publications

2020

  1. A network-based integrated framework for predicting virus–prokaryote interactions
    Wang, Weili, Ren, Jie, Tang, Kujin, Dart, Emily, Ignacio-Espinoza, Julio Cesar, Fuhrman, Jed A, Braun, Jonathan, Sun, Fengzhu, and Ahlgren, Nathan A
    NAR Genomics and Bioinformatics 2020

2019

  1. Long-term stability and Red Queen-like strain dynamics in marine viruses
    Ignacio-Espinoza, J. Cesar, Ahlgren, Nathan A., and Fuhrman, Jed A.
    Nature Microbiology 2019
  2. Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes
    Sieradzki, Ella T, Ignacio-Espinoza, J Cesar, Needham, David M, Fichot, Erin B, and Fuhrman, Jed A
    Nature Communications 2019
  3. Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.
    Martinez, Miguel A., Woodcroft, Ben J., Ignacio-Espinoza, J. Cesar, Zayed, Ahmed A., Singleton, Caitlin M., Boyd, Joel A., Li, Yueh Fen, Purvine, Samuel, Maughan, Heather, Hodgkins, Suzanne B., Anderson, Darya, Sederholm, Maya, Temperton, Ben, Bolduc, Benjamin, Saleska, Scott R., Tyson, Gene W., and Rich, Virginia I.
    Systematic and Applied Microbiology 2019

2016

  1. Illuminating structural proteins in viral "dark matter" with metaproteomics
    Brum, Jennifer R., Ignacio-Espinoza, J. Cesar, Kim, Eun Hae, Trubl, Gareth, Jones, Robert M., Roux, Simon, VerBerkmoes, Nathan C., Rich, Virginia I., and Sullivan, Matthew B.
    Proceedings of the National Academy of Sciences of the United States of America 2016
  2. Plankton networks driving carbon export in the oligotrophic ocean
    Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R., Coelho, Luis Pedro, Ignacio-Espinoza, J. Cesar, 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, and Gorsky, Gabriel
    Nature 2016
  3. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
    Gregory, Ann C., Solonenko, Sergei A., Ignacio-Espinoza, J. Cesar, LaButti, Kurt, Copeland, Alex, Sudek, Sebastian, Maitland, Ashley, Chittick, Lauren, Santos, Filipa, Weitz, Joshua S., Worden, Alexandra Z., Woyke, Tanja, and Sullivan, Matthew B.
    BMC Genomics 2016

2015

  1. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea
    Lara, Elena, Holmfeldt, Karin, Solonenko, Natalie, Sà, Elisabet Laia, Ignacio-Espinoza, J. Cesar, Cornejo-Castillo, Francisco M., Verberkmoes, Nathan C., Vaqué, Dolors, Sullivan, Matthew B., and Acinas, Silvia G.
    PLoS ONE 2015
  2. Patterns and ecological drivers of ocean viral communities
    Brum, Jennifer R., Ignacio-Espinoza, J. Cesar, Roux, Simon, Doulcier, Guilhem, Acinas, Silvia G., Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, De Vargas, Colomban, Gasol, Josep M., Gorsky, Gabriel, Gregory, Ann C., Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T., Schwenck, Sarah M., Speich, Sabrina, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Sullivan, Matthew B., Boss, Emmanuel, Follows, Michael, Grimsley, Nigel, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Stemmann, Lars, Velayoudon, Didier, and Weissenbach, Jean
    Science 2015
  3. Determinants of community structure in the global plankton interactome
    Lima-Mendez, Gipsi, Faust, Karoline, Henry, Nicolas, Decelle, Johan, Colin, Sébastien, Carcillo, Fabrizio, Chaffron, Samuel, Ignacio-Espinoza, J. Cesar, Roux, Simon, Vincent, Flora, Bittner, Lucie, Darzi, Youssef, Wang, Jun, Audic, Stéphane, Berline, Léo, Bontempi, Gianluca, Cabello, Ana M., Coppola, Laurent, Cornejo-Castillo, Francisco M., D’Ovidio, Francesco, De Meester, Luc, Ferrera, Isabel, Garet-Delmas, Marie José, Guidi, Lionel, Lara, Elena, Pesant, Stéphane, Royo-Llonch, Marta, Salazar, Guillem, Sánchez, Pablo, Sebastian, Marta, Souffreau, Caroline, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Gorsky, Gabriel, Not, Fabrice, Ogata, Hiroyuki, Speich, Sabrina, Stemmann, Lars, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G., Sunagawa, Shinichi, Bork, Peer, Sullivan, Matthew B., Karsenti, Eric, Bowler, Chris, De Vargas, Colomban, Raes, Jeroen, Boss, Emmanuel, Follows, Michael, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, and Velayoudon, Didier
    Science 2015
  4. Closing the gaps on the viral photosystem-IpsaDCAB gene organization
    Roitman, Sheila, Flores-Uribe, José, Philosof, Alon, Knowles, Ben, Rohwer, Forest, Ignacio-Espinoza, J. Cesar, Sullivan, Matthew B., Cornejo-Castillo, Francisco M., Sánchez, Pablo, Acinas, Silvia G., Dupont, Chris L., and Béjà, Oded
    Environmental Microbiology 2015

2014

  1. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
    Deng, Li, Ignacio-Espinoza, J. Cesar, Gregory, Ann C., Poulos, Bonnie T., Weitz, Joshua S., Hugenholtz, Philip, and Sullivan, Matthew B.
    Nature 2014

2013

  1. The global virome: Not as big as we thought?
    Ignacio-Espinoza, J. Cesar, Solonenko, Sergei A., and Sullivan, Matthew B.
    2013
  2. Sequencing platform and library preparation choices impact viral metagenomes
    Solonenko, Sergei A., Ignacio-Espinoza, J. Césa, Alberti, Adriana, Cruaud, Corinne, Hallam, Steven, Konstantinidis, Kostas, Tyson, Gene, Wincker, Patrick, and Sullivan, Matthew B.
    BMC Genomics 2013

2012

  1. Phylogenomics of T4 cyanophages: Lateral gene transfer in the ’core’ and origins of host genes
    Ignacio-Espinoza, J. Cesar, and Sullivan, Matthew B.
    Environmental Microbiology 2012

2020

  1. A network-based integrated framework for predicting virus–prokaryote interactions
    Wang, Weili, Ren, Jie, Tang, Kujin, Dart, Emily, Ignacio-Espinoza, Julio Cesar, Fuhrman, Jed A, Braun, Jonathan, Sun, Fengzhu, and Ahlgren, Nathan A
    NAR Genomics and Bioinformatics 2020