Aram Avila-Herrera


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.

Academic and Professional History

2019–

Lawrence Livermore National Laboratory (AIS), Livermore, CA

2016–2019

Lawrence Livermore National Laboratory, Livermore, CA

2015–2016

Gladstone Institutes, San Francisco, CA

2009–2015

University of California San Francisco, San Francisco, CA

2005–2009

University of California Santa Cruz, Santa Cruz, CA

Honors and Awards

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
Minority Access to Research Careers (MARC) Fellow
2007
International Scholar Laureate Program (Delegation on Engineering, China)

Publications

Presentations

Research Experience

2016–present

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.

2015–2016

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.

2010–2015

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.

2009–2010

I completed three research rotations with Profs. Joseph DeRisi, Alan Frankel, Katherine Pollard.

  1. (experimental) Under the supervision of Florencia Caro, I cultured Plasmodium falciparum in blood, coimmunoprecipitated RNA binding proteins and isolated their RNA cargo.
  2. (computational) I implemented two methods for predicting intraprotein evolutionary constraints and applied them to HIV Rev.
  3. (computational) I implemented a metagenomics pipeline for identifying CRISPRs in oceanic samples and tested for associations between their abundance and environmental variables.

Our PhD training program included two Team Challenges:

  1. We conducted microarray experiments and analyses to determine cause of death for yeast samples.
  2. We built a rudimentary fluorescence microscope / spectrometer.
Summer 2008

Minority Access to Research Careers (MARC) Summer Research Institute:

2007–2008

In the lab of Prof. Phillip Berman, I tested sera for immunoreactivity and automated the digitization of critical biological sequence records.

Teaching Experience

2010–2012 (Falls)

Integrated Program in Quantitative Biology, UCSF

Bootcamp Bioinformatics Leader

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.

Bootcamp Instructor

Gave introductory lectures on probability and statistics to students from diverse fields.

2010 (Fall)

School of Pharmacy, UCSF

Assistant in Instuction

Developed course material, led weekly discussions, held office hours, and administered course website. BPS 112: “Biostatistics”.

Service

Referee

BMC Bioinformatics, Bioinformatics, PLOS Computational Biology

2017–

Reviewed research manuscripts for publication.

Early Career Panelist

LLNL; Gladstone Institutes

Feb 2019; Apr 2017

Shared early career experiences with undergraduate and graduate students.

Dec 2014

Science Education and Outreach, Gladstone Institutes

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

Built a team to fundraise and participate in the 2014 Bay Area Heart Walk.

2012–2015

Minority Graduate Student Organization, UCSF

Peer Mentor

Provide longterm mentorship for new students.

Professional Development

Nov 2018

National Laboratory Entrepreneurship Academy, UC Davis GSM

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

Fall 2013

CATALYST Award Student Internship Program, UCSF

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

2012

Graduate Student Internships and Career Exploration, UCSF

Participated in career exploration and professional development workshops

Programming Languages

(and frequently used libraries)

Foreign Languages