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, Depts of Bioengineering & Computer Science
Co-Director, Bioinformatics and Systems Biology PhD Program

Director, NIGMS National Resource for Network Biology (NRNB)
Co-Director, NCI Cancer Cell Map Initiative (CCMI)
Co-Director, NIMH Psychiatric Cell Map Initiative (PCMI)

Office: (858) 822-4558



Jason F. Kreisberg, Ph.D.
(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
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.


Charlotte Curtis 
(858) 534-7726

Administrator (On Leave)

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

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.


John Lee

Staff Research Associate

Fund Managers

Julie Wilkes
(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
(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

Anton Kratz, Ph.D.

Assistant 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.

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


Dexter Pratt

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.


Jing Chen
(858) 246-1698

Software Architect


Chris Churas

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.

Sophie Liu

Bioinformatics 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.


Keiichiro (Kei) Ono

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. 


Rudolf T. Pillich, Ph.D.
(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.

Willy Markuske

Systems Admin for Cluster


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


David Otasek

Software Programmer

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.

Postdoctoral Scholars

Maayan Baron, Ph.D. 

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.

Mark Kelly, Ph.D.

Postdoctoral Scholar

Brent Kuenzi, Ph.D.

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.

Karen Mei, Ph.D.

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. 

Devin N. Patel, MD

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.

Leah Schaffer, PhD

Postdoctoral Scholar

I am a Postdoctoral Scholar in the Department of Medicine. My research involves developing hierarchical models of cell structure using protein imaging and interaction data. Outside of lab, I enjoy hiking, music, and learning to surf.

Fan Zheng, Ph.D.

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

Samson Fong


Rob Loughnan

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


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.

Yue Qin

Bioinformatics & Systems Biology

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

Erica Silva

Biomedical Sciences

I am a MD/PhD student in the BMS program

Akshat Singhal

Computer Science

I’m a 2nd-year Computer Science PhD student. My research interests lie in applying computational techniques to improve drug discovery. I’m currently working on building deep learning models using data-driven hierarchies of molecular systems to predict drug response. In my free time, I like to play tennis, watch anime and cricket, and read sci-fi/fantasy novels.

Patrick Wall


Sarah Wright

Bioinformatics & Systems Biology

Research Lab Assistants

Likitha Aradhyula
Human Biology (BS) 

Undergraduate Lab Assistant

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.

Audrey Bogosian
Molecular and Cell Biology (BS)

Undergraduate Lab Assistant

I have been working with the Ideker Lab since summer 2020, under the supervision of Jason Kreisberg. 

Ximena Gonzalez 
General Biology (BS)

Undergraduate Lab Assistant

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.

Delina Kambo
Bioengineering (BS)

Undergraduate Lab Assistant

I began my work with the lab as a Genentech Scholars Summer Research Program participant. I am now an undergraduate student research working under the supervision of Samson Fong.

Isabella Panagiotou 
General Biology (BS)

Undergraduate Lab Assistant

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
Biological Sciences (BS/MS)

Lab Assistant

I am pursuing my Masters degree in Biology under UCSD’s BS/MS program. 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.