User:J. Cesar Ignacio Espinoza: Difference between revisions

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*J. Cesar Ignacio Espinoza, PhD
*J. Cesar Ignacio Espinoza, PhD
*Ecology and Evolutionary Biology
* Ecology and Evolutionary Biology
*315 Sahuaro Hall
*315 Sahuaro Hall
*1110 East South Campus
* 1110 East South Campus
*The University of Arizona  
*The University of Arizona
*Tucson, AZ 85721
*Tucson, AZ 85721
*[[Special:Emailuser/J. Cesar Ignacio Espinoza|ignacioel@email.arizona.edu]]
*[[Special:Emailuser/J. Cesar Ignacio Espinoza|ignacioel@email.arizona.edu]]


Line 22: Line 23:
==Research interests==
==Research interests==
<!-- Feel free to add brief descriptions to your research interests as well -->
<!-- Feel free to add brief descriptions to your research interests as well -->
# Interest 1
# Microbial and phage genomics
# Interest 2
# Microbial ecology
# Interest 3
# Microbes and biogeochemical cycles


==Publications==
==Publications==
* '''1. '''Sullivan, M.B., K.H. Huang, '''J.C. Ignacio-Espinoza''', A. Berlin, L. Kelly, P.R. Weigele, A.S. DeFrancesco, S.E. Kern, L.R. Thompson, S. Young, S.Yandava, R. Fu, B. Krastins, M. Chase, D. Sarracino, M.S. Osburne, M.R. Henn & S.W. Chisholm. (2010). [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02280.x/full Genomic analysis of oceanic cyanobacterial myoviruses compared to T4- like myoviruses from diverse hosts and environments] Environmental Microbiology 12:3035-56.
* '''1. '''Sullivan, M.B., K.H. Huang, '''J.C. Ignacio-Espinoza''', A. Berlin, L. Kelly, P.R. Weigele, A.S. DeFrancesco, S.E. Kern, L.R. Thompson, S. Young, S.Yandava, R. Fu, B. Krastins, M. Chase, D. Sarracino, M.S. Osburne, M.R. Henn & S.W. Chisholm. (2010). [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02280.x/full Genomic analysis of oceanic cyanobacterial myoviruses compared to T4- like myoviruses from diverse hosts and environments] Environmental Microbiology 12:3035-56.
* '''2.''' '''Ignacio-Espinoza J.C.''' & M.B. Sullivan. (2012). [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02704.x/full Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes.] Environmental Microbiology 14:2113-26.
* '''2.''' '''Ignacio-Espinoza J.C.''' & M.B. Sullivan. (2012). [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02704.x/full Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes.] Environmental Microbiology 14:2113-26.
* '''3.''' Solonenko S., '''J.C. Ignacio-Espinoza''', A. Alberti, C. Cruaud, S. Hallam, K. Kostantinidis, G. Tyson, P. Wincker & MB Sullivan. (2013). [http://www.biomedcentral.com/1471-2164/14/320/ Impact of sequencing platform and library preparation choices on viral metagenomes.] BMC Genomics, 14:320.
* '''3.''' Solonenko S., '''J.C. Ignacio-Espinoza''', A. Alberti, C. Cruaud, S. Hallam, K. Kostantinidis, G. Tyson, P. Wincker & MB Sullivan. (2013). [http://www.biomedcentral.com/1471-2164/14/320/ Impact of sequencing platform and library preparation choices on viral metagenomes.] BMC Genomics, 14:320.
* '''4.''' '''Ignacio-Espinoza J.C.''', S.A. Solonenko & M.B. Sullivan. (2013). [http://www.sciencedirect.com/science/article/pii/S1879625713001168 The global virome: not as big as we thought?] Current Opinion Virology, 3:566–571.
* '''4.''' '''Ignacio-Espinoza J.C.''', S.A. Solonenko & M.B. Sullivan. (2013). [http://www.sciencedirect.com/science/article/pii/S1879625713001168 The global virome: not as big as we thought?] Current Opinion Virology, 3:566–571.
* '''5.''' Deng, L.*,'''J.C. Ignacio-Espinoza'''*, A. Gregory, B.T. Poulos, P. Hugenholtz & M.B. Sullivan. (2014). [http://www.nature.com/nature/journal/v513/n7517/full/nature13459.html Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.] Nature. 513: 242– 245.
