Angela Brooks
Assistant Professor
Biomolecular Engineering
Postdoctoral Fellow,
Dana-Farber Cancer Institute/Broad Institute with Matthew Meyerson
Ph.D., Molecular and Cell Biology,
UC Berkeley with Steven Brenner
B.S., Biology with Specialization in Bioinformatics,
UC San Diego

When I'm not sciencing, I like to run to offset my love of food and cooking. I also like to sing and play guitar.
Eva Hrabeta-Robinson
Lab Manager

Postdoctoral Fellow, UC Santa Cruz with Charles Daniel
B.A. and Ph.D., Biochemistry and Comparative Biochemistry, UC Berkeley

As a senior scientist in the lab, I enjoy developing experimental approaches for new projects inspired by hypotheses derived from computational analysis of high throughput sequencing data. I provide preliminary data and support to our students who chose to take up and lead these projects as part of our team effort to understand the connection between genomic mutations and RNA processing in diseases like cancer.

I am happiest spending time with my family swimming, hiking, and camping in the mountains. I also love ballet and teach at local studios on occasions.

Amit Behera
Postdoctoral Researcher

Ph.D., Molecular and Cell Biology,
JNCASR with Tapas K. Kundu
M.Sc., Molecular and Human Genetics,
Banaras Hindu University
B.Sc., Botany, Zoology, and Chemistry,
Ravenshaw University

I am mostly interested in studying and exploring the interdependence and functional interplay among chromatin remodeling, transcription and splicing processes in cells. Currently, I am studying how mutations in splicing factors affect chromatin state and transcription in the context of cancer.

Outside lab research, I enjoy spending time amidst nature, hiking, camping, looking at ocean waves and staring at stars on the sky.

Jon Akutagawa
Graduate Student, BME

B.S., Bioengineering
UC Berkeley

I want to develop better models to predict disease progression and drug resistance in cancers that arise from mutations that alter splicing and the transcriptome. My current project involves uncovering mutations in the 5' untranslated regions of genes and characterizing their effects on transcription and translation.

When I'm not in lab, I enjoy discovering new rock walls to climb, re-imagining childhood Japanese dishes, and fiddling with new frameworks for data visualization.

Brandon Saint-John
Graduate Student, BME

B.Sc., Biochemistry
University of Virginia

There are a number of chromatin factors that are recurrently mutated in lung cancer, and how these mutations affect DNA accessibility and contribute to cancer is poorly understood. To this end, my research focuses on developing new methods with long-read nanopore sequencing to determine changes in DNA accessibility on a genome-wide scale and also determine how DNA accessibility is coordinated to influence gene expression.

In my spare time, I like to go to trivia nights at bars across town, surf, rock climb at Pacific Edge, and play basketball with labmates and friends.

Alison Tang
Graduate Student, BME

B.A., Molecular and Cell Biology
UC Berkeley

My work is primarily focused on investigating splicing alterations, RNA modifications, and allele-specific expression of transcripts associated with human disease. To do so, I work on various methods to analyze long reads as these studies are powered by hybrid RNA-Seq approaches. More generally, I’m interested in furthering our understanding of cancer and other genetic diseases through the development of computational methods.

I like hiking (especially if there are water features involved!), doing jigsaw puzzles, reading, drinking pearl milk tea, and watching movies.

Megan Durham
Graduate Student, MCD

B.S., Biology
Cal Poly San Luis Obispo

I work on the ssCRISPR project, which uses CRISPR/Cas9 targeting splice sites to force exon skipping events. I’m using this method to find new cancer driver mutations that result from aberrant exon skipping in lung adenocarcinoma.

When I’m not in lab, I enjoy backpacking, breakfast bonfires on the beach, and hammocking with beers and friends.

Alexis Thornton
Graduate Student, BME

B.S., Biology
University of Florida

My research aims to predict the impact of somatic cancer mutations by using Expression-based Variant Impact Phenotyping (eVIP). I’m also taking advantage of the vast amounts of existing RNA-seq datasets to create a database of splice variants and the cellular conditions (e.g. immune responses) they are associated with. This will be a valuable resource for the types of isoform-specific analysis we do in the Brooks Lab.

In my free time, I like to surf in Santa Cruz as much as possible. I also enjoy reading, playing basketball, and cheering for the Florida Gators.

