Meet the Ideker Lab

The Ideker Lab is a dynamic group of enthusiastic scientists with expertise across a variety of disciplines, including systems biology, cellular modeling, cancer genomics, computational biology, epigenetics, and psychiatric diseases. Current lab members and their contact information are shown below. Visit the Lab Alumni page to meet our distinguished alumni. Visit our Photo Gallery to see what fun our group has been up to! 

Trey Ideker, Ph.D

University of California San Diego
Professor, Department of Medicine
Adjunct Professor, Departments of Bioengineering and Computer Science

Director, National Resource for Network Biology
Director, Cancer Cell Map Initiative
Director, Psychiatric Cell Map Initiative 

Office: (858) 822-4558
Fax:     (858) 246-1396
Email:  tideker@ucsd.edu

Mailing Address:
UC San Diego
Dr. Trey Ideker, Dept of Medicine
9500 Gilman Drive, MC-0688
La Jolla, CA 92093-0688

Staff

JasonKreisberg

Jason F. Kreisberg, Ph.D.
jkreisberg@ucsd.edu
(858) 534-3578

Academic Program Manager
Asst Director, Cancer Cell Map Initiative

As a Program Manager, I work closely with many members of the lab to plan projects, troubleshoot experiments, analyze results, prepare manuscripts and write grants. I also serve as the Assistant Director of the Cancer Cell Map Initiative where I help coordinate research activities across the ten labs supported by the Center.

Kate Licon
klicon@ucsd.edu
Tel (858) 822-4667
Fax (858) 246-1396

Lab Manager

 I am the Lab Manager in Dr. Ideker’s experimental part of the lab. I assist postdocs, graduate, and undergraduate students with their projects.

CharlotteCurtis

Charlotte Curtis
cacurtis@ucsd.edu 
(858) 534-7726

Administrator


I provide Administrative support to Dr. Ideker, our lab members, and our research centers. When not in lab, I enjoy painting and baking.  I am also a professionally trained Pastry Chef and received my BFA in Visual Arts from UC San Diego. 

Michael Chen
mic024@ucsd.edu

Staff Research Associate

Currently assisting the graduate students in their studies in the DNA damage response mechanism. When not in lab, I enjoy playing FFXIV.

JohnLee

John Lee
jjl047@ucsd.edu

Staff Research Associate

Fund Managers

Julie Wilkes
jwilkes@ucsd.edu
(858) 822-2137

Assistant Director of Sponsored Projects

I am the Assistant Director of the Sponsored Projects Office for the Dept of Medicine. I handle Pre-Awards for the Ideker Lab. When not working, I enjoy listening to music and gardening.

Jeane Lee
jel079@ucsd.edu
(858) 534-1725

Fund Manager

I serve as a Fund Manager handling Post-Awards for the Ideker Lab.  In my off time, I enjoy exploring San Diego with my dog! 

Senior Scientists

Daniel Carlin, Ph.D.
carlin.daniel@gmail.com
(412) 841-6852

Asst. Project Scientist

I am an Assistant Project Scientist, and former Postdoc, in the Ideker Lab. I study network and ontology interpretations of genetics results. Currently I am working to bring the best possible combination of networks, algorithms, and data to bear on the problems of cardiac disease, addiction, and diabetes. I’m also interested in multi-omics approaches, especially single cell data. In my free time I enjoy being outdoors in sunny San Diego!

Anton Kratz, Ph.D.
akratz@ucsd.edu

Asst. Research Scientist

My research is concerned with the creation and functionalization of a data-driven Systems Biology model of DNA damage response and repair. Prior to joining the Ideker Lab, I earned my PhD in Systems Biology at Keio University, Japan, in the lab of Dr. Masaru Tomita, and completed my postdoctoral research at RIKEN CLST, Japan.

Sara Brin Rosenthal, Ph.D.
sbrosenthal@ucsd.edu

Senior Bioinformatics Scientist

Working with the Ideker lab and the Center for Computational Biology and Bioinformatics (CCBB), my research focuses on understanding neuronal and developmental disorders, including autism and congenital heart disease.  By integrating common and rare variation in a hierarchical framework, we seek to uncover novel biological pathways underlying these disorders.  Outside of work I enjoy going on long runs around campus, and playing flute and piccolo in a local community orchestra.

