Bioinformatics Applications in Human Disease

Niema Moshiri

Faculty Status
Active
Title
Assistant Teaching Professor
Email
a1moshir@ucsd.edu
Phone
(619) 993-1642
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Brief Research Description
Computational HIV epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development
Lab Description

We are interested in developing scalable methods for performing epidemiological analyses of large viral (primarily HIV) sequence and phylogenetic datasets. Topics of interest include large-scale phylogenetic analyses, developing novel models of sequence and tree evolution, performing epidemiological simulation experiments, and developing methods for predicting epidemic outcomes.

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
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.

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

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

Yingxiao (Peter) Wang

Faculty Status
Active
Title
Professor
Email
yiw015@eng.ucsd.edu
Phone
(858) 822-4502
Track(s)
Bioinformatics and Systems Biology
Biomedical Informatics
Department
Brief Research Description
Live cell imaging, genetic and epigenetic regulations, immunoengineering, therapeutics
Lab Description

Our research focuses on molecular engineering for cellular imaging and reprogramming, and image-based bioinformatics, with applications in stem cell differentiation and cancer treatment.