* '''5.''' Deng, L.*,'''J.C. Ignacio-Espinoza'''*, A. Gregory, B.T. Poulos, P. Hugenholtz & M.B. Sullivan. (2014). [http://www.nature.com/nature/journal/v513/n7517/full/nature13459.html Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.] Nature. 513: 242– 245.
* '''6.''' Lara E., K. Holmfeldt, N. Solonenko, E. Laia-Sà, '''J.C. Ignacio-Espinoza''', F.M. Cornejo-Castillo, N.C. Verberkmoes, D. Vaqué, M.B. Sullivan & S.G. Acinas. (2015 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114829 Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the Northwestern Mediterranean Sea.] PLoS One 10(1): e0114829.
* '''6.''' Lara E., K. Holmfeldt, N. Solonenko, E. Laia-Sà, '''J.C. Ignacio-Espinoza''', F.M. Cornejo-Castillo, N.C. Verberkmoes, D. Vaqué, M.B. Sullivan & S.G. Acinas. (2015 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114829 Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the Northwestern Mediterranean Sea.] PLoS One 10(1): e0114829.
* '''7.''' Brum, J.R.*, '''Ignacio-Espinoza* J.C.''', Roux* S., G. Doulcier, S. Acinas, A. Alberti, S. Chaffron, L. Coppola, C. Cruaud, C. de Vargas, P. Gasol, G. Gorsky, A.C. Gregory, L. Guidi, P. Hingamp, F. Not, H. Ogata, S. Pesant, B.T. Poulos, S.M., Schwenck1, S. Speich, C. Dimier, M. Pichera, S. Searson, S. Kandels-Lewis, Tara Oceans Coordinators, P. Bork, C. Bowler, E. Karsenti, S. Sunagawa, P. Wincker, & M.B. Sullivan. Global patterns and ecological drivers of ocean viral communities. Science. In Press
* '''7.''' Brum, J.R.*, '''Ignacio-Espinoza* J.C.''', Roux* S., G. Doulcier, S. Acinas, A. Alberti, S. Chaffron, L. Coppola, C. Cruaud, C. de Vargas, P. Gasol, G. Gorsky, A.C. Gregory, L. Guidi, P. Hingamp, F. Not, H. Ogata, S. Pesant, B.T. Poulos, S.M., Schwenck1, S. Speich, C. Dimier, M. Pichera, S. Searson, S. Kandels-Lewis, Tara Oceans Coordinators, P. Bork, C. Bowler, E. Karsenti, S. Sunagawa, P. Wincker, & M.B. Sullivan. Global patterns and ecological drivers of ocean viral communities. Science. In Press
* '''8.''' Lima-Mendez G, K. Faust, N. Henry, J. Decelle, S. Colin, F. Carcilli, S. CHaffron, '''J.C. Ignacio-Espinoza''', S. Roux, F. Vincent, L. Bittner, Y. Darzi, J. Wang, S Audic, L Berline, G Bontempi, L. Copola, F.M. Cornejo- Castillo, F. D’Ovidio, L. Demeester, M.J. Garet-Delmas, L. Guidi, S. Pesant, G. Salazar, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, Tara Oceans coordinators, S.G. Acinas, G. Gorsky, F. Not, H. Ogata, S. Speich, J. Weissenbach, P. Wincker, S. Sunagawa, P. Boork, M.B. Sullivan, C. Bowler, E. Karsenti, C. de Vargas & J. Raes. Top-Down determinants of community structure in the global plankton interactome. Science. In Press
* '''8.''' Lima-Mendez G, K. Faust, N. Henry, J. Decelle, S. Colin, F. Carcilli, S. CHaffron, '''J.C. Ignacio-Espinoza''', S. Roux, F. Vincent, L. Bittner, Y. Darzi, J. Wang, S Audic, L Berline, G Bontempi, L. Copola, F.M. Cornejo- Castillo, F. D’Ovidio, L. Demeester, M.J. Garet-Delmas, L. Guidi, S. Pesant, G. Salazar, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, Tara Oceans coordinators, S.G. Acinas, G. Gorsky, F. Not, H. Ogata, S. Speich, J. Weissenbach, P. Wincker, S. Sunagawa, P. Boork, M.B. Sullivan, C. Bowler, E. Karsenti, C. de Vargas & J. Raes. Top-Down determinants of community structure in the global plankton interactome. Science. In Press
* '''9.''' '''Ignacio-Espinoza J.C.''', V.T. Dang, O. Jaillon, P. Winker & M.B. Sullivan. Comparative viromics across four Mediterranean Sea dsDNA viral communities from the Tara Oceans Expedition. Submitted to Environmental Microbiology
* '''9.''' '''Ignacio-Espinoza J.C.''', V.T. Dang, O. Jaillon, P. Winker & M.B. Sullivan. Comparative viromics across four Mediterranean Sea dsDNA viral communities from the Tara Oceans Expedition. Submitted to Environmental Microbiology


