eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses von Huerta-Cepas, Jaime, Szklarczyk, Damian, Heller, Davide, Hernández-Plaza, Ana, Forslund, Sofia K, Cook, Helen, Mende, Daniel R, Letunic, Ivica, Rattei, Thomas, Jensen, Lars J, von Mering, Christian, Bork, Peer

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Metabolic dependencies drive species co-occurrence in diverse microbial communities von Zelezniak, Aleksej, Andrejev, Sergej, Ponomarova, Olga, Mende, Daniel R., Bork, Peer, Patil, Kiran Raosaheb

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Accurate and universal delineation of prokaryotic species von Mende, Daniel R, Sunagawa, Shinichi, Zeller, Georg, Bork, Peer

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GUNC: detection of chimerism and contamination in prokaryotic genomes von Orakov, Askarbek, Fullam, Anthony, Coelho, Luis Pedro, Khedkar, Supriya, Szklarczyk, Damian, Mende, Daniel R., Schmidt, Thomas S. B., Bork, Peer

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Microbial abundance, activity and population genomic profiling with mOTUs2 von Milanese, Alessio, Mende, Daniel R, Paoli, Lucas, Salazar, Guillem, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Hingamp, Pascal, Alves, Renato, Costea, Paul I, Coelho, Luis Pedro, Schmidt, Thomas S. B., Almeida, Alexandre, Mitchell, Alex L, Finn, Robert D., Huerta-Cepas, Jaime, Bork, Peer, Zeller, Georg, Sunagawa, Shinichi

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Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review von Luchen, Charlie C, Chibuye, Mwelwa, Spijker, Rene, Simuyandi, Michelo, Chisenga, Caroline, Bosomprah, Samuel, Chilengi, Roma, Schultsz, Constance, Mende, Daniel R, Harris, Vanessa C

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Assessment of metagenomic assembly using simulated next generation sequencing data von Mende, Daniel R, Waller, Alison S, Sunagawa, Shinichi, Järvelin, Aino I, Chan, Michelle M, Arumugam, Manimozhiyan, Raes, Jeroen, Bork, Peer

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Genomic variation landscape of the human gut microbiome von Schloissnig, Siegfried, Arumugam, Manimozhiyan, Sunagawa, Shinichi, Mitreva, Makedonka, Tap, Julien, Zhu, Ana, Waller, Alison, Mende, Daniel R., Kultima, Jens Roat, Martin, John, Kota, Karthik, Sunyaev, Shamil R., Weinstock, George M., Bork, Peer

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Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean von Boiteau, Rene M., Mende, Daniel R., Hawco, Nicholas J., McIlvin, Matthew R., Fitzsimmons, Jessica N., Saito, Mak A., Sedwick, Peter N., DeLong, Edward F., Repeta, Daniel J.

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A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators von Needham, David M., Yoshizawa, Susumu, Hosaka, Toshiaki, Poirier, Camille, Choi, Chang Jae, Hehenberger, Elisabeth, Irwin, Nicholas A. T., Wilken, Susanne, Yung, Cheuk-Man, Charles Bachy, Rika Kurihara, Nakajima, Yu, Kojima, Keiichi, Kimura-Someya, Tomomi, Leonard, Guy, Malmstrom, Rex R., Mende, Daniel R., Olson, Daniel K., Sudo, Yuki, Sudek, Sebastian, Richards, Thomas A., DeLong, Edward F., Keeling, Patrick J., Santoro, Alyson E., Shirouzu, Mikako, Iwasaki, Wataru, Worden, Alexandra Z.

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Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone von Aylward, Frank O., Boeuf, Dominique, Mende, Daniel R., Wood-Charlson, Elisha M., Vislova, Alice, Eppley, John M., Romano, Anna E., DeLong, Edward F.

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MOCAT: a metagenomics assembly and gene prediction toolkit von Kultima, Jens Roat, Sunagawa, Shinichi, Li, Junhua, Chen, Weineng, Chen, Hua, Mende, Daniel R, Arumugam, Manimozhiyan, Pan, Qi, Liu, Binghang, Qin, Junjie, Wang, Jun, Bork, Peer

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Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity von Maistrenko, Oleksandr M., Mende, Daniel R., Luetge, Mechthild, Hildebrand, Falk, Schmidt, Thomas S. B., Li, Simone S., Rodrigues, João F. Matias, von Mering, Christian, Pedro Coelho, Luis, Huerta-Cepas, Jaime, Sunagawa, Shinichi, Bork, Peer

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Deciphering a global network of functionally associated post‐translational modifications von Minguez, Pablo, Parca, Luca, Diella, Francesca, Mende, Daniel R, Kumar, Runjun, Helmer‐Citterich, Manuela, Gavin, Anne‐Claude, van Noort, Vera, Bork, Peer

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Role for urea in nitrification by polar marine Archaea von Alonso-Sáez, Laura, Waller, Alison S, Mende, Daniel R, Bakker, Kevin, Farnelid, Hanna, Yager, Patricia L, Lovejoy, Connie, Tremblay, Jean-Éric, Potvin, Marianne, Heinrich, Friederike, Estrada, Marta, Riemann, Lasse, Bork, Peer, Pedrós-Alió, Carlos, Bertilsson, Stefan

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Bacteriophage Distributions and Temporal Variability in the Ocean's Interior von Luo, Elaine, Aylward, Frank O, Mende, Daniel R, DeLong, Edward F

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proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes von Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas S B, Ducarmon, Quinten R, Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M, Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, Mende, Daniel R

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Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments von Ruscheweyh, Hans-Joachim, Milanese, Alessio, Paoli, Lucas, Karcher, Nicolai, Clayssen, Quentin, Keller, Marisa Isabell, Wirbel, Jakob, Bork, Peer, Mende, Daniel R, Zeller, Georg, Sunagawa, Shinichi

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Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage von Boeuf, Dominique, Eppley, John M., Mende, Daniel R., Malmstrom, Rex R., Woyke, Tanja, DeLong, Edward F.

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Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre von Mende, Daniel R., Boeuf, Dominique, DeLong, Edward F.

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