| Year |
Citation |
Score |
| 2023 |
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. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Research. PMID 37897342 DOI: 10.1093/nar/gkad943 |
0.788 |
|
| 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 |
0.718 |
|
| 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, ... ... Mende DR, et al. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research. PMID 36408900 DOI: 10.1093/nar/gkac1078 |
0.826 |
|
| 2022 |
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research. PMID 36399505 DOI: 10.1093/nar/gkac1022 |
0.814 |
|
| 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, ... ... Mende DR, 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 |
0.584 |
|
| 2022 |
Bongrand C, Koch E, Mende D, Romano A, Lawhorn S, McFall-Ngai M, DeLong EF, Ruby EG. Evidence of Genomic Diversification in a Natural Symbiotic Population Within Its Host. Frontiers in Microbiology. 13: 854355. PMID 35300477 DOI: 10.3389/fmicb.2022.854355 |
0.608 |
|
| 2022 |
van der Putten BCL, Huijsmans NAH, Mende DR, Schultsz C. Benchmarking the topological accuracy of bacterial phylogenomic workflows using evolution. Microbial Genomics. 8. PMID 35290758 DOI: 10.1099/mgen.0.000799 |
0.412 |
|
| 2022 |
Muratore D, Boysen AK, Harke MJ, Becker KW, Casey JR, Coesel SN, Mende DR, Wilson ST, Aylward FO, Eppley JM, Vislova A, Peng S, Rodriguez-Gonzalez RA, Beckett SJ, Virginia Armbrust E, et al. Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nature Ecology & Evolution. PMID 35058612 DOI: 10.1038/s41559-021-01606-w |
0.74 |
|
| 2021 |
Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, et al. Towards the biogeography of prokaryotic genes. Nature. PMID 34912116 DOI: 10.1038/s41586-021-04233-4 |
0.786 |
|
| 2021 |
Boeuf D, Eppley JM, Mende DR, Malmstrom RR, Woyke T, DeLong EF. Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage. Microbiome. 9: 172. PMID 34389059 DOI: 10.1186/s40168-021-01119-5 |
0.549 |
|
| 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 |
0.558 |
|
| 2021 |
Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biology. 22: 178. PMID 34120611 DOI: 10.1186/s13059-021-02393-0 |
0.758 |
|
| 2020 |
Becker KW, Harke MJ, Mende DR, Muratore D, Weitz JS, DeLong EF, Dyhrman ST, Van Mooy BAS. Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean. The Isme Journal. PMID 33033374 DOI: 10.1038/s41396-020-00793-x |
0.524 |
|
| 2020 |
Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, et al. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. The Isme Journal. PMID 32636492 DOI: 10.1038/S41396-020-0710-7 |
0.631 |
|
| 2020 |
Luo E, Eppley JM, Romano AE, Mende DR, DeLong EF. Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. The Isme Journal. PMID 32060418 DOI: 10.1038/S41396-020-0604-8 |
0.804 |
|
| 2020 |
Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. The Isme Journal. PMID 32047279 DOI: 10.1038/S41396-020-0600-Z |
0.708 |
|
| 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 |
0.815 |
|
| 2019 |
Mende DR, Boeuf D, DeLong EF. Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre. Frontiers in Microbiology. 10: 2273. PMID 31632377 DOI: 10.3389/Fmicb.2019.02273 |
0.789 |
|
| 2019 |
Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, ... ... Mende DR, et al. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences of the United States of America. PMID 31548428 DOI: 10.1073/Pnas.1907517116 |
0.782 |
|
| 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, et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nature Communications. 10: 1014. PMID 30833550 DOI: 10.1038/S41467-019-08844-4 |
0.816 |
|
| 2018 |
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. PMID 30418610 DOI: 10.1093/Nar/Gky1085 |
0.82 |
|
| 2017 |
Luo E, Aylward FO, Mende DR, DeLong EF. Bacteriophage Distributions and Temporal Variability in the Ocean's Interior. Mbio. 8. PMID 29184020 DOI: 10.1128/Mbio.01903-17 |
0.808 |
|
| 2017 |
Sosa OA, Repeta DJ, Ferrón S, Bryant JA, Mende DR, Karl DM, DeLong EF. Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter. Frontiers in Microbiology. 8: 1786. PMID 29085339 DOI: 10.3389/Fmicb.2017.01786 |
0.771 |
|
| 2017 |