* '''10.'''  Brum* J.R., '''Ignacio-Espinoza* J.C.''', Kim E.H*., G. Trubl, R.M. Jones, N.C. VerBerkmoes, V.I. Rich, & M.B. Sullivan. Virion structural metaproteomics sheds light on marine ‘viral dark matter’. In preparation.
* '''10.'''  Brum* J.R., '''Ignacio-Espinoza* J.C.''', Kim E.H*., G. Trubl, R.M. Jones, N.C. VerBerkmoes, V.I. Rich, & M.B. Sullivan. Virion structural metaproteomics sheds light on marine ‘viral dark matter’. In preparation.
* '''11.''' '''Ignacio-Espinoza J.C.*''', A. Gregory*, Deng, L., B.T. Poulos, P. Hugenholtz & M.B. Sullivan. Genomic population landscape of cyanophage viral communities. In preparation.
* '''11.''' '''Ignacio-Espinoza J.C.*''', A. Gregory*, Deng, L., B.T. Poulos, P. Hugenholtz & M.B. Sullivan. Genomic population landscape of cyanophage viral communities. In preparation.
* '''12.''' '''Ignacio-Espinoza J.C.''', D. Anderson, B. Woodcroft, S.B. Hodgkins, J.P. Chanton, G. Tyson, S. Saleska, V. Rich. Candidatus Caldiserium septentrionalis a novel sulfate reducing bacteria in thawing permafrost. In preparation.
* '''12.''' '''Ignacio-Espinoza J.C.''', D. Anderson, B. Woodcroft, S.B. Hodgkins, J.P. Chanton, G. Tyson, S. Saleska, V. Rich. Candidatus Caldiserium septentrionalis a novel sulfate reducing bacteria in thawing permafrost. In preparation.


'''Star denotes shared first authorship.'''
'''Star denotes shared first authorship.'''


==Useful links==
==Outreach and press==
*[[OpenWetWare:Welcome|Introductory tutorial]]
 
*[[Help|OpenWetWare help pages]]
 
* Finalist, top 10, in the Oceans180 video competition: '''[http://ocean180.org/innocence-by-viral-tagging.html Innocence by viral tagging]''', seen by more than 30 thousand students world wide.
 
* [http://uanews.org/story/tiniest-catch-ua-scientists-fishing-expedition-reveals-viral-diversity-in-the-sea Tiniest Catch: UA Scientists' Fishing Expedition Reveals Viral Diversity in the Sea]
Featured also in ScienceDaily, EurekAlert, PhysOrg, NSF, RealClearScience.
 
