Publications of G. Zeller

Publications of G. Zeller

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2023 1 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
2022 4 publication(s).
41.
A faecal microbiota signature with high specificity for pancreatic cancer.
Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, MAGIC Study investigators , PanGenEU Study investigators , Benes V, Zeller G, Trebicka J, X Real F, Malats N, Bork P
Gut.
2022 Jul 8; 71(7): 1359-1372. PubMed: 35260444.
Abstract + PDF
40.
Biosynthetic potential of the global ocean microbiome.
Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlström CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sánchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J, Sunagawa S
2022 Jul 22; 607(7917): 111-118. PubMed: 35732736.
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39.
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S
2022 Dec 5; 10(1): 212. PubMed: 36464731.
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38.
Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial.
Sowah SA, Milanese A, Schübel R, Wirbel J, Kartal E, Johnson TS, Hirche F, Grafetstätter M, Nonnenmacher T, Kirsten R, López-Nogueroles M, Lahoz A, Schwarz KV, Okun JG, Ulrich CM, Nattenmüller J, von Eckardstein A, Müller D, Stangl GI, Kaaks R, Kühn T, Zeller G
2022 Mar 14; 14(1): 30. PubMed: 35287713.
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2021 2 publication(s).
37.
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
36.
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G
2021 Mar 30; 22(1): 93. PubMed: 33785070.
Abstract + PDF
2020 2 publication(s).
35.
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P
2020 Jan 8; 48: D621-D625. PubMed: 31647096.
Abstract + PDF
34.
Die Erforschung des menschlichen Mikrobioms
Trojahn U, Wirbel J, Bork P, Zeller G
In: Von der Datenanalyse zum Verstehen komplexer biologischer Systems01 pp.64-69. BID: 23.
Publisher: Bruns Druckwelt GmbH & Co. KG, Minden
PDF
2019 7 publication(s).
33.
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves RJ, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S
2019 Mar 4; 10(1): 1014. PubMed: 30833550.
Abstract + PDF
32.
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Tara Oceans Consortium Coordinators , Acinas SG, Babin M, Bork P, Bowler C, De Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S
2019 Nov 14; 179(5): 1068-1083.e21. PubMed: 31730850.
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31.
Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P
2019 Feb 12; 8: . PubMed: 30747106.
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30.
Effects of Weight-Loss Interventions on Short-Chain Fatty Acid Concentrations in Blood and Feces of Adults: A Systematic Review.
Sowah SA, Riedl L, Damms-Machado A, Johnson TS, Schübel R, Graf M, Kartal E, Zeller G, Schwingshackl L, Stangl GI, Kaaks R, Kühn T
2019 Jul 1; 10(4): 673-684. PubMed: 31075175.
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29.
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N
2019 Apr 1; 25(4): 667-678. PubMed: 30936548.
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28.
Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N
2019 Dec 29; 25(12): 1948. PubMed: 31664237.
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27.
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G
2019 Apr 1; 25(4): 679-689. PubMed: 30936547.
Abstract + PDF
2018 4 publication(s).
26.
Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
2018 Jan; 3(1): 8-16. PubMed: 29255284.
Abstract + PDF
25.
Publisher Correction: Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
2018 Mar 13; 3(3): 388. PubMed: 29440750.
Abstract + PDF
24.
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.
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23.
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 3 publication(s).
22.
Subspecies in the global human gut microbiome.
2017 Dec 14; 13(12): 960. PubMed: 29242367.
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21.
Towards standards for human fecal sample processing in metagenomic studies.
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P
2017 Nov 2; 35(11): 1069-1076. PubMed: 28967887.
Abstract + PDF
20.
[Microbial Biomarkers for Early Cancer Detection].
Voigt AY, Zeller G, Bork P
2017 Feb; 142(4): 267-274. PubMed: 28235227.
Abstract + PDF
2016 5 publication(s).
19.
CART - a chemical annotation retrieval toolkit.
Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P
2016 Sep 15; 32(18): 2869-71. Epub 2016 Jun 2; PubMed: 27256313.
Abstract + PDF
18.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed: 27153620.
Abstract + PDF
17.
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P
2016 Apr 29; 352(6285): 586-9. PubMed: 27126044.
Abstract + PDF
16.
Gut Microbiota Linked to Sexual Preference and HIV Infection.
Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R
2016 Mar; 5: 135-46. PubMed: 27077120.
Abstract + PDF
15.
Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.
Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R
2016; 11(5): e0155362. PubMed: 27171425.
Abstract + PDF
2015 2 publication(s).
14.
Structure and function of the global ocean microbiome.
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, De Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
2015 May 22; 348(6237): 1261359. PubMed: 25999513.
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13.
Temporal and technical variability of human gut metagenomes.
2015 Apr 8; 16(1): 73. Epub 2015 Apr 8; PubMed: 25888008.
Abstract + PDF
2014 3 publication(s).
12.
A fair comparison.
2014 Apr 28; 11(4): 359. PubMed: 24681719.
PDF
11.
Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling.
van Noort V, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P
2014 Oct 15; 74(20): 5690-9. Epub 2014 Jul 18; PubMed: 25038229.
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10.
Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P
2014 Nov 28; 10(11): 766. PubMed: 25432777.
Abstract + PDF
2013 3 publication(s).
9.
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
8.
Accurate and universal delineation of prokaryotic species.
2013 Sep 28; 10(9): 881-4. Epub 2013 Jul 28; PubMed: 23892899.
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7.
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
2013 Dec 20; 10(12): 1196-9. Epub 2013 Oct 20; PubMed: 24141494.
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2012 1 publication(s).
6.
Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
2012 Aug 5; 23(4): 609-16. Epub 2011 Dec 5; PubMed: 22153034.
Abstract + PDF
2011 3 publication(s).
5.
Network neighbors of drug targets contribute to drug side-effect similarity.
2011; 6(7): e22187. PubMed: 21765950.
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4.
Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans.
Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM, Horvitz HR, Sternberg PW, Ringstad N
2011 Jan 4; 108(1): 254-9. PubMed: 21173231.
Abstract
3.
Prediction of drug combinations by integrating molecular and pharmacological data.
2011 Dec; 7(12): e1002323. PubMed: 22219721.
Abstract + PDF
2010 2 publication(s).
2.
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium , Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH
2010 Dec 24; 330(6012): 1775-87. PubMed: 21177976.
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1.
Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.
Laubinger S, Zeller G, Henz SR, Buechel S, Sachsenberg T, Wang JW, Rätsch G, Weigel D
2010 Oct 12; 107(41): 17466-73. PubMed: 20870966.
Abstract