Software Development Team

DexterPratt

Dexter Pratt
depratt@ucsd.edu

Director of Software Development

I direct the Software Development Team as they work to build the Cytoscape ecosystem, including Cytoscape Desktop, NDEx, cytoscape.js, and new web services.  We maintain and extend the lab’s computing resources and help researchers in the lab translate their work into useful prototypes and sometimes to new released software.

JingChen

Jing Chen
jic002@ucsd.edu
(858) 246-1698

Software Architect

ChrisC

Chris Churas
cchuras@ucsd.edu

Software Developer

I am a Software Developer with the Ideker lab who splits time between development on NDEx and other lab projects. When I’m not in the lab, I enjoy hiking, backpacking, and board games.

Iris

Tongqiu (Iris) Jia
t1jia@ucsd.edu

Applications Programmer

My research is focused on applying network knowledge to GWAS and sequencing data to find disease-related pathways and mechanisms. I am also interested in algorithms, especially those can be applied to biological systems. When not in lab, I enjoy running on the beach and hikes out in nature. 

Sophie Liu
sol015@ucsd.edu

Applications Programmer

I’m a member of the software development team working on NDEx. When not in the lab, I enjoy hiking, baking, and salsa dancing.

Willy Markuske 
wmarkuske@ucsd.edu

Systems Admin for Cluster

(Consultant)

Willy is a Systems Admin for the NRNB Cluster. Please post cluster related issues directly to the NRNB cluster google group. 

KeiOno

Keiichiro (Kei) Ono
kono@ucsd.edu

Bioinformatics Programmer

I am a Software Engineer specialized in bioinformatics and data visualization. My primary project is the development of new data visualization systems for biologists, including Cytoscape and HiView. 

DavidOtasek

David Otasek

Software Programmer
(Consultant)

I help build and maintain software components in the Cytoscape ecosystem. These include the Cytoscape Desktop application, and web libraries for sharing its data with NDEx and Cytoscape.js. In my spare time, I powerlift and build very noisy guitar pedals.

RudiPillich

Rudolf T. Pillich, Ph.D.
rpillich@ucsd.edu
(858) 822-4068

NDEx Application Manager

I am a research scientist with 10+ years of hands-on experience in Cell & Molecular Biology mainly focused on pancreas biology and diabetes. I am excited to bridge the gap between biologists and software engineers, while ensuring that the NDEx Project understands and satisfies the needs of our vibrant biomedical research community.

PaulTatarsky

Paul Tatarsky

Systems Admin for Cluster
(Consultant)

Paul is a Systems Admin for the NRNB Cluster. Please post cluster related issues directly to the NRNB cluster google group. 

Postdoctoral Scholars

Maayan Baron, Ph.D. 
m2baron@ucsd.edu 

Postdoctoral Scholar

My research in the Ideker lab focuses on linking genomics and transcriptomics to functional properties of tumors such as early stages of tumor initiation and progression. I am interested in applying interpretable machine learning techniques such as visible neural network to understand cancer drug resistance in single cell resolution. Outside of the lab, I enjoy being in nature with my family.

Brent Kuenzi, Ph.D.
bkuenzi@ucsd.edu

Postdoctoral Scholar

My research in the Ideker lab focuses on using CRISPR/Cas9 to identify new synthetic lethal interactions in cancer. I am also interested in using advanced machine learning technologies to improve cancer therapy. Outside of the lab, I enjoy taking my kids hiking/camping and am avid home cook.

Mark Kelly, Ph.D.
m3kelly@health.ucsd.edu

Postdoctoral Scholar

Jisoo Park, Ph.D.
jisoopark@ucsd.edu

Postdoctoral Scholar

I am a Postdoctoral Scholar at the Ideker lab. My research interests include Systems Biology, Computational Biology, and Bioinformatics. I am currently working on 1) building a Visible Neural Network for interpretable human genotype-phenotype translation and 2) understanding differential protein-protein interaction across head and neck, breast cancer cell lines. 

Devin N. Patel, MD
d4patel@ucsd.edu

Urologic Oncology Fellow

I am a current urologic oncology fellow. My research with the Ideker Lab is focused on using a network based bioinformatics approach to urothelial carcinoma. Outside lab, I enjoy running, playing basketball and all things related to the NBA.

