Bioinformatics Applications in Human Disease

Lilia Iakoucheva

Faculty Status
Active
Title
Associate Professor
Email
lilyak@ucsd.edu
Phone
(858) 822-1878
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
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 risk mutations derived from exome and whole genome sequencing of the patients. We created mouse models carrying some of these mutations using CRISPR/Cas9, and also produced patient-derived cerebral organoids with autism risk mutations. We performed bulk RNA-seq from various brain regions or time periods in these models. Gene-level analyses of RNA-seq data has been completed (manuscripts in preparation). We are now pursuing isoform-level analyses of these data to better understand functional impact of autism risk mutations on splicing isoform transcriptome.

Joel Wertheim

Faculty Status
Active
Title
Assistant Professor
Email
jwertheim@ucsd.edu
Phone
(619) 543-5069
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Department
BISB Research Area(s)
Brief Research Description
Molecular epidemiology of HIV and other RNA viruses; Virus phylogenetics and evolution

Jill Mesirov

Faculty Status
Active
Title
Professor
Title 2
Associate Vice Chancellor, Computational Health Sciences
Title 3
Professor of Medicine
Email
jmesirov@ucsd.edu
Phone
(858) 534-5096
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Department
Brief Research Description
Algorithms and analytic methodologies for pattern recognition and discovery with applications to cancer genomics, to better diagnose, stratify, and treat patients. Development of biologist-friendly biomedical software tools.
Lab Description

Research in the Mesirov Lab focuses on cancer genomics applying machine-learning methods to functional data derived from patient tumors. The lab analyzes these molecular data to determine the underlying biological mechanisms of specific tumor subtypes, to stratify patients according to their relative risks of relapse, and to identify candidate compounds for new treatments. The overall goal is to treat patients as individuals specific to their tumors. Importantly, the lab is committed to the development of practical, accessible software tools to bring these methods to the general biomedical research community.

Hannah Carter

Faculty Status
Active
Title
Assistant Professor
Email
hkcarter@health.ucsd.edu
Phone
(858) 822-4706
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Brief Research Description
Genomics and systems biology for precision cancer medicine, variant interpretation, network analysis, immunogenomics

Christopher Woelk

Faculty Status
Inactive
Title
Assistant Professor; Dir., Genomics Core, CFAR
Email
cwoelk@ucsd.edu
Phone
(858) 552-8585 x7193
Track(s)
Biomedical Informatics
Department
Brief Research Description
Infectious diseases, biomarker identification, gene expression, microbial genomics, molecular evolution, innate immunity

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

Olivier Harismendy

Faculty Status
Active
Title
Assistant Professor
Email
oharismendy@ucsd.edu
Phone
858-246-0248
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Brief Research Description
My laboratory develops genome-wide assays and analysis for personalized cancer care. Particular focus includes genetics of cancer susceptibility and drug response, secure computing and data sharing.
Lab Description

The Oncogenomics laboratory is located in the Moores Cancer Center. Its research program is focused on the identification of genetic and epigenetic markers for cancer prevention and progression as well as drug response. The laboratory is a humid laboratory, combining both wet-lab techniques and bioinformatics analysis to study cancer samples from patients and animal models of cancer. The laboratory is also an important partner for multiple principal investigators at the Moores Cancer Center, collaborating on the design, analysis and interpretation of their genomic experiments.