Comparative and Population Genomics

Vikas Bansal

Faculty Status
Active
Title
Assistant Professor
Email
vibansal@ucsd.edu
Phone
(858) 246-1810
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Computational tools for variant calling, haplotyping and analysis of rare variants in disease association studies
Lab Description

Research in our lab is focused on developing computational methods for the discovery and analysis of human genetic variation using high-throughput sequencing technologies. We develop algorithms and software tools for accurate and comprehensive assembly of human genomes and identifying disease associated variants.

Konrad Scheffler

Faculty Status
Inactive
Title
Associate Professor
Phone
(619) 543-6347
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Probabilistic models of molecular evolution
Lab Description

The Viral Evolution Group (located near the UCSD hospital in Hillcrest) studies computational and statistical models of evolution, with applications to viral pathogens and other systems. Solid programming skills and knowledge of probabilistic modeling (e.g. as covered in CSE250A and CSE250B) are required. There is no wet lab component.

Jonathan Sebat

Faculty Status
Active
Title
Chief, Beyster Center for Molecular Genomics of Neuropsychiatric Diseases; Associate Professor of Psychiatry and Cellular & Molecular Medicine
Email
jsebat@ucsd.edu
Phone
(858)534-6526
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Genome informatics, psychiatric genetics, copy number variation (CNV), de novo mutation
Lab Description

Our laboratory is interested in how rare and de novo mutations in the human genome contribute to patterns of genetic variation and risk for disease in humans. To this end, we are developing novel approaches to gene discovery that are based on advanced technologies for the detection of rare variants, including studies of copy number variation (CNV) and deep whole genome sequencing (WGS). Our goal is to identify genes related to psychiatric disorders and determine how genetic variants impact the function of genes and corresponding cellular pathways.

Nicholas Schork

Faculty Status
Active
Title
Professor
Email
nschork@scripps.edu
Phone
(858) 554-5704
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
BMI Research Area(s)
Brief Research Description
Developing mathematical, statistical, and computational models and tools to study the genetic basis of complex traits and diseases

Gene Yeo

Faculty Status
Active
Title
Professor
Title 2
Graduate Program Associate Director
Email
geneyeo@ucsd.edu
Phone
(858) 534-9321
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
We develop computational, molecular, biochemical and cellular approaches to understanding and treating human diseases such as neurodegeneration and autism.
Lab Description

We have a wide scope of projects ranging from developing novel algorithms for studying RNA processing in diseases, development and personalized medicine, and for analyzing single-cell RNA-seq data.

Doug Richman

Faculty Status
Inactive
Title
Professor (Active Emeritus)
Email
drichman@ucsd.edu
Phone
(858) 552-8585
Track(s)
Bioinformatics and Systems Biology
Department
BISB Research Area(s)
Brief Research Description
HIV disease and pathogenesis
Lab Description

The Richman Laboratory is a translational HIV research laboratory that uses basic science techniques to answer clinically relevant questions. These laboratory techniques include a wide range and combination of wet lab and computational methods. Prospective students will have exposure to aspects of both wet laboratory and computational investigation. They will also have exposure to clinical aspects of HIV disease to place their research into clinical perspective. Currently available projects include:

Sergei L. Kosakovsky Pond

Faculty Status
Inactive
Title
Assistant Adjunct Professor
Email
spond@ucsd.edu
Phone
(619) 543-8898
Track(s)
Biomedical Informatics
Department
BISB Research Area(s)
Brief Research Description
Computational biology, molecular evolution, phylogenetics and statistical genetics with an emphasis on HIV evolution

Pavel Pevzner

Faculty Status
Active
Title
Professor and Ronald R Taylor Chair
Email
ppevzner@ucsd.edu
Phone
(858) 822-4365
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Computational Molecular Biology

Joseph Gleeson

Faculty Status
Active
Title
Professor
Title 2
Director of Neurogenetics
Email
jogleeson@ucsd.edu
Phone
(858) 822-3535
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Autism, Whole genome sequencing, Epigenome, Single cell sequencing, Gene-environment interactions, Somatic mosaicism, Systems biology, Protein interactions
Lab Description

Our lab is interested in how the human brain is assembled. We use genetic strategies to explore causes of human disease and then link these genes to function using model systems. We are focused on diseases like mental retardation, epilepsy and autism, where brain development is disrupted. We have two full time bioinformatics (graduate student and staff programmer) developing computational solutions, database design and machine learning paradigms for large datasets in the area of genome sequencing.