Genetic and Molecular Networks

Wendy Huang

Faculty Status
Active
Title
Assistant Professor
Email
wjh003@ucsd.edu
Phone
(858) 246-2258
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Non-coding RNA, RNA binding proteins, gene expression analysis, immune pathologies
Lab Description

We strive to better understand how diverse members of the non-coding RNA family and their RNA binding protein partners, through their ability to modulate gene expression in the nucleus, contribute to immune pathologies in mouse models of colitis, multiple sclerosis, and cancers. Deeper understanding of how immune gene expression programs are controlled will facilitate development of new intervention strategies against inflammatory diseases.

Mohit Jain

Faculty Status
Active
Title
Associate Professor
Email
mjain@ucsd.edu
Phone
(858) 822-5854
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Human Biology, Metabolic Biochemistry, Integrative Biology, Mass Spectrometry, Metabolomics
Lab Description

Bringing together Disease Research, Analytical Chemistry, Computational Methods and Drug Discovery

Abraham Palmer

Faculty Status
Active
Title
Professor
Email
aap@ucsd.edu
Phone
(858) 534-2093
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Quantitative genetic studies of behavior using fish, mice, rats and humans. Applying statistical genetics and genomics approaches to understanding behavior.
Lab Description

We are interested in the relationship between genes and behavior. By identifying genes that influence behavior we hope to obtain fundamental mechanistic insights into the molecular basis of both health and disease. Our research uses mice, rats and humans in pursuit of these goals.

Andrew Allen

Faculty Status
Active
Title
Associate Professor
Email
aallen@ucsd.edu
Phone
(858) 200-1826
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Ecological, comparative, and functional genomics of marine phytoplankton, Systems biology of microalgae, Genome evolution and evolutionary origins of metabolic function in marine microbes, Transcriptional regulatory networks, Metagenomics, Metatranscriptomics, Microbes, Evolution

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 of Medicine and Pediatrics, Division of Endocrinology
Email
amajithia@ucsd.edu
Phone
(858) 822-0727
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
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
Lab Description

The main objective of the Chavez laboratory is the molecular characterization of malignant childhood cancers in order to identify drug targets and improve treatment options. Our focus is mainly on pediatric brain tumors such as medulloblastoma, glioblastoma, and ependymoma. Recently, we have demonstrated how to leverage epigenetic information such as DNA methylation and enhancer profiling in pediatric brain tumors and normal human tissues to identify clinically relevant tumor subgroups, oncogenic enhancers, transcription factors, and pathways amenable to pharmacologic targeting. To reveal regulatory circuitries disturbed in childhood brain tumors, we generate and integrate public high-dimensional data from primary tumors and patient-derived cell lines. We are specifically interested in the analysis of somatic and germline DNA mutations, chromatin and DNA modifications, transcription factor binding, and gene expression.

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 Adjunct Professor
Email
ferhatay@lji.org
Phone
(858) 752-6612
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
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.