15; 36(4): 1213-1218. PubMed: 31605112.
Abstract + PDF
2019 1 publication(s).
32.
Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals.
Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P
2019 May 16; 177(5): 1308-1318.e10. PubMed: 31031010.
Abstract + PDF
2018 2 publication(s).
31.
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
2018 Mar 29; 555(7698): 623-628. PubMed: 29555994.
Abstract + PDF
30.
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
2018 Apr 19; 3(4): 514-522. PubMed: 29556107.
Abstract + PDF
2017 1 publication(s).
29.
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
2017 Jan 4; 45(D1): D362-D368. PubMed: 27924014.
Abstract + PDF
2016 3 publication(s).
28.
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
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
27.
The SIDER database of drugs and side effects.
2016 Jan 4; 44: D1075-9. Epub 2015 Oct 19; PubMed: 26481350.
Abstract + PDF
26.
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
2016 Jan 4; 44: D380-4. Epub 2015 Nov 20; PubMed: 26590256.
Abstract + PDF
2015 1 publication(s).
25.
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C
2015 Jan 28; 43: D447-52. Epub 2014 Oct 28; PubMed: 25352553.
Abstract + PDF
2014 2 publication(s).
24.
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
2014 Jan 1; 42(Database issue): D401-7. Epub 2013 Nov 28; PubMed: 24293645.
Abstract + PDF
23.
eggNOG v4.0: nested orthology inference across 3686 organisms.
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
Abstract + PDF
2013 3 publication(s).
22.
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
2013 Jan 1; 41: D808-15. Epub 2012 Nov 29; PubMed: 23203871.
Abstract + PDF
21.
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
2013 Apr 30; 9: 662. PubMed: 23632384.
Abstract + PDF
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
2013 Apr 30; 9: 663. PubMed: 23632385.
Abstract + PDF
2012 2 publication(s).
19.
STITCH 3: zooming in on protein-chemical interactions.
Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P
2012 Jan 1; 40: D876-80. Epub 2011 Nov 9; PubMed: 22075997.
Abstract + PDF
18.
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
2012 Jan 1; 40: D284-9. Epub 2011 Nov 16; PubMed: 22096231.
Abstract + PDF
2011 2 publication(s).
17.
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
2011 Jan 2; 39: D561-8. Epub 2010 Nov 2; PubMed: 21045058.
Abstract + PDF
16.
Prediction of drug combinations by integrating molecular and pharmacological data.
2011 Dec; 7(12): e1002323. PubMed: 22219721.
Abstract + PDF
2010 5 publication(s).
15.
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
2010 Nov 30; 6: 430. PubMed: 21119626.
Abstract + PDF
14.
Drug-Induced Regulation of Target Expression.
2010 Sep 9; 6(9): . PubMed: 20838579.
Abstract + PDF
13.
A side effect resource to capture phenotypic effects of drugs.
2010; 6: 343. PubMed: 20087340.
Abstract + PDF
12.
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
2010 Jan 6; 38: D552-6. Epub 2009 Nov 6; PubMed: 19897548.
Abstract + PDF
11.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
2010 Jan 9; 38: D190-5. Epub 2009 Nov 9; PubMed: 19900971.
Abstract + PDF
2009 4 publication(s).
10.
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey CJ, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C
2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.
Abstract + PDF
9.
Reflect: augmented browsing for the life scientist.
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R
2009 Jun; 27(6): 508-10. PubMed: 19513049.
PDF
8.
OnTheFly: A Tool for automated document-based text annotation, data linking and network generation.
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R
2009 Feb 17; 25(7): 977-8. PubMed: 19223449.
Abstract + PDF
7.
Microblogging the ISMB: a new approach to conference reporting.
Saunders N, Beltrão P, Jensen LJ, Jurczak D, Krause R, Kuhn M, Wu S
2009 Jan; 5(1): e1000263. PubMed: 19180175.
PDF
2008 5 publication(s).
6.
Drug target identification using side-effect similarity.
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P
2008 Jul 11; 321(5886): 263-6. PubMed: 18621671. Media echos.
Abstract + PDF
5.
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
2008 Jan 16; 36: D919-22. Epub 2007 Oct 16; PubMed: 17942422.
Abstract + PDF
4.
eggNOG: automated construction and annotation of orthologous groups of genes.
2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.
Abstract + PDF
3.
Large-scale prediction of drug-target relationships.
Kuhn M, Campillos M, González P, Jensen LJ, Bork P
2008 Apr 9; 582(8): 1283-90. Epub 2008 Feb 20; PubMed: 18291108.
Abstract + PDF
2.
STITCH: interaction networks of chemicals and proteins.
2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.
Abstract + PDF
2007 1 publication(s).
1.
STRING 7--recent developments in the integration and prediction of protein interactions.
2007 Jan 10; 35: D358-62. Epub 2006 Nov 10; PubMed: 17098935.
Abstract + PDF