Karen Mei, Ph.D.
yumei@ucsd.edu

Postdoctoral Scholar

I am a Postdoctoral Scholar in the Department of Medicine. My interests are to use bioinformatic analysis and machine learning methods to better understand the biological mechanisms of psychiatric diseases. When not in lab, I enjoy reading history, hiking, and seeking out good food. 

Fan Zheng, Ph.D.
f6zheng@ucsd.edu

Postdoctoral Scholar

My research interest with the Ideker lab is mainly on the structures of molecular networks, including data-driven hierarchical models and ontologies, and applying those models to interpret cancer genomes.  Before joining the Ideker lab, I obtained my Ph.D. at Dartmouth College, focused on computational modeling and design of protein structures.

Graduate Student Researchers

Mitchell Flagg
meflagg@ucsd.edu

Medical Student

I am Medical Student interested in clinical applications of hierarchical modeling. 

Samson Fong
shfong@ucsd.edu

Bioengineering

Rob Loughnan
rloughna@ucsd.edu

Cognitive Science,
Center for Human Development

I am interested in linking human genetic risk for psychiatric disorders to regulatory changes. My research involves applying machine learning  methods to large population genetic datasets. In my free time I like sailing, surfing and playing jazz piano. 

Brenton Munson
bpmunson@eng.ucsd.edu

Bioengineering

I am a PhD student in the Bioengineering Department. In the Ideker Lab my research is chiefly focused on the development of analytical and experimental frameworks for quantifying genetic interactions, which are utilize to investigate cellular reorganization in response to environmental perturbations. Outside the lab, I enjoy getting out into nature through backpacking and rock climbing.

Erica Silva
e5silva@ucsd.edu

Biomedical Sciences

I am a MD/PhD student in the BMS program

Akshat Singhal
a2singha@eng.ucsd.edu

Computer Science

Vikram Sirupurapu
vsirupur@eng.ucsd.edu 

Master’s Student

Yue Qin
y8qin@ucsd.edu

Bioinformatics & Systems Biology

I am a Bioinformatics PhD student. My research with the Ideker Lab is primarily related to cellular hierarchy and deep learning.

Patrick Wall
pgwall@eng.ucsd.edu

Bioengineering

Undergraduate Lab Assistants

Likitha Aradhyula
laradhyu@ucsd.edu

Human Biology (BS) 

I am an Undergraduate Lab Assistant with the Ideker lab, and majoring in Human Biology. I am passionate about medical research and planning to become a medical professional in the future.

Ximena Gonzales
xigonzal@ucsd.edu 

General Biology (BS)

I’m an undergraduate lab assistant majoring in general biology and minoring is music at UCSD. My favorite things to do outside of lab are playing the piano, going on hikes, and traveling.

Isabella Panagiotou
ipanagio@ucsd.edu 

General Biology (BS)

I am an undergraduate student pursuing a General Biology degree and a Music minor. In my free time I enjoy reading, singing and making origami.

Lily Rajaee
lirajaee@ucsd.edu

Human Biology (BS)

I am a third-year undergraduate student studying Human Biology. I plan to pursue a career as a physician in the Medical Field, while continuing to explore my interest in biomedical research. When I am not in lab or classes, I enjoy art and music in my free time.

Summer Research Students

Audrey Bogosian
abogosia@ucsd.edu

Undergraduate Assistant

Undergraduate Assistant in Summer 2020. Audrey will be working with Jason Kreisberg. 

Delina Kambo
dkambo@ucsd.edu

Undergraduate Assistant

Genentech Scholars Summer Research Program. Delina will be working with Samson Fong. 

Dalia Sebat
daliasebat@gmail.com

High School Intern

Summer 2020. Dalia will be working with Iris Jia. 

Nicholas Wilson
n4wilson@ucsd.edu

Undergraduate Assistant

Undergraduate Assistant in Summer 2020. Nicolas will be working with Fan Zheng.

Visiting Scholars

Hidenori Tanaka, Ph.D.
htanaka@ucsd.edu

Visiting Scholar
Toyota Central Research & Development Laboratories, Inc.
Genome Engineering Program

I’m a visiting scholar from Japan. My research with Ideker Lab is focused on phenotypic prediction using machine learning. When not in lab, I enjoy riding a bike and playing with my children.