EXPERT: transfer learning-enabled context-aware microbial community classification

por Chong, Hui, Zha, Yuguo, Yu, Qingyang, Cheng, Mingyue, Xiong, Guangzhou, Wang, Nan, Huang, Xinhe, Huang, Shijuan, Sun, Chuqing, Wu, Sicheng, Chen, Wei-Hua, Coelho, Luis Pedro, Ning, Kang
Publicado 2022

Software testing in microbial bioinformatics: a call to action

por van der Putten, Boas C.L., Mendes, C. I., Talbot, Brooke M., de Korne-Elenbaas, Jolinda, Mamede, Rafael, Vila-Cerqueira, Pedro, Coelho, Luis Pedro, Gulvik, Christopher A., Katz, Lee S.
Publicado 2022

Similarity of the dog and human gut microbiomes in gene content and response to diet

por Coelho, Luis Pedro, Kultima, Jens Roat, Costea, Paul Igor, Fournier, Coralie, Pan, Yuanlong, Czarnecki-Maulden, Gail, Hayward, Matthew Robert, Forslund, Sofia K., Schmidt, Thomas Sebastian Benedikt, Descombes, Patrick, Jackson, Janet R., Li, Qinghong, Bork, Peer
Publicado 2018

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

por Mende, Daniel R, Letunic, Ivica, Maistrenko, Oleksandr M, Schmidt, Thomas S B, Milanese, Alessio, Paoli, Lucas, Hernández-Plaza, Ana, Orakov, Askarbek N, Forslund, Sofia K, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, Coelho, Luis Pedro, Bork, Peer
Publicado 2020

Microbial abundance, activity and population genomic profiling with mOTUs2

por 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
Publicado 2019

Computational exploration of the global microbiome for antibiotic discovery

por Santos-Júnior, Célio Dias, Der Torossian Torres, Marcelo, Duan, Yiqian, del Río, Álvaro Rodríguez, Schmidt, Thomas S.B., Chong, Hui, Fullam, Anthony, Kuhn, Michael, Zhu, Chengkai, Houseman, Amy, Somborski, Jelena, Vines, Anna, Zhao, Xing-Ming, Bork, Peer, Huerta-Cepas, Jaime, de la Fuente-Nunez, Cesar, Coelho, Luis Pedro
Publicado 2023

Drivers and determinants of strain dynamics following fecal microbiota transplantation

por Schmidt, Thomas S. B., Li, Simone S., Maistrenko, Oleksandr M., Akanni, Wasiu, Coelho, Luis Pedro, Dolai, Sibasish, Fullam, Anthony, Glazek, Anna M., Hercog, Rajna, Herrema, Hilde, Jung, Ferris, Kandels, Stefanie, Orakov, Askarbek, Thielemann, Roman, von Stetten, Moritz, Van Rossum, Thea, Benes, Vladimir, Borody, Thomas J., de Vos, Willem M., Ponsioen, Cyriel Y., Nieuwdorp, Max, Bork, Peer
Publicado 2022

Plankton networks driving carbon export in the oligotrophic ocean

por Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G., Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B., Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Gorsky, Gabriel
Publicado 2016

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

por Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M., Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C., Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A., Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, de Vargas, Colomban, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Ogata, Hiroyuki, Pesant, Stephane, Speich, Sabrina, Sullivan, Matthew B., Wincker, Patrick, Sunagawa, Shinichi
Publicado 2019

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

por Andrikopoulos, Petros, Aron-Wisnewsky, Judith, Chakaroun, Rima, Myridakis, Antonis, Forslund, Sofia K., Nielsen, Trine, Adriouch, Solia, Holmes, Bridget, Chilloux, Julien, Vieira-Silva, Sara, Falony, Gwen, Salem, Joe-Elie, Andreelli, Fabrizio, Belda, Eugeni, Kieswich, Julius, Chechi, Kanta, Puig-Castellvi, Francesc, Chevalier, Mickael, Le Chatelier, Emmanuelle, Olanipekun, Michael T., Hoyles, Lesley, Alves, Renato, Helft, Gerard, Isnard, Richard, Køber, Lars, Coelho, Luis Pedro, Rouault, Christine, Gauguier, Dominique, Gøtze, Jens Peter, Prifti, Edi, Froguel, Philippe, Zucker, Jean-Daniel, Bäckhed, Fredrik, Vestergaard, Henrik, Hansen, Torben, Oppert, Jean-Michel, Blüher, Matthias, Nielsen, Jens, Raes, Jeroen, Bork, Peer, Yaqoob, Muhammad M., Stumvoll, Michael, Pedersen, Oluf, Ehrlich, S. Dusko, Clément, Karine, Dumas, Marc-Emmanuel
Publicado 2023

Global Trends in Marine Plankton Diversity across Kingdoms of Life

por Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, de Vargas, Colomban, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, Zinger, Lucie
Publicado 2019

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

por Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E, Prifti, Edi, Aron-Wisnewsky, Judith, Debédat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouyal, Chloé, André, Sébastien, Andreelli, Fabrizio, Blüher, Matthias, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue H, Holmes, Bridget, Ji, Boyang, Krogh Pedersen, Helle, Le, Phuong, Le Chatelier, Emmanuelle, Lewinter, Christian, Mannerås-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B, Touch, Sothea, Vieira-Silva, Sara, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvoll, Michael, Pedersen, Oluf Borbye, Bork, Peer, Ehrlich, Stanislav Dusko, Zucker, Jean-Daniel, Bäckhed, Fredrik, Raes, Jeroen, Clément, Karine
Publicado 2022

Microbiome and metabolome features of the cardiometabolic disease spectrum

por Fromentin, Sebastien, Forslund, Sofia K., Chechi, Kanta, Aron-Wisnewsky, Judith, Chakaroun, Rima, Nielsen, Trine, Tremaroli, Valentina, Ji, Boyang, Prifti, Edi, Myridakis, Antonis, Chilloux, Julien, Andrikopoulos, Petros, Fan, Yong, Olanipekun, Michael T., Alves, Renato, Adiouch, Solia, Bar, Noam, Talmor-Barkan, Yeela, Belda, Eugeni, Caesar, Robert, Coelho, Luis Pedro, Falony, Gwen, Fellahi, Soraya, Galan, Pilar, Galleron, Nathalie, Helft, Gerard, Hoyles, Lesley, Isnard, Richard, Le Chatelier, Emmanuelle, Julienne, Hanna, Olsson, Lisa, Pedersen, Helle Krogh, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Schmidt, Thomas S. B., Vieira-Silva, Sara, Li, Peishun, Zimmermann-Kogadeeva, Maria, Lewinter, Christian, Søndertoft, Nadja B., Hansen, Tue H., Gauguier, Dominique, Gøtze, Jens Peter, Køber, Lars, Kornowski, Ran, Vestergaard, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Hercberg, Serge, Letunic, Ivica, Bäckhed, Fredrik, Oppert, Jean-Michel, Nielsen, Jens, Raes, Jeroen, Bork, Peer, Stumvoll, Michael, Segal, Eran, Clément, Karine, Dumas, Marc-Emmanuel, Ehrlich, S. Dusko, Pedersen, Oluf
Publicado 2022