aramavilaherrera-cv

Aram Avila-Herrera, PhD

Versatile group leader, data scientist, and software developer with 15+ years experience.

Academic and Professional History

2016–

Lawrence Livermore National Laboratory, Livermore, CA

Biomolecular Design and Development Group Leader
Software Developer
Bioinformatics Data Engineer
Bioinformatics Scientist

2016–2019

Postdoctoral Research Staff

2015–2016

Gladstone Institutes, San Francisco, CA

Bioinformatics Fellow. Adviser: Prof. Katherine Pollard

2009–2015

University of California San Francisco, San Francisco, CA

PhD in Biological and Medical Informatics. Adviser: Prof. Katherine Pollard

Statistical evaluation of coevolution methods for predicting inter-protein contacts

2005–2009

University of California Santa Cruz, Santa Cruz, CA

BS in Bioinformatics. Advisers: Prof. Kevin Karplus, Prof. Phillip Berman

Honors and Awards

2021

Physical and Life Sciences Directorate Award

2015

Gladstone Institute of Cardiovascular Disease Award for Excellence in Leadership

2011–2012

UCSF Graduate Research Mentorship Fellowship

2011

National Science Foundation Graduate Research Fellowship Program (*Honorable Mention)

2008–2009

Maximizing Access to Research Careers (MARC) Fellow

2007

International Scholar Laureate Program (Delegation on Engineering, China)

Publications

Martí JM, Kok CR, Thissen JB, Mulakken NJ, Avila-Herrera A, Jaing CJ, Allen JE, and Be NA (2025) Addressing the dynamic nature of reference data: A new nucleotide database for robust metagenomic classification. mSystems, 10, e0123924.

Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, and Borucki MK (2024) Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PloS one, 19, e0289198.

Kok CR, Mulakken N, Thissen JB, Grey SF, Avila-Herrera A, Upadhyay MM, Lisboa FA, Mabery S, Elster EA, Schobel SA, and Be NA (2023) Targeted metagenomic assessment reflects critical colonization in battlefield injuries. Microbiology spectrum, 11, e0252023.

Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, and Boston PJ (2023) Astrovirology: How viruses enhance our understanding of life in the Universe. International journal of astrobiology, 22, 247–271.

Avila-Herrera A, Thissen JB, Mulakken N, Schobel SA, Morrison MD, Zhou X, Grey SF, Lisboa FA, Unselt D, Mabery S, Upadhyay MM, Jaing CJ, Elster EA, and Be NA (2022) Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds. Scientific reports, 12, 13816.

Kimbrel J, Moon J, Avila-Herrera A, Martí JM, Thissen J, Mulakken N, Sandholtz SH, Ferrell T, Daum C, Hall S, Segelke B, Arrildt KT, Messenger S, Wadford DA, Jaing C, Allen JE, and Borucki MK (2022) Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses, 14.

Avila-Herrera A, Thissen J, Urbaniak C, Be NA, Smith DJ, Karouia F, Mehta S, Venkateswaran K, and Jaing C (2020) Crewmember microbiome may influence microbial composition of ISS habitable surfaces. PloS one, 15, e0231838.

Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp J-M, Stern DL, Davis GW, Pollard KS, and Shah NM (2019) Evolution of Mechanisms that Control Mating in Drosophila Males. Cell reports, 27, 2527–2536.e4.

Wyman SK, Avila-Herrera A, Nayfach S, and Pollard KS (2018) A most wanted list of conserved microbial protein families with no known domains. PloS one, 13, e0205749.

Be NA, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, and Venkateswaran K (2017) Whole metagenome profiles of particulates collected from the International Space Station. Microbiome, 5, 81.

Avila-Herrera A and Pollard KS (2015) Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC bioinformatics, 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, and Greene WC (2014) Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. Journal of virology, 88, 7221–7234.

Presentations

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.

Service

2017-2019

Referee. Reviewed research manuscripts for publication in Bioinformatics, BMC Bioinformatics, PLOS Comp. Bio.

2/2019, 4/2017

LLNL, Gladstone Institutes, Early career panelist

Dec 2014

Gladstone Institutes, Science Education and Outreach Guest Lecturer

Co-led lesson on biology, prevention, and history of HIV/AIDS to students of Balboa High School, San Francisco.
Co-led hands-on activity demonstrating the importance of HIV testing.

Sep 2014

American Heart Association, San Francisco, Heart Walk Team Leader

Professional Development

2025

Crucial Conversations for Mastering Dialogue, LLNL Computing Leadership Training

Moments That Matter, LLNL Computing Leadership Training

2018

National Laboratory Entrepreneurship Academy, UC Davis Graduate School of Management

Received interactive entrepreneurship training from experts in academia, government, and industry.

2013

CATALYST Award Student Internship Program, UCSF

Reviewed funding proposals with academic and industry experts in translational research.

2012

Graduate Student Internships and Career Exploration, UCSF

Programming

HPC
- flux
- slurm
- merlin
- parsl
Python
- pandas
- numpy/scipy
- biopython
- matplotlib
- BeautifulSoup
- scikit-learn
- networkx/igraph
R
- quarto, rmarkdown
- tidyverse
- igraph
- phyloseq
- vegan
- caret
- batchtools
- future
Web/Viz.
- Django/DRF
- Jekyll
- JavaScript
- CoffeeScript
- CSS
- Stylus
- plot.ly
- HTML5
- D3.js
Misc.
- bash
- Perl
- SQL
- C
- XML
- Java
- ruby
- lua
- C++