Year |
Citation |
Score |
2022 |
Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. Microbiome. 10: 212. PMID 36464731 DOI: 10.1186/s40168-022-01410-z |
0.725 |
|
2022 |
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, ... ... Zeller G, et al. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research. PMID 36408900 DOI: 10.1093/nar/gkac1078 |
0.783 |
|
2022 |
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, ... ... Zeller G, et al. Biosynthetic potential of the global ocean microbiome. Nature. PMID 35732736 DOI: 10.1038/s41586-022-04862-3 |
0.487 |
|
2022 |
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, ... ... Zeller G, et al. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 19: 429-440. PMID 35396482 DOI: 10.1038/s41592-022-01431-4 |
0.638 |
|
2022 |
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, ... ... Zeller G, et al. A faecal microbiota signature with high specificity for pancreatic cancer. Gut. PMID 35260444 DOI: 10.1136/gutjnl-2021-324755 |
0.35 |
|
2021 |
Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, ... ... Zeller G, et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. PMID 34789871 DOI: 10.1038/s41591-021-01552-x |
0.716 |
|
2021 |
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, ... ... Zeller G, et al. Unravelling the collateral damage of antibiotics on gut bacteria. Nature. PMID 34646011 DOI: 10.1038/s41586-021-03986-2 |
0.729 |
|
2021 |
Ruscheweyh HJ, Milanese A, Paoli L, Sintsova A, Mende DR, Zeller G, Sunagawa S. mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities. Current Protocols. 1: e218. PMID 34387940 DOI: 10.1002/cpz1.218 |
0.635 |
|
2021 |
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. Genome Biology. 22: 93. PMID 33785070 DOI: 10.1186/s13059-021-02306-1 |
0.39 |
|
2020 |
Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, ... ... Zeller G, et al. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biology. 21: 138. PMID 32513234 DOI: 10.1186/S13059-020-02042-Y |
0.357 |
|
2020 |
Garza DR, Taddese R, Wirbel J, Zeller G, Boleij A, Huynen MA, Dutilh BE. Metabolic models predict bacterial passengers in colorectal cancer. Cancer & Metabolism. 8: 3. PMID 32055399 DOI: 10.1186/S40170-020-0208-9 |
0.554 |
|
2020 |
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G. Abstract A40: The SIAMCAT R package enables statistical and machine learning analyses for case-control microbiome datasets Cancer Research. 80. DOI: 10.1158/1538-7445.Mvc2020-A40 |
0.474 |
|
2019 |
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, ... ... Zeller G, et al. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell. 179: 1068-1083.e21. PMID 31730850 DOI: 10.1016/J.Cell.2019.10.014 |
0.716 |
|
2019 |
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, ... ... Zeller G, et al. Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. PMID 31664237 DOI: 10.1038/S41591-019-0663-4 |
0.581 |
|
2019 |
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. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Research. PMID 31647096 DOI: 10.1093/Nar/Gkz1002 |
0.768 |
|
2019 |
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, ... ... Zeller G, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. PMID 30936548 DOI: 10.1038/S41591-019-0405-7 |
0.705 |
|
2019 |
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, ... ... Zeller G, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine. PMID 30936547 DOI: 10.1038/S41591-019-0406-6 |
0.79 |
|
2019 |
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, ... ... Zeller G, et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nature Communications. 10: 1014. PMID 30833550 DOI: 10.1038/S41467-019-08844-4 |
0.805 |
|
2019 |
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, et al. Extensive transmission of microbes along the gastrointestinal tract. Elife. 8. PMID 30747106 DOI: 10.7554/Elife.42693 |
0.708 |
|
2019 |
Milanese A, Mende DR, Zeller G, Sunagawa S. Reference-independent taxonomic profiling of metagenomes with an extended version of mOTUs F1000research. 8. DOI: 10.7490/F1000Research.1116490.1 |
0.34 |
|
2018 |
