Genetic and Molecular Networks

Pablo Tamayo

Faculty Status
Active
Title
Professor
Email
ptamayo@ucsd.edu
Phone
(858) 246-2385
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Development of analysis methods for the functional characterization of cancer genomes including RNAi and CRISPR genetic dependencies. Computational methods, probability and statistics, data analysis, machine learning, computational biology and cancer research.

Amit Majithia

Faculty Status
Active
Title
Assistant Professor
Email
amajithia@ucsd.edu
Phone
(858) 822-0727
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Insulin resistance, functional genomics, pharmacogenetics, cardiometabolic disease, diabetes
Lab Description

Our goal is to identify genes causing insulin resistance in humans in order to find new therapeutic targets for diabetes and cardiometabolic diseases. Our approach to discovery is grounded in human genetics, clarified through systematic, high throughput experimentation in human cells, and calibrated by its relevance to clinical disease. We use massively parallel genome engineering to re-create mutations identified in patients and develop high-throughput assays to interrogate function in human cell models. We apply bioinformatics and statistics to make sense of this data integrating 1) human mutations, 2) cellular function, and 3) metabolic/glycemic phenotypes of the individuals who harbor them. Using this approach, we have discovered novel missense mutations that greatly increase risk for type 2 diabetes. As a complementary aim towards precision medicine, we develop tools for clinical genome interpretation powered by high-throughput experimental data.

Lukas Chavez

Faculty Status
Active
Title
Assistant Professor
Email
lukaschavez@ucsd.edu
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Department
Brief Research Description
Chromatin and Gene Regulation in Childhood Cancers

Louise Laurent

Faculty Status
Active
Title
Associate Professor
Email
llaurent@ucsd.edu
Phone
(858) 246-1403
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Gene Interaction Networks, Biomarker Discovery, Pluripotency, Embryonic Development, Placental Dysfunction, Preeclampsia, Pregnancy complications
Lab Description

Our lab applies our expertise in human pluripotent stem cell research and genomics to understand the molecular mechanisms underlying normal and abnormal human development, in order to improve the health of mothers and babies.

Ferhat Ay

Faculty Status
Active
Title
Assistant Professor
Email
ferhatay@lji.org
Phone
(858) 752-6612
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Epigenetics, genomics, chromatin structure, 3D/4D genome/nucleome, statistical methods for analysis of Hi-C and HiChIP data, gene regulation in immune cells, cancer genomics
Lab Description

We are interested in the analysis and modeling of the three-dimensional chromatin structure from high-throughput sequencing experiments. We develop methods that are based in statistics, machine learning, optimization and graph theory to understand how changes in the 3D genome affect cellular outcome such as development, differentiation and gene expression. We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases.

Elizabeth Winzeler

Faculty Status
Active
Title
Professor
Email
ewinzeler@ucsd.edu
Phone
(858) 822-3339
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
My laboratory uses big data approaches to solve problems in global health. The lab also offers training in cheminformatics and chemical genomics.

Alon Goren

Faculty Status
Active
Title
Assistant Professor
Email
agoren@ucsd.edu
Phone
(858) 246-0943
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Dynamics of epigenomic mechanisms during development and along the cell cycle
Lab Description

Our overall goal is to understand how chromatin structure is employed in making cellular fate decisions, its dynamics, and how it is shaped and maintained by different chromatin regulators (CRs). We merge basic biology, genomics and technology development.

Lilia Iakoucheva

Faculty Status
Active
Title
Associate Professor
Email
lilyak@ucsd.edu
Phone
(858) 822-1878
Track(s)
Bioinformatics and Systems Biology
Department
BISB Research Area(s)
Brief Research Description
Autism, genetics, gene expression, protein interactions, systems biology, networks, psychiatric diseases, whole genome sequencing
Lab Description

The lab has a variety of bioinformatics projects aimed at improving understanding of the functional impact of autism mutations derived from exome and genome sequencing of the patients. We build spatio-temporal gene co-expression and protein interaction networks for psychiatric diseases and we use these networks to generate the testable hypothesis about the mechanisms of disease. We also test these hypothesis experimentally in the lab, thereby adding a translational aspect to our work.