Nadav Ahituv, PhD

Associate Professor of Bioengineering and Therapeutic Sciences
Graduate Program Membership:  BMIBMSDSCB, PSPG

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Nadav Ahituv, PhD
Dr. Ahituv’s research focuses on understanding the role of regulatory sequences in human biology and disease. Through a combination of comparative genomic strategies, regulatory element analysis, human patient samples, and mouse and fish genetic engineering technologies, he is working to elucidate mechanisms whereby genetic variation within these sequences lead to changes in human phenotypes. The research focuses on three clinically relevant phenotypic categories: monogenic disease, using limb malformations as a model; complex disease, analyzing how nucleotide changes in regulatory sequences contribute to obesity; and pharmacogenomics, characterizing how genetic differences in regulatory sequences lead to clinical variation in response to drugs.

Sourav Bandyopadhyay, PhD

Assistant Professor of Bioengineering and Therapeutic Sciences
Graduate Program Membership:  BMIBMSDSCB, PSPG

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Sourav Bandyopadhyay, PhD
The Bandyopadhyay lab uses systems biology approaches to understand how cellular pathways are organized and reshaped in diseases. We are developing new high throughput protein-protein and genetic interaction mapping platforms and computational approaches for integrating experimental data with larger pictures of pathways and networks. The major focus of the lab is on developing networks maps to dissect components of oncogene addiction and to identify new precision therapies in cancer.

Sergio E. Baranzini, PhD

Professor in Residence of Neurology
Graduate Program Membership: BMI

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Sergio E. Baranzini, PhD
Dr. Baranzini’s research focuses on mechanisms underlying susceptibility to common diseases, prediction of therapeutic response, and innovative approaches to drug discovery. Through a combination of wet lab (genetic and immunological approaches) and computational methods, the Baranzini lab investigates combinations of DNA variants that confer susceptibility to diseases in the context of the biological pathways, gene networks, and regulatory influences. In particular, efforts to integrate multiple data domains to understand susceptibility and phenotype heterogeneity (including response to therapeutic drugs) in multiple sclerosis (MS) are underway. In addition, research about the influence of the microbiome in MS susceptibility and expressivity is ongoing.

Steven Brenner, PhD

Adjunct Professor of Bioengineering and Therapeutic Sciences
Department of Molecular & Cell Biology, UC Berkeley
Graduate Program Membership: BMI

Website | UC Berkeley Plant & Microbial Biology

Steven Brenner, PhD
Dr. Brenner is a computational biologist with a variety of interests spanning from cell biology to human genetics. Areas of current interest include gene regulation by alternative splicing and nonsense-mediated mRNA decay; prediction of protein function using Bayesian phylogenetics; medical and environmental metagenomis; structural genomics and protein complexes; and application of next generation sequencing in the clinical genetic setting.

Atul Butte, MD, PhD

Director of Institute for Computational Health Sciences
Professor of Pediatrics
Executive Director for Clinical Informatics, University of California Health Sciences and Services
Graduate Program Membership:  BMI, iPQBPSPG

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Atul Butte, MD, PhD
Dr. Butte builds and applies tools that convert more than 400 trillion points of molecular, clinical, and epidemiological data — measured by researchers and clinicians over the past decade and now colloquially known as “big data” — into diagnostics, therapeutics, and new insights into disease. His lab has developed tools to analyze genomic data sets, and has used these tools to develop new uses for existing drugs, and new diagnostics. Dr. Butte was part of the team treating the first patient presenting with a whole genome. A major new focus is the analysis of clinical data from electronic health records.

Farid Chehab, PhD

Professor of Laboratory Medicine, Division of Molecular Diagnostics
Medical Genetics and Molecular Pathology Training programs

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Farid Chehab, PhD
Dr. Chehab’s research efforts are centered on elucidating the mechanisms causing ichthyosis and lipoatrophy in a knockout mouse model for a novel gene that is highly conserved in mammals. These investigations will uncover the function of the encoded protein in epidermal lipid metabolism and its interplay with dermal adipocytes, using primarily inducible mouse knockout models in the epidermis and adipocytes. Dr. Chehab is also working on the role of FoxO4 in the late steps of cholesterol biosynthesis. Furthermore, he is using NGS and microarrays to uncover genes and variants associated with obesity in neonatal syndromes without a firm clinical diagnosis.

Aaron Diaz, PhD

Assistant Professor of Neurological Surgery
Graduate Program Membership:  BMS

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Aaron Diaz, PhD
Dr. Diaz studies the role of neurodevelopmental programs in malignant gliomas, using computational and systems approaches. By contrasting genetic and epigenetic signatures between the developing human cortex and human brain tumors, Dr. Diaz is elucidating developmental pathways that are aberrantly activated during oncogenesis, promoting tumor growth and self-renewal. The Diaz lab is currently using high-throughput, single-cell assays, coupled with modern techniques from machine learning and data science, to identify therapeutic targets within these critical pathways.