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature Microbiology. 3: 514-522. PMID 29556107 DOI: 10.1038/S41564-018-0123-9 |
0.623 |
|
2018 |
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. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. PMID 29555994 DOI: 10.1038/Nature25979 |
0.628 |
|
2018 |
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, ... ... Zeller G, et al. Publisher Correction: Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. PMID 29440750 DOI: 10.1038/S41564-018-0114-X |
0.688 |
|
2018 |
Costea PI, Hildebrand F, Manimozhiyan A, 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, ... ... Zeller G, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 3: 8-16. PMID 29255284 DOI: 10.1038/S41564-017-0072-8 |
0.632 |
|
2018 |
Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, Beaufort Cd, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, et al. Author response: Extensive transmission of microbes along the gastrointestinal tract Elife. DOI: 10.7554/Elife.42693.037 |
0.404 |
|
2018 |
Voigt A, Zeller G, Bork P. Mikrobielle Biomarker zur Krebsfrüherkennung Tumordiagnostik & Therapie. 39: 55-62. DOI: 10.1055/S-0043-124940 |
0.383 |
|
2017 |
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. Subspecies in the global human gut microbiome. Molecular Systems Biology. 13: 960. PMID 29242367 DOI: 10.15252/Msb.20177589 |
0.756 |
|
2017 |
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, et al. Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology. PMID 28967887 DOI: 10.1038/Nbt.3960 |
0.701 |
|
2017 |
Voigt AY, Zeller G, Bork P. [Microbial Biomarkers for Early Cancer Detection]. Deutsche Medizinische Wochenschrift (1946). 142: 267-274. PMID 28235227 DOI: 10.1055/S-0042-110193 |
0.496 |
|
2016 |
Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P. CART - a chemical annotation retrieval toolkit. Bioinformatics (Oxford, England). PMID 27256313 DOI: 10.1093/Bioinformatics/Btw233 |
0.773 |
|
2016 |
Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R. Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing. Plos One. 11: e0155362. PMID 27171425 DOI: 10.1371/Journal.Pone.0155362 |
0.53 |
|
2016 |
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. MOCAT2: a metagenomic assembly, annotation and profiling framework. Bioinformatics (Oxford, England). PMID 27153620 DOI: 10.1093/Bioinformatics/Btw183 |
0.725 |
|
2016 |
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. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science (New York, N.Y.). 352: 586-9. PMID 27126044 DOI: 10.1126/Science.Aad8852 |
0.44 |
|
2016 |
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, et al. Gut Microbiota Linked to Sexual Preference and HIV Infection. Ebiomedicine. 5: 135-46. PMID 27077120 DOI: 10.1016/J.Ebiom.2016.01.032 |
0.402 |
|
2015 |
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, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science (New York, N.Y.). 348: 1261359. PMID 25999513 DOI: 10.1126/Science.1261359 |
0.785 |
|
2015 |
Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. Temporal and technical variability of human gut metagenomes. Genome Biology. 16: 73. PMID 25888008 DOI: 10.1186/S13059-015-0639-8 |
0.486 |
|
2015 |
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, et al. Gut Microbiota Linked to Sexual Preference and HIV Infection Ebiomedicine. DOI: 10.1016/j.ebiom.2016.01.032 |
0.303 |
|
2014 |
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, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Molecular Systems Biology. 10: 766. PMID 25432777 DOI: 10.15252/Msb.20145645 |
0.773 |
|
2014 |
van Noort V, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P. Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling. Cancer Research. 74: 5690-9. PMID 25038229 DOI: 10.1158/0008-5472.Can-13-3540 |
0.771 |
|
2014 |
Costea PI, Zeller G, Sunagawa S, Bork P. A fair comparison. Nature Methods. 11: 359. PMID 24681719 DOI: 10.1038/Nmeth.2897 |
0.403 |
|
2013 |
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, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods. 10: 1196-9. PMID 24141494 DOI: 10.1038/Nmeth.2693 |
