CGL and CGP Team

A photo of Benedict Paten in front of a banner for the Genomics Institute at UCSC.

Principal Investigator: Dr. Benedict Paten

Dr. Paten is an associate professor in the Department of Biomolecular Engineering at the University of California, Santa Cruz. He received his Ph.D. in computational biology from the University of Cambridge and the European Molecular Biology Laboratory. Dr. Paten’s work is broadly focused on the growing field of computational genomics. He leads the Computational Genomics Lab and sister Computational Genomics Platform groups within the Genomics Institute. He is involved in many large-scale genomics efforts. Through these efforts and many smaller collaborations, he is helping to develop methods to further our ability to read and interpret genomes.

Computational Genomics Team

A B C D E F G H I J K L M N O P Q R S U V W X Y Z Alumni

A

Mobin Asri

Graduate Student Researcher, CGL

Comparative Genomics

masri@ucsc.edu

B

Lon Blauvelt

Software Engineer, CGP

BioData Catalyst, Dockstore, AnVIL, TOIL

lblauvel@ucsc.edu

C

Xian Hui Chang

Graduate Student Researcher, CGL

Human Genome Variation Map

xhchang@ucsc.edu

Abraham Chavez Jr.

Software Engineer, CGP

Human Cell Atlas

achave11@ucsc.edu

Cecilia Cisar

Graduate Student Researcher, CGL

Spatial Transcriptomics

ccisar@ucsc.edu

Melissa Cline

Associate Research Scientist, CGL

BRCA Exchange, GA4GH

mcline@ucsc.edu

Brian Craft

Software Engineer, CGL

Xena

bcraft@ucsc.edu

Kimberley Czupil

Administrative Coordinator, CGL

kczupil@ucsc.edu

D

Mark Diekhans

Technical Director, CGL

GENCODE, TOIL, Genome10K, Comparative Genomics, T2T

markd@ucsc.edu

Noah Dove

Junior Software Engineer, CGP

Human Cell Atlas

nadove@ucsc.edu

E

Jordan Eizenga

Postdoctoral Scholar, CGL

Human Genome Variation Map

jeizenga@ucsc.edu

Parsa Eskander

Graduate Student Researcher, CGL

seeskand@ucsc.edu

G

Mary Goldman

Design and Outreach Engineer, CGL

UCSC Xena

mgoldman@ucsc.edu

H

Maximilian Haeussler

Assistant Research Scientist, CGL

max@soe.ucsc.edu

David Haussler

Scientific Co-Director, CGL

haussler@ucsc.edu

Prajna Hebbar

Graduate Student Researcher, CGL

pnhebbar@ucsc.edu

J

Nafiseh Jafarzadeh

Postdoctoral Scholar, CGL

njafarza@ucsc.edu

K

Nick Keener

Graduate Student Researcher, CGL

nkeener@ucsc.edu

M

Mira Mastoras

Graduate Student Researcher, CGL

mmastora@ucsc.edu

Melissa Meredith

Graduate Student Researcher, CGL

Computational Nanopore Genomics

mmmeredi@ucsc.edu

N

Shloka Negi

Graduate Student Researcher, CGL

shnegi@ucsc.edu

Uyen Nguyen

Graduate Student Researcher, CGL

uydnguye@ucsc.edu

Adam M Novak

Senior Software Engineer, CGL

TOIL, Human Genome Variation

anovak1@ucsc.edu

O

Nneka Olunwa

Security Compliance Analyst, CGP

Dockstore, BioData Catalyst, AnVIL, Human Cell Atlas

nolunwa@ucsc.edu

Charles Overbeck

Senior Software Engineer, CGP

Dockstore, BioData Catalyst, AnVIL

coverbec@ucsc.edu

P

Jimin Park

Graduate Student Researcher, CGL

jpark621@ucsc.edu

Benedict Paten

Director, CGL

bpaten@ucsc.edu

R

Robin Rounthwaite

Graduate Student Researcher, CGL

Comparative Genomics

rrounthw@ucsc.edu

S

Hannes Schmidt

Technical Lead, CGP

Human Cell Atlas

hannes@ucsc.edu

Jouni Sirén

Assistant Research Scientist, CGL

Human Genome Variation Map

jlsiren@ucsc.edu

Daniel Sotirhos

Software Engineer, CGP

Human Cell Atlas

dsotirho@ucsc.edu

David Steinberg

Senior Software Engineer, CGP

Dockstore, BioData Catalyst, AnVIL

davidcs@ucsc.edu

V

Ben Vizzier

Program Manager, CGP

bvizzier@ucsc.edu

Steve Von Worley