Aylward FO, Boeuf D, Mende DR, Wood-Charlson EM, Vislova A, Eppley JM, Romano AE, DeLong EF. Diel cycling and long-term persistence of viruses in the ocean's euphotic zone. Proceedings of the National Academy of Sciences of the United States of America. 114: 11446-11451. PMID 29073070 DOI: 10.1073/Pnas.1714821114 |
0.788 |
|
| 2017 |
Mende DR, Bryant JA, Aylward FO, Eppley JM, Nielsen T, Karl DM, DeLong EF. Environmental drivers of a microbial genomic transition zone in the ocean's interior. Nature Microbiology. PMID 28808230 DOI: 10.1038/S41564-017-0008-3 |
0.827 |
|
| 2017 |
Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Research. 45: D529-D534. PMID 28053165 DOI: 10.1093/Nar/Gkw989 |
0.764 |
|
| 2016 |
Boiteau RM, Mende DR, Hawco NJ, McIlvin MR, Fitzsimmons JN, Saito MA, Sedwick PN, DeLong EF, Repeta DJ. Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean. Proceedings of the National Academy of Sciences of the United States of America. PMID 27911777 DOI: 10.1073/Pnas.1608594113 |
0.454 |
|
| 2016 |
Mende DR, Aylward FO, Eppley JM, Nielsen TN, DeLong EF. Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies. Frontiers in Microbiology. 7: 143. PMID 26904016 DOI: 10.3389/Fmicb.2016.00143 |
0.775 |
|
| 2016 |
Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Research. PMID 26773059 DOI: 10.1093/Nar/Gkw004 |
0.785 |
|
| 2015 |
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. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. PMID 26582926 DOI: 10.1093/Nar/Gkv1248 |
0.769 |
|
| 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 |
0.821 |
|
| 2015 |
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America. 112: 6449-54. PMID 25941371 DOI: 10.1073/Pnas.1421834112 |
0.487 |
|
| 2015 |
Zhu A, Sunagawa S, Mende DR, Bork P. Inter-individual differences in the gene content of human gut bacterial species. Genome Biology. 16: 82. PMID 25896518 DOI: 10.1186/S13059-015-0646-9 |
0.534 |
|
| 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 |
0.77 |
|
| 2014 |
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Addendum: Enterotypes of the human gut microbiome Nature. 506: 516-516. DOI: 10.1038/Nature13075 |
0.752 |
|
| 2013 |
Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, et al. Individuality and temporal stability of the human gut microbiome. Central Asian Journal of Global Health. 2: 120. PMID 29805877 DOI: 10.5195/Cajgh.2013.120 |
0.79 |
|
| 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 |
0.8 |
|
| 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 |
0.648 |
|
| 2013 |
Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-specific antibiotic use practices impact the human gut resistome. Genome Research. 23: 1163-9. PMID 23568836 DOI: 10.1101/Gr.155465.113 |
0.597 |
|
| 2013 |
van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. Consistent mutational paths predict eukaryotic thermostability. Bmc Evolutionary Biology. 13: 7. PMID 23305080 DOI: 10.1186/1471-2148-13-7 |
0.8 |
|
| 2013 |
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. Genomic variation landscape of the human gut microbiome. Nature. 493: 45-50. PMID 23222524 DOI: 10.1038/Nature11711 |
0.78 |
|
| 2012 |
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P. MOCAT: a metagenomics assembly and gene prediction toolkit. Plos One. 7: e47656. PMID 23082188 DOI: 10.1371/Journal.Pone.0047656 |
0.612 |
|
| 2012 |
Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JÉ, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S. Role for urea in nitrification by polar marine Archaea. Proceedings of the National Academy of Sciences of the United States of America. 109: 17989-94. PMID 23027926 DOI: 10.1073/Pnas.1201914109 |
0.632 |
|
| 2012 |
Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. Deciphering a global network of functionally associated post-translational modifications. Molecular Systems Biology. 8: 599. PMID 22806145 DOI: 10.1038/Msb.2012.31 |
0.642 |
|
| 2012 |
Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. Assessment of metagenomic assembly using simulated next generation sequencing data. Plos One. 7: e31386. PMID 22384016 DOI: 10.1371/Journal.Pone.0031386 |
0.783 |
|
| 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, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/Nature09944 |
0.796 |
|
| 2010 |
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464: 59-65. PMID 20203603 DOI: 10.1038/Nature08821 |
0.821 |
|
| Show low-probability matches. |