0.772 |
|
2013 |
Mende DR, Sunagawa S, Zeller G, Bork P. Accurate and universal delineation of prokaryotic species. Nature Methods. 10: 881-4. PMID 23892899 DOI: 10.1038/Nmeth.2575 |
0.708 |
|
2013 |
Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P. Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Molecular Systems Biology. 9: 662. PMID 23632384 DOI: 10.1038/Msb.2013.20 |
0.756 |
|
2012 |
Iskar M, Zeller G, Zhao XM, van Noort V, Bork P. Drug discovery in the age of systems biology: the rise of computational approaches for data integration. Current Opinion in Biotechnology. 23: 609-16. PMID 22153034 DOI: 10.1016/J.Copbio.2011.11.010 |
0.774 |
|
2011 |
Zhao XM, Iskar M, Zeller G, Kuhn M, van Noort V, Bork P. Prediction of drug combinations by integrating molecular and pharmacological data. Plos Computational Biology. 7: e1002323. PMID 22219721 DOI: 10.1371/Journal.Pcbi.1002323 |
0.768 |
|
2011 |
Brouwers L, Iskar M, Zeller G, van Noort V, Bork P. Network neighbors of drug targets contribute to drug side-effect similarity. Plos One. 6: e22187. PMID 21765950 DOI: 10.1371/Journal.Pone.0022187 |
0.762 |
|
2011 |
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, ... ... Zeller G, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/Nature09944 |
0.779 |
|
2011 |
Eichner J, Zeller G, Laubinger S, Rätsch G. Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. Bmc Bioinformatics. 12: 55. PMID 21324185 DOI: 10.1186/1471-2105-12-55 |
0.362 |
|
2011 |
Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina SE, Katz M, et al. A spatial and temporal map of C. elegans gene expression. Genome Research. 21: 325-41. PMID 21177967 DOI: 10.1101/Gr.114595.110 |
0.335 |
|
2010 |
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, ... ... Zeller G, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914 |
0.347 |
|
2010 |
Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, Laubinger S, Naouar N, Patrignani A, Rombauts S, Shu H, Van de Peer Y, Vuylsteke M, Weigel D, Zeller G, Hennig L. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiology. 152: 487-99. PMID 20032078 DOI: 10.1104/Pp.109.150185 |
0.33 |
|
2010 |
Behr J, Bohnert R, Zeller G, Schweikert GB, Hartmann L, Rätsch G. Next generation genome annotation with mGene.ngs Bmc Bioinformatics. 11: 1-2. DOI: 10.1186/1471-2105-11-S10-O8 |
0.365 |
|
2009 |
McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America. 106: 12273-8. PMID 19597147 DOI: 10.1073/Pnas.0900992106 |
0.33 |
|
2009 |
Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A, Krüger N, Sonnenburg S, Rätsch G. mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Research. 19: 2133-43. PMID 19564452 DOI: 10.1101/Gr.090597.108 |
0.376 |
|
2009 |
Schweikert G, Behr J, Zien A, Zeller G, Ong CS, Sonnenburg S, Rätsch G. mGene.web: a web service for accurate computational gene finding. Nucleic Acids Research. 37: W312-6. PMID 19494180 DOI: 10.1093/Nar/Gkp479 |
0.368 |
|
2009 |
Plantegenet S, Weber J, Goldstein DR, Zeller G, Nussbaumer C, Thomas J, Weigel D, Harshman K, Hardtke CS. Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance. Molecular Systems Biology. 5: 242. PMID 19225455 DOI: 10.1038/Msb.2008.79 |
0.353 |
|
2009 |
Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, van Hummelen P, Weigel D, Rätsch G, Inzé D, Kuiper M, De Veylder L, Vuylsteke M. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. The Plant Journal : For Cell and Molecular Biology. 57: 184-94. PMID 18764924 DOI: 10.1111/J.1365-313X.2008.03662.X |
0.339 |
|
2008 |
Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Schölkopf B, Rätsch G, Weigel D. At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biology. 9: R112. PMID 18613972 DOI: 10.1186/Gb-2008-9-7-R112 |
0.301 |
|
2008 |
Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D, Rätsch G. Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Research. 18: 918-29. PMID 18323538 DOI: 10.1101/Gr.070169.107 |
0.333 |
|
2007 |
Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (New York, N.Y.). 317: 338-42. PMID 17641193 DOI: 10.1126/Science.1138632 |
0.352 |
|
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