Epigenomics and Gene Expression Control

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.

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.

Emma Farley

Faculty Status
Active
Title
Assistant Professor
Email
efarley@ucsd.edu
Phone
(858) 246-2559
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Department
Brief Research Description
High-throughput functional assays in developing embryos to decipher how genomes instruct development

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.

Kyle Gaulton

Faculty Status
Active
Title
Assistant Professor
Email
kgaulton@ucsd.edu
Phone
(858) 822-3640
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Statistical genetics, epigenomics, chromatin, gene regulatory networks, diabetes
Lab Description

The Gaulton lab studies the effects of human genetic variation on gene regulation and diabetes risk. We use computational and statistical methods to integrate genome sequence information with epigenomic annotation and molecular QTL data.

Graham McVicker

Faculty Status
Active
Title
Assistant Professor
Email
gmcvicker@salk.edu
Phone
(858) 453-4100
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Human genetic variation, chromatin and gene regulation in immune cells
Lab Description

The McVicker laboratory aims to understand how chromatin state and organization are encoded by the human genome. Our approach to this problem is to exploit naturally occurring human genetic variation to identify sequence variants that disrupt chromatin function. We are currently focused on chromatin within immune cells and we are also interested in how variants that affect chromatin and gene regulation lead to disease risk. The problems that we work on often require the development of sophisticated computational and statistical methods that can extract subtle signals from noisy experimental data.