Software Engineer, CGP

svonworl@ucsc.edu

Z

Jingchun Zhu

Associate Research Scientist, CGL

Xena

jzhu2@ucsc.edu

Alumni

Andrew Bailey

Graduate Student Researcher, CGL

Epigenetics, Computational Nanopore Genomics

andbaile@ucsc.edu

Colleen Bosworth

Graduate Student Researcher, CGL

Computational Nanopore Genomics, Notch2nl

cboswort@ucsc.edu

Alden Deran

Graduate Student Researcher

Hongxu Ding

Postdoctoral Scholar, CGL

hding16@ucsc.edu

Alden Douglas

Undergraduate Student Researcher

Ian Fiddes

Graduate Student Researcher

Zack Fischmann

Senior Software Engineer, CGL

BRCA

zfischma@ucsc.edu

Mason Hargrave

Undergraduate Student Researcher

Tim Harris

Director, CGP

tijharri@ucsc.edu

Miten Jain

Assistant Research Scientist, CGL

mjain3@ucsc.edu

Amar Jandu

Junior Software Engineer, CGP

Human Cell Atlas

ajandu@ucsc.edu

Christopher Kethcum

Software Engineer

cketchum@ucsc.edu

Avani Khadilkar

Bioinformatics Systems Analyst

Emily Kobayashi

Undergraduate Student Researcher

Mikhail Kolmogorov

Postdoctoral Scholar, CGL

mkolmogo@ucsc.edu

Justin Krupp

Undergraduate Student Researcher

Natan Lao

Undergraduate Student Researcher, CGP

Human Cell Atlas

Fariha Lateef

Undergraduate Student Researcher, CGP

Dockstore

flateef@ucsc.edu

Melaina Legaspi

Scrum Master, CGP

Dockstore, BioData Catalyst, Human Cell Atlas

meelegas@ucsc.edu

Julian Lucas

Bioinformatics Systems Analyst, CGP

Human Pangeome Project, AnVIL, Dockstore

juklucas@ucsc.edu

Charles Markello

Graduate Student Researcher, CGL

BRCA Exchange, Human Genome Variation Map

cmarkell@ucsc.edu

Karen Miga

Associate Professor and Associate Director of Genomics Institute

khmiga@ucsc.edu

Jean Monlong

Postdoctoral Scholar, CGL

Human Genome Variation Map

flateef@ucsc.edu

Letitia Mueller

Graduate Student Researcher, CGL

BRCA Exchange

leamuell@ucsc.edu

Audrey Musselman-Brown

Graduate Student Researcher

Jake Narkizian

Undergraduate Student Researcher

Natalie Perez

Junior Software Engineer, CGP

Dockstore, BioData Catalyst, AnVIL

nperez9@ucsc.edu

Trevor Pesout

Graduate Student Researcher, CGL

Computational Nanopore Genomics

tpesout@ucsc.edu

Arthur Rand

Graduate Student Researcher

Kishwar Shafin

Graduate Student Researcher, CGL

Computational Nanopore Genomics

mshafin@ucsc.edu

Beth Sheets

Project Manager, CGP

BioData Catalyst, Dockstore, AnVIL, Human Pangenome Project

esheets@ucsc.edu

Jonas Sibbesen

Postdoctoral Scholar, CGL

Human Genome Variation Map

jsibbese@ucsc.edu

Yatish Turakhia

Postdoctoral Scholar, CGL

Computational Nanopore Genomics, Comparative Genomics

yturakhi@ucsc.edu

John Vivian

Graduate Student Researcher

Jeffrey Wu

Undergraduate Student Researcher, CGP

TOIL

jwu157@ucsc.edu

Walt Shands

Software Engineer, CGP

Dockstore, BioData Catalyst, AnVIL

jshands@ucsc.edu

William Gao

Undergraduate Research Assistant, CGL

wlgao@ucsc.edu

Marina Haukness

Graduate Student Researcher, CGL

Computational Nanopore Genomics

mhauknes@ucsc.edu

Trevor Heathorn

Program Manager, CGP

Human Cell Atlas, LungMAP

theathor@ucsc.edu

Stephen Hwang

Graduate Student Researcher, CGL

sjhwang@ucsc.edu

Ryan Lorig-Roach

Graduate Student Researcher, CGL

Computational Nanopore Genomics

rlorigro@ucsc.edu

Ash O’Farrell

Bioinformatics Systems Analyst, CGP

BioData Catalyst, Dockstore, AnVIL

aofarrel@ucsc.edu

Jonathan Xu

Undergraduate Student Researcher, CGP

TOIL

jxu125@ucsc.edu

Avani Khadilkar

Bioinformatics Systems Analyst, CGP

akhadilk@ucsc.edu

James Casaletto

Graduate Student Researcher, CGL

BRCA Exchange

jcasalet@ucsc.edu