Faculty & Staff

Julio ("Cesar") Espinoza, PhD

Julio Cesar Ignacio Espinoza, PhDContact
Areas of Expertise

Bioinformatics, Data Science, Genomics, Scientific Cloud Computing, Virus Discovery, Virus Host Interactions

Featured Links

Research group website

Google Scholar

J. Cesar Ignacio Espinoza, who joined KGI in September 2023, earned his Bachelor of Science in Biology from the Oaxacan Institute of Technology in Oaxaca, Mexico. He then received his Masters in Ecology and Evolutionary Biology from the University of Arizona in Tucson. His master’s thesis studied the evolutionary biology of T4-like phages. After obtaining his Masters, Cesar pursued a PhD in Molecular and Cellular Biology with an emphasis on bioinformatics, training within the IGERT Comparative Genomics program. During his time at the U of A, he was generously founded thought a Fulbright Fellowship, and several of the objects of his doctoral research were published in Nature and Science.

After his PhD, Cesar trained as a postdoctoral fellow at USC, having secured the competitive USC-Provost fellowship. There, he examined the evolutionary dynamics of marine viruses using -omics and bioinformatic techniques. His work was published in Nature Microbiology.

Before becoming a part of KGI, Cesar had a successful tenure in a couple of startups. Initially, he worked as a Data and Bioinformatics Scientist at Curative, where he established the bioinformatics infrastructure that secured some early contracts. He further established workflows that sequenced, assembled, and annotated over 35,000 SARS-CoV-2 genomes. Post-pandemic, his expertise was channeled towards building fast variant calling workflows for human genome sequencing and direct-to-consumer genomic services. After departing from Curative, Cesar joined as a senior engineer at FormBio, contributing significantly to the creation of software designed to analyze NGS data and extract biological insights from it. Cesar is proficient in both AWS and Google Cloud environments.

His research interests sit at the intersection of microbiology, virus-host interactions, bioinformatics, and data science.

  1. 2022 N. Kojima, E. Khorosheva, L. Lopez, M. Hanewich-Hollatz, J.C Ignacio-Espinoza [12 authors]. Local monitoring of SARS-CoV-2 variants in two large California counties in 2021. Scientific Reports 12(1):17046
  2. 2021 A.M. Long, S. Hou, J.C. Ignacio-Espinoza and J.A. Fuhrman. Benchmarking microbial growth rate predictions from metagenomes. The ISME Journal 15:183-195
  3. 2020 Wang, W., J. Ren, K. Tang, E. Dart, J.C. Ignacio-Espinoza, J.A. Fuhrman, J. Braun, F. Sun & N. Ahlgren A network-based integrated framework for predicting virus-host interactions. NAR Genomics and Bioinformatics 2(2):lqaa044
  4. 2019 Ignacio-Espinoza J.C., N. Ahlgren & J.A. Fuhrman. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nature Microbiology 5:265–271
  5. 2019 Sieradzki E.T., J.C. Ignacio-Espinoza, D.M. Needham, E. Fichot & J.A. Fuhrman. Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporalpicoplankton metatranscriptomes Nature Communications 10:1169
  6. 2018 Ignacio-Espinoza, J.C. & J.A. Fuhrman. A non-tailed twist in the viral tale. Nature 554:38
  7. 2016 Gregory A.C., S.A. Solonenko, J.C. Ignacio-Espinoza, K. LaButti, A. Copeland, S. Sudek, A. Maitland, L. Chittick, F. dos Santos, J.S. Weitz, A.Z. Worden, T. Woyke and M.B. Sullivan. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC genomics 17:930
  8. 2016 Brum*, J.R., Ignacio-Espinoza*, J.C., Kim*, EH, G. Trubl, R.M. Jones, S. Roux, N.C. VerBerkmoes, V.I. Rich, M.B. Sullivan. Illuminating structural proteins in viral “dark matter” with metaproteomics. PNAS 113:2436-2441
  9. 2015 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 348:e1261498 doi:10.1126/science.1261498.
  10. 2014 Deng, L.*, Ignacio-Espinoza*, J.C., A. Gregory, B.T. Poulos, P. Hugenholtz & M.B. Sullivan. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513:242–245.

Our research lies at the intersection of environmental microbiology, genomics, and evolutionary biology, leveraging cutting-edge ‘omics technologies, bioinformatics, and data science to explore the roles of viruses, microbes, and their interactions in environments critical to human health and well-being.

We use metagenomic big data to uncover novel viruses, investigate their ecological significance, and understand their evolutionary dynamics. By studying viral evolution and ecological interactions, we develop predictive and causal models to better understand their emergence and behavior.

To complement this work, we integrate proteomic and metagenomic data from naturally occurring parallel evolution experiments. This approach enhances virus annotation, links genomic features to phenotype, and allows for comparative analyses across environmental gradients. By combining these insights, we create more robust models to explore viral functions and their ecological impacts.

Building on these foundations, we are now applying deep learning to model species distributions and the emergence of ecological traits, expanding our ability to predict how organisms interact with and adapt to their environments.