Cindy Liang
Graduate Student, MCD

B.S., Neurobiology, Physiology, and Behavior
UC Davis

Although splicing factor mutations are recurrent in lung cancer, the biological impacts of the resulting transcript isoforms remain largely unknown. To shed light on this subject, my research project is focused on understanding the functional consequences of isoforms created by the splicing factor mutation U2AF1 S34F on lung adenocarcinoma.

When not in lab, I love creating digital art and character designs based off fantasy settings.

Colette Felton
Graduate Student, BME

B.S., Biochemistry
University of Washington

I want to develop long read sequencing tools for diagnostic or prognostic predictions of multiple cancer types. My current research involves developing a tool using nanopore data to identify gene fusions in chronic lymphocytic leukemia with the SF3B1 K700E mutation.

When I'm not in lab, I love doing tactile, creative things, especially cooking, baking, and sewing. My evenings are mostly spent reading speculative fiction or walking along the beach and on the weekends I can be found engrossed in a baking project or hiking in the redwood forest.

Dennis Mulligan
Graduate Student, BME

B.S., Genetics & Plant Biology
UC Berkeley

I develop computational tools to help understand complex biological data. I’m currently working on a project to quantify mutually exclusive splicing events, in hopes of helping researchers study alternative splicing in transcriptome sequencing data. I also am interested in data visualization, making pretty and occasionally useful graphs and plots.

Outside of my research, I enjoy making art with my kids, hiking, gardening, and building furniture.

Nathan Cook
Undergrad Researcher

Major: Biomolecular Engineering
Minor: Bioinformatics

I am currently studying the role of alternative splicing in oncogenesis. We hope to develop a CRISPR screen that can identify therapeutic targets in lung cancer. My interests in biotechnology extend broadly to medical research and I hope to one day work on chronic diseases such as diabetes.

When I’m not in the lab, I enjoy fencing, playing Catan, and talking about almost anything interesting.

Swetha Vadde
Undergrad Researcher

Major: Human Biology
Minor: Classical Studies

I am studying aberrant alternative splicing and its role in oncogenesis. Currently, I am contributing to a CRISPR screen that targets the splice sites of exons to cause exon skipping and investigating how much skipping is needed to see a cancer phenotype.

In my free time, I like to spend time with friends, ski/snowboard, read novels, and bake.

Carlos Arevalo
Undergrad Researcher

Major: Molecular, Cell, and Developmental Biology
Minor: Bioinformatics

I am interested in understanding the role of spliceosomal mutations and protein isoform functions in lung adenocarcinoma. I am currently developing validation approaches for nanopore sequencing data and molecular characterization methods for U2AF1 S34F-associated transcript isoforms, which can hopefully lead to novel treatments for lung adenocarcinoma.

In my free time, I like to read about new topics in science journals and explore new offerings at the bookstore.


Lab Alumni

Undergraduate Students

Kevyn Hart

Sept 2015-July 2017, Research Specialist Jan-July 2017, Currently: Graduate Student, UCLA

Maximillian Marin

Sep 2015-Jun 2017, Awards: Crown College Undergraduate Research Fellowship, Koret Scholarship, Dean’s Award, Currently: Graduate Student, Harvard Systems Biology

Pratibha Jagannatha

March 2016-July 2019, Research Specialist July 2018-July 2019, Currently: Graduate Student, UC San Diego

Dominic Schenone

Sept 2016-Oct 2017, Research Specialist June-July 2017, Currently: Graduate Student, UC San Diego

Jacob Runyan

June 2017-June 2018, Currently: Software Engineer, Egnyte

Tyler Myers

Sept 2017-April 2018, Awards: Koret Scholarship, Currently: Graduate Student, UC San Diego

Maelia Uy-Gomez

Jan 2018-March 2019, Currently: Senior Research Associate, Genentech

Chang Kim

March 2018-June 2019, Currently: Bioinformatician, UCSF

Stefanie Brizuela

June 2017-June 2020, Awards: NIH Undergraduate Scholarship Program

Carmelle Catamura

June 2017-June 2020, Awards: Koret Scholarship, Currently: Graduate Student, UC Berkeley

Matthew Cattle

April 2018-June 2020, Awards: Koret Scholarship, Dean’s Award, Currently: Graduate Student, NYU

Graduate Students

Allysia Mak

M.S., Jan 2018-July 2018, Currently: Bioinformatics Analyst, Guardant Health

Elizabeth DeVogelaere

M.S., April 2019-Dec 2019, Currently: Bioinformatics Analyst, Takeda

Cameron Soulette

Ph.D., March 2016-June 2020, Currently: Bioinformatics Analyst, Gilead Sciences