Laboratory

• Haussler lab alumni
• Lab photos and events

Research Projects

UCSC Genome Browser
Funded by HHMI, NHGRI, NCI, and QB3

UCSC Cancer Genomics Browser
Funded by I-SPY, TCGA, QB3, NIH

ENCODE
Funded by NHGRI

Genome 10K
Funded by NHGRI, American Genetic Association, Moore Foundation, UCSC Foundation, STEPS Institute

NISC comparative genomes
Funded by NHGRI

Mammalian gene collection
Funded by NCI

Translational research—exploratory wet-lab validation of computational predictions
Funded by HHMI

Postdocs

Benedict Paten

(831) 459-5232
Ancestral genome reconstruction, sequence analysis, and molecular evolution; further development of the genome alignment tools Pecan and Ortheus

Jason Underwood

(831) 459-1014
Applying biochemical and cellular approaches to investigating the role of conserved non-coding regions of the vertebrate genome with emphasis on regions that may encode structured RNAs

Daniel Zerbino

(831) 459-5232
Genome assembly and comparative genomics, focusing on methods to identify and compare patterns of structural variation, either between species or between healthy and tumor cells, with the ultimate goal of associating genomic rearrangements with phenotype

Jing Zhu

(831) 459-5232
Comparative genomic analysis of the malaria and mammalian genomes

UCSC Research Collaborators

Jim Kent

Genome browser research and development

Mark Akeson

Nanopore technology for the analysis of single RNA and DNA molecules

Manny Ares

Alternative splicing

Josh Stuart

Gene networks

Christopher Benz

or benz@itsa.ucsf.edu
Cancer research

Joseph Costello

Cancer research

Laura J Esserman
Cancer research

Joe W Gray

Cancer research

Stephen J O'Brien

Genome 10K project

Nader Pourmand

Genome sequencing center

Oliver Ryder

Genome 10K project

Thorgeir Thorgeirsson

Medical genomics

Wet Lab Research Staff

Wet lab phone (831) 459-1014

Sofie Salama
Translational research—exploratory wet-lab validation of computational predictions

Robert Sellers

Laboratory Manager

Bryan King

Research Technician

Graduate Students

Robert Baertsch

Processed pseudogenes and mammalian synteny/orthology relationships (read about Robert's work on the SARS genome)

Tracy Ballinger 

Steven Benz

Mark Diekhans

Computational gene finding, UCSC Mammalian Gene Collection project (read about Mark's work on the Consensus Coding Sequence gene set in UCSC Currents) and the database of the Genome 10K Project

James Durbin

Data mining in integrated cancer genomics data sets

Ted Goldstein

(831) 459-1874
Tools for understanding evolution and disease in the context of rare alleles and structural variation of transposition and gene duplication within the genome

David Greenberg

Characterizing the biological function in mammalian brain development of genome regions that show accelerated changes in humans

Sol Katzman

Recent positive selection in the evolution of the human genome

Craig Lowe

Contributions of mobile elements to the human genome

Ngan Nguyen

Database of the Genome 10K Project

Courtney Onodera

Gene regulation, distal enhancers, human ultraconserved elements

Krishna Roskin

Mammalian comparative genomics focusing on conserved, non-coding regions (read about Krishna in the HHMI Bulletin)

Zack Sanborn

Using ancestral genomes to computationally identify gene losses that occurred during primate evolution

Bernard Suh

Genome evolution and chromosomal rearrangements

Chris Szeto

Development and use of the UCSC Cancer Genomics Browser

Affiliations

Center for Biomolecular Science & Engineering

Howard Hughes Medical Institute

UCSC Biomolecular Engineering Department

Bioinformatics & Computational Biology at UCSC

California Institute for Quantitative Biosciences (QB3)

Resources

UCSC Genome Browser

UCSC Bioinformatics Research Projects