* [http://uanews.org/story/microbial-murder-mystery-lands-two-ua-students-in-top-10-of-ocean-science-video-challenge Microbial Murder Mystery Lands Two UA Students in Top 10 of Ocean Science Video Challenge]
 
* twitter handle: [https://twitter.com/Phagenomics @phagenomics]

Latest revision as of 16:04, 23 April 2015

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Contact Info

Cesar on board of the RV Urania, Fall 2009.
  • J. Cesar Ignacio Espinoza, PhD
  • Ecology and Evolutionary Biology
  • 315 Sahuaro Hall
  • 1110 East South Campus
  • The University of Arizona
  • Tucson, AZ 85721

Education

  • 2015, PhD, University of Arizona

Thesis title: "Functional and Population Based Viral Ecology". Advisor Dr. Matthew B. Sullivan

  • 2010, MS, University of Arizona

Thesis title: "Phylogenomics of T4-like phages". Advisor Dr. Matthew B. Sullivan

  • 2007, BS, Instituto Tecnologico del Valle de Oaxaca

Research interests

  1. Microbial and phage genomics
  2. Microbial ecology
  3. Microbes and biogeochemical cycles

Publications

  • 7. Brum, J.R.*, Ignacio-Espinoza* J.C., Roux* S., G. Doulcier, S. Acinas, A. Alberti, S. Chaffron, L. Coppola, C. Cruaud, C. de Vargas, P. Gasol, G. Gorsky, A.C. Gregory, L. Guidi, P. Hingamp, F. Not, H. Ogata, S. Pesant, B.T. Poulos, S.M., Schwenck1, S. Speich, C. Dimier, M. Pichera, S. Searson, S. Kandels-Lewis, Tara Oceans Coordinators, P. Bork, C. Bowler, E. Karsenti, S. Sunagawa, P. Wincker, & M.B. Sullivan. Global patterns and ecological drivers of ocean viral communities. Science. In Press
  • 8. Lima-Mendez G, K. Faust, N. Henry, J. Decelle, S. Colin, F. Carcilli, S. CHaffron, J.C. Ignacio-Espinoza, S. Roux, F. Vincent, L. Bittner, Y. Darzi, J. Wang, S Audic, L Berline, G Bontempi, L. Copola, F.M. Cornejo- Castillo, F. D’Ovidio, L. Demeester, M.J. Garet-Delmas, L. Guidi, S. Pesant, G. Salazar, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, Tara Oceans coordinators, S.G. Acinas, G. Gorsky, F. Not, H. Ogata, S. Speich, J. Weissenbach, P. Wincker, S. Sunagawa, P. Boork, M.B. Sullivan, C. Bowler, E. Karsenti, C. de Vargas & J. Raes. Top-Down determinants of community structure in the global plankton interactome. Science. In Press
  • 9. Ignacio-Espinoza J.C., V.T. Dang, O. Jaillon, P. Winker & M.B. Sullivan. Comparative viromics across four Mediterranean Sea dsDNA viral communities from the Tara Oceans Expedition. Submitted to Environmental Microbiology
  • 10. Brum* J.R., Ignacio-Espinoza* J.C., Kim E.H*., G. Trubl, R.M. Jones, N.C. VerBerkmoes, V.I. Rich, & M.B. Sullivan. Virion structural metaproteomics sheds light on marine ‘viral dark matter’. In preparation.
  • 11. Ignacio-Espinoza J.C.*, A. Gregory*, Deng, L., B.T. Poulos, P. Hugenholtz & M.B. Sullivan. Genomic population landscape of cyanophage viral communities. In preparation.
  • 12. Ignacio-Espinoza J.C., D. Anderson, B. Woodcroft, S.B. Hodgkins, J.P. Chanton, G. Tyson, S. Saleska, V. Rich. Candidatus Caldiserium septentrionalis a novel sulfate reducing bacteria in thawing permafrost. In preparation.

Star denotes shared first authorship.

Outreach and press

  • Finalist, top 10, in the Oceans180 video competition: Innocence by viral tagging, seen by more than 30 thousand students world wide.

Featured also in ScienceDaily, EurekAlert, PhysOrg, NSF, RealClearScience.

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