iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria von Roux, Simon, Camargo, Antonio Pedro, Coutinho, Felipe H, Dabdoub, Shareef M, Dutilh, Bas E, Nayfach, Stephen, Tritt, Andrew

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Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT von von Meijenfeldt, F A Bastiaan, Arkhipova, Ksenia, Cambuy, Diego D, Coutinho, Felipe H, Dutilh, Bas E

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Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans von Coutinho, Felipe H., Silveira, Cynthia B., Gregoracci, Gustavo B., Thompson, Cristiane C., Edwards, Robert A., Brussaard, Corina P. D., Dutilh, Bas E., Thompson, Fabiano L.

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Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal von Cabello-Yeves, Pedro J, Zemskaya, Tamara I, Rosselli, Riccardo, Coutinho, Felipe H, Zakharenko, Alexandra S, Blinov, Vadim V, Rodriguez-Valera, Francisco

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Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes von Fernández-Ruiz, Iris, Coutinho, Felipe H, Rodriguez-Valera, Francisco

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Ecogenomics and Taxonomy of Cyanobacteria Phylum von Walter, Juline M, Coutinho, Felipe H, Dutilh, Bas E, Swings, Jean, Thompson, Fabiano L, Thompson, Cristiane C

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Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19 von Ventero, Maria Paz, Cuadrat, Rafael R C, Vidal, Inmaculada, Andrade, Bruno G N, Molina-Pardines, Carmen, Haro-Moreno, Jose M, Coutinho, Felipe H, Merino, Esperanza, Regitano, Luciana C A, Silveira, Cynthia B, Afli, Haithem, López-Pérez, Mario, Rodríguez, Juan Carlos

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Environmental and Sanitary Conditions of Guanabara Bay, Rio de Janeiro von Fistarol, Giovana O, Coutinho, Felipe H, Moreira, Ana Paula B, Venas, Tainá, Cánovas, Alba, de Paula, Jr, Sérgio E M, Coutinho, Ricardo, de Moura, Rodrigo L, Valentin, Jean Louis, Tenenbaum, Denise R, Paranhos, Rodolfo, do Valle, Rogério de A B, Vicente, Ana Carolina P, Amado Filho, Gilberto M, Pereira, Renato Crespo, Kruger, Ricardo, Rezende, Carlos E, Thompson, Cristiane C, Salomon, Paulo S, Thompson, Fabiano L

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Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes von Silveira, Cynthia B, Coutinho, Felipe H, Cavalcanti, Giselle S, Benler, Sean, Doane, Michael P, Dinsdale, Elizabeth A, Edwards, Robert A, Francini-Filho, Ronaldo B, Thompson, Cristiane C, Luque, Antoni, Rohwer, Forest L, Thompson, Fabiano

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Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake von Bhattarai, Bishav, Bhattacharjee, Ananda S., Coutinho, Felipe H., Goel, Ramesh K.

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Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities von Coutinho, Felipe H, Silveira, Cynthia B, Sebastián, Marta, Sánchez, Pablo, Duarte, Carlos M, Vaqué, Dolors, Gasol, Josep M, Acinas, Silvia G

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Prophage Genomics and Ecology in the Family Rhodobacteraceae von Forcone, Kathryn, Coutinho, Felipe H., Cavalcanti, Giselle S., Silveira, Cynthia B.

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Putative mobilized colistin resistance genes in the human gut microbiome von Andrade, Bruno G N, Goris, Tobias, Afli, Haithem, Coutinho, Felipe H, Dávila, Alberto M R, Cuadrat, Rafael R C

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Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition von Sánchez, Pablo, Coutinho, Felipe H., Sebastián, Marta, Pernice, Massimo C., Rodríguez-Martínez, Raquel, Salazar, Guillem, Cornejo-Castillo, Francisco Miguel, Pesant, Stéphane, López-Alforja, Xabier, López-García, Ester María, Agustí, Susana, Gojobori, Takashi, Logares, Ramiro, Sala, Maria Montserrat, Vaqué, Dolors, Massana, Ramon, Duarte, Carlos M., Acinas, Silvia G., Gasol, Josep M.

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Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia von Walter, Juline M., Coutinho, Felipe H., Leomil, Luciana, Hargreaves, Paulo I., Campeão, Mariana E., Vieira, Verônica V., Silva, Beatriz S., Fistarol, Giovana O., Salomon, Paulo S., Sawabe, Tomoo, Mino, Sayaka, Hosokawa, Masashi, Miyashita, Hideaki, Maruyama, Fumito, van Verk, Marcel C., Dutilh, Bas E., Thompson, Cristiane C., Thompson, Fabiano L.

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Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters von Bhattarai, Bishav, Bhattacharjee, Ananda Shankar, Coutinho, Felipe H., Goel, Ramesh

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Bacteriophages carry auxiliary metabolic genes related to energy, sulfur and phosphorus metabolism during a harmful algal bloom in a freshwater lake von Bhattarai, Bishav, Bhattacharjee, Ananda Shankar, Coutinho, Felipe H., Li, Hanyan, Chadalavada, Sreeni, Goel, Ramesh

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Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp von Serrano-Gamboa, José Germán, Fócil-Espinosa, Carlos Abraham, Cabello-Yeves, Pedro J, Coutinho, Felipe H, Rojas-Herrera, Rafael Antonio, Sánchez-González, Mónica Noel

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Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle von Silveira, Cynthia B, Gregoracci, Gustavo B, Coutinho, Felipe H, Silva, Genivaldo G Z, Haggerty, John M, de Oliveira, Louisi S, Cabral, Anderson S, Rezende, Carlos E, Thompson, Cristiane C, Francini-Filho, Ronaldo B, Edwards, Robert A, Dinsdale, Elizabeth A, Thompson, Fabiano L

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Integrating Computational Methods to Investigate the Macroecology of Microbiomes von Mascarenhas, Rilquer, Ruziska, Flávia M, Moreira, Eduardo Freitas, Campos, Amanda B, Loiola, Miguel, Reis, Kaike, Trindade-Silva, Amaro E, Barbosa, Felipe A S, Salles, Lucas, Menezes, Rafael, Veiga, Rafael, Coutinho, Felipe H, Dutilh, Bas E, Guimarães, Jr, Paulo R, Assis, Ana Paula A, Ara, Anderson, Miranda, José G V, Andrade, Roberto F S, Vilela, Bruno, Meirelles, Pedro Milet

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