Versatile data scientist with computational biology expertise.
10+ yrs of collaboration experience to deliver basic and applied research products. Deep technical skill in R and Python development, building high-performance computing workflows, and next-generation sequencing analysis. Enjoys connecting across teams, and engaging customers to identify opportunities and needs. Passionate about advancing solutions that improve healthcare.
Lawrence Livermore National Laboratory, Livermore, CA
Lawrence Livermore National Laboratory, Livermore, CA
Lawrence Livermore National Laboratory, Livermore, CA
Gladstone Institutes, San Francisco, CA
University of California San Francisco, San Francisco, CA
PhD in Biological and Medical Informatics
Statistical evaluation of coevolution methods for predicting inter-protein contacts
Adviser: Prof. Katherine Pollard
University of California Santa Cruz, Santa Cruz, CA
Kok C, Mulakken N, Thissen J, Grey S, Avila-Herrera A, Upadhyay M, Lisboa F, Mabery S, Elster E, Schobel S, Be NA. Targeted metagenomic assessment reflects critical colonization in battlefield injuries. Microbiology Spectrum October 2023.
Trubl G, Stedman KM, Bywaters KF, et al. Astrovirology: how viruses enhance our understanding of life in the Universe. International Journal of Astrobiology. 2023;22(4):247-271.
Kimbrel J, Moon J, Avila-Herrera A, Martí JM, Thissen J, Mulakken N, Sandholtz SH, Ferrell T, Daum C, Hall S, et al. Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses. 2022; 14(12):2775.
Avila-Herrera A, Thissen J, Mulakken N, et al. Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds. Sci Rep 12, 13816 (2022).
Avila-Herrera A, Thissen J, Urbaniak C, Be NA, Smith DJ, Karouia F, et al. Crewmember microbiome may influence microbial composition of ISS habitable surfaces. PLoS ONE April 2020 15(4):e0231838.
Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp J-M, Stern DL, Davis GW, Pollard KS, Shah NM. Evolution of mechanisms that control mating in Drosophila males. Cell Reports May 2019 27(9):2527-2536.e4
Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. A most wanted list of conserved microbial protein families with no known domains. PLoS ONE October 2018 13(10):e0205749.
Be N, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K. Whole metagenome profiles from ISS particulates. BMC Microbiome July 2017 5:81
Avila-Herrera A, Pollard K. Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinformatics August 2015 16:268
Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M, Kumar ST, Smith JF, Pollard KS, Fändrich M, Kirchhoff F, Münch J, Witkowska HE, Greene WC. Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. Journal of Virology July 2014 88:13 7221-7234.
Avila-Herrera A. Counting on Microbes. Mathematics Colloquium, November 2019. Sonoma State University, Sonoma, CA.
Avila-Herrera A, Be N, Thissen J, Urbaniak C, Karouia F, Smith DJ, Mehta S, Venkateswaran K, Jaing C. Building a Microbial Catalog of the International Space Station. Poster presented at American Society for Gravitational and Space Research. Nov 2018. Washington, DC.
Avila-Herrera A, Be N, Thissen J, Urbaniak C, Karouia F, Smith DJ, Mehta S, Venkateswaran K, Jaing C. Building a Microbial Catalog of the International Space Station. Bioinformatics for the Microbiome Symposium. September 2018. Stanford, CA.
Avila-Herrera A. Search strategies for antimicrobial resistance associated genes. LLNL and UC Inaugural Data Science Workshop. Aug 2018. Livermore, CA.
Avila-Herrera A., Zemla A, Ames SK, Pearce R, Allen JE. Maximal match weights and sequence motifs for detection of antimicrobial resistance genes in shotgun metagenomic sequences. Poster presented at LLNL Postdoc Symposium. June 2018. Livermore, CA.
Avila-Herrera A, Be N, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K. Whole metagenome profiles from ISS particulates. American Society for Gravitational and Space Research. Oct 2017. Seattle, WA.
Avila-Herrera A, Pollard K. Performance of methods used to identify coevolving residues between proteins. Poster presented at 14th Biomedical Computation at Stanford Symposium. 2014. Stanford, CA.
Avila-Herrera A, Hernandez R, Krogan N, Pollard K. Measuring correlated evolution in HIV-human protein complexes. Poster presented at XVIth Bay Area Microbial Pathogenesis Symposium. 2013. San Francisco, CA.
I support an automated antibody engineering capability and consult for various genomics projects.
I maintained and developed web services that provide data to biosurveillance programs. My responsibilities included configuring web servers, creating continuous integration and deployment (CI/CD) pipelines, authentication, authorization, database maintenance, automating report generation and visualizations to increase situational awareness.
I provided bioinformatics and biostatistics support for multiple projects. I used compositional data analysis methods to help characterize the microbial taxonomy of the International Space Station surfaces and crew. We explored machine learning models of complex blast injuries for the purpose of identifying potential medical interventions using patient, treatment, and microbiome measurements taken over time. I also co-developed and benchmarked in-house tools for antimicrobial resistance detection and reporting.
Microbes have fascinating relationships with their environments, be they natural or man-made. This includes other microbes and host organisms, such as humans and plants, in addition to their surroundings, like ocean, soil, and buildings. I want to understand how these relationships affect us on Earth and in manned spaceflight.
In the lab of Prof. Katherine Pollard, I analyzed metagenomic data sets from human and ocean microbiomes for associations between environmental variables and novel gene families of unknown function.
For my dissertation, advised by Prof. Katherine Pollard, I investigated statistical methods for identifying coevolving residues—the building blocks of proteins. Residues may coevolve in order to conserve important functions or structures between phylogenetically broad protein families, for example, those involved in signaling complexes across bacteria, or in evolutionary arms race between a virus and host.
I completed three research rotations with Profs. Joseph DeRisi, Alan Frankel, Katherine Pollard.
Our PhD training program included two Team Challenges:
Minority Access to Research Careers (MARC) Summer Research Institute:
In the lab of Prof. Phillip Berman, I tested sera for immunoreactivity and automated the digitization of critical biological sequence records.
Integrated Program in Quantitative Biology, UCSF
Responsible for the organization and design of three-day theoretical and applied bioinformatics crash course. Prepared simulated data sets for coursework and led journal club discussions.
Gave introductory lectures on probability and statistics to students from diverse fields.
School of Pharmacy, UCSF
Developed course material, led weekly discussions, held office hours, and administered course website. BPS 112: “Biostatistics”.
BMC Bioinformatics, Bioinformatics, PLOS Computational Biology
Reviewed research manuscripts for publication.
LLNL; Gladstone Institutes
Shared early career experiences with undergraduate and graduate students.
Science Education and Outreach, Gladstone Institutes
Co-led lesson on biology, prevention, and history of HIV/AIDS to students of Balboa High School, San Francisco.
American Heart Association, San Francisco
Built a team to fundraise and participate in the 2014 Bay Area Heart Walk.
Minority Graduate Student Organization, UCSF
Provide longterm mentorship for new students.
National Laboratory Entrepreneurship Academy, UC Davis GSM
Received interactive entrepreneurship training from experts in academia, government, and industry.
CATALYST Award Student Internship Program, UCSF
Reviewed funding proposals with academic and industry experts in translational research for
Graduate Student Internships and Career Exploration, UCSF
Participated in career exploration and professional development workshops
(and frequently used libraries)