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
UC San Diego
Dr. Trey Ideker, Dept of Medicine
9500 Gilman Drive, MC-0688
La Jolla, CA 92093-0688
Jason F. Kreisberg, Ph.D.
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.
Tel (858) 822-4667
Fax (858) 246-1396
I am the Lab Manager in Dr. Ideker’s experimental part of the lab. I assist postdocs, graduate, and undergraduate students with their projects.
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.
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.
Staff Research Associate
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.
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!
Daniel Carlin, Ph.D.
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.
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.
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
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.
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.
Tongqiu (Iris) Jia
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.
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 is a Systems Admin for the NRNB Cluster. Please post cluster related issues directly to the NRNB cluster google group.
Keiichiro (Kei) Ono
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.
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.
Rudolf T. Pillich, Ph.D.
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.
Systems Admin for Cluster
Paul is a Systems Admin for the NRNB Cluster. Please post cluster related issues directly to the NRNB cluster google group.
Maayan Baron, Ph.D.
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.
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.
Jisoo Park, Ph.D.
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
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.
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.
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
I am Medical Student interested in clinical applications of hierarchical modeling.
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.
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.
I am a MD/PhD student in the BMS program
Bioinformatics & Systems Biology
I am a Bioinformatics PhD student. My research with the Ideker Lab is primarily related to cellular hierarchy and deep learning.
Undergraduate Lab Assistants
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.
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.
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.
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
Undergraduate Assistant in Summer 2020. Audrey will be working with Jason Kreisberg.
Genentech Scholars Summer Research Program. Delina will be working with Samson Fong.
High School Intern
Summer 2020. Dalia will be working with Iris Jia.
Undergraduate Assistant in Summer 2020. Nicolas will be working with Fan Zheng.
Hidenori Tanaka, Ph.D.
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.