Su Guo, PhD

Professor of Bioengineering and Therapeutic Sciences
Graduate Membership: DSCB, Neuroscience, PSPG, Tetrad

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Su Guo, PhD
Dr. Guo has a broad background in molecular biology, genetics, developmental biology, neurobiology, and is interested in the molecular genetic mechanisms that regulate brain development and function. Dr. Guo’s laboratory employs zebrafish and mammalian cell models to study the molecular genetics of neural development and behavior, with the ultimate goal of broadening our basic understanding of the brain and the mind, as well as to help treat neuropsychiatric disorders.

Katherine Pollard, PhD

Senior Investigator, Gladstone Institutes
Professor of Epidemiology & Biostatistics
Graduate Program Membership:  BMI, ETS

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Katherine Pollard, PhD
Dr. Pollard develops statistical and computational methods for the analysis of genomic datasets. Her research focuses on genome evolution, in particular identifying DNA sequences that differ significantly between or within species, and the sequences’ relationship to biomedical traits. Many of these sequences are non-coding, such as enhancers and RNA genes. The group aims to pinpoint specific DNA alterations in these sequences that are responsible for changes in gene expression. Current projects focus on two major areas: identifying the genetic basis for human-specific traits, such as our susceptibility to AIDS and atherosclerosis; and characterizing the human microbiome through metagenomic data.

Mark Segal, PhD

Professor of Epidemiology and Biostatistics
Director, Center for Bioinformatics and Molecular Biostatistics
Graduate Program Membership: BMI, PSPG, ETS

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Mark Segal, PhD
Dr. Segal focuses on the development and application of statistical methods to address problems in computational biology and genomics. He has devised methods for addressing several aspects of analyzing data deriving from high-throughput biotechnologies, straddling low-level (e.g., pre-processing) to high-level (e.g., linked survival phenotypes, regulatory module elicitation) approaches. He is currently engaged in developing and comparing methods for inferring 3D genome architecture utilizing data from chromatin conformation capture assays.

Licia Selleri, MD, PhD

Professor of Craniofacial Biology
Graduate Program Membership:  BMS, OCS DSCB

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Licia Selleri, MD, PhD
Dr. Selleri studies the genetic basis of how elaborately patterned tissues form during development. Her laboratory combines different genetic approaches, using the mouse as a model, to understand basic developmental processes related to cranial and appendicular morphogenesis. The laboratory discovered that homeodomain-containing transcription factors of the Pbx family, also known as Hox-cofactors, are critical developmental regulators through the transcriptional control of target genes within tissue-specific regulatory networks.Using genetically-engineered and ethylnitrosourea (ENU)-mutagenized mouse models the ultimate goal of the laboratory is to identify novel genes and regulatory networks underlying morphogenesis of embryonic structures, morphological variation, evolution, and human congenital disease.

Yin Shen, PhD

Assistant Professor of Neurology
Graduate Program Membership:  BMS

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Yin Shen, PhD
Dr. Shen studies the fundamental mechanisms of transcriptional control underlying cellular function. Her research utilizes human pluripotent stem cells to model development and complex diseases as well as innovative genomic and genetic tools to investigate how regulatory elements affect gene expression. Her lab focuses on elucidating the causal relationship between genetic and epigenetic variations at regulatory sequences, e.g. enhancers and neurodevelopment and neurological diseases, and how these factors interplay to control gene regulation in mammalian cells.

Marina Sirota, PhD

Associate Professor, Institute for Computational Health Sciences

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Marina Sirota, PhD
Dr. Sirota is interested in developing computational methods in integrative biology and applying these approaches in the context of disease diagnostic and therapeutics. She has extensive background in bioinformatics and data integration in the context of drug repositioning, drug target identification, clinical and molecular data analysis. Dr. Sirota has a long standing interest in studying genetic architecture in complex disease as well as novel applications of next-generation sequencing techniques with a special focus on autoimmune disease.

Chun Jimmie Ye, PhD

Assistant Professor
Department of Epidemiology and Biostatistics
Department of Bioengineering and Therapeutic Sciences
Graduate Program Membership:  BMIBMS

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Chun Jimmie Ye, PhD
The Ye lab is interested in how genetics and environment interact to affect molecular phenotypes. The general strategy is to couple high-throughput sequencing with population genetics to measure and model cellular response to environmental challenges across large patient cohorts. The lab develops experimental approaches that enable the collection of functional genomic data en masse and computational methods that translate the data into biological insights. The initial focus is to study human immune cells in healthy and diseased patients to understand host pathogen interactions and its role in autoimmunity.