Katherine S. Pollard, PhD

Associate Investigator

Phone: (415) 734-2711
Fax: (415) 355-0960
Fewer scientific details, please
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Founder and Faculty Supervisor, Gladstone Bioinformatics Core

Associate Professor, Department of Epidemiology & Biostatistics, Institute for Human Genetics at University of California, San Francisco

Administrative Assistant

Audrey Le
(415) 734-2768
audrey.le@gladstone.ucsf.edu

More about Dr. Pollard

Dr. Pollard’s lab develops statistical and computational methods for the analysis of massive 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 regulatory signals, structural sites and RNA genes.

Dr. Pollard’s 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.

Previously, Dr. Pollard was an assistant professor in the University of California, Davis Genome Center and Department of Statistics. She was awarded the Thomas J. Watson Fellowship in 1995 and the Sloan Research Fellowship in 2008.

Dr. Pollard earned her master’s degree and PhD in biostatistics from the University of California, Berkeley. At Berkeley, she developed computationally intensive statistical methods for the analysis of microarray data with applications in cancer biology. She implemented these approaches in Bioconductor, an open source software program used with high-throughput genomic data. As a comparative genomics postdoctoral fellow at the University of California, Santa Cruz, Dr. Pollard participated in the Chimpanzee Genome Project and used this sequence to identify the fastest evolving regions in the human genome, known as Human Accelerated Regions.

 

More scientific details, please

Other Professional Titles

Founder and Faculty Supervisor, Gladstone Bioinformatics Core

Associate Professor, Department of Epidemiology & Biostatistics, Institute for Human Genetics at University of California, San Francisco

Administrative Assistant

Audrey Le
(415) 734-2768
audrey.le@gladstone.ucsf.edu

Areas of Investigation

Our laboratory develops statistical and computational methods for the analysis of massive genomic datasets. We are interested in genome evolution, in particular identifying genome sequences that differ significantly between or within species and their relationship to biomedical traits of interest. We pioneered the statistical phylogenetic approach for identifying Human Accelerated Regions (HARs), the fastest evolving sequences in the human genome. Most HARs are non-coding elements, such as regulatory signals, structural sites, and RNA genes. One of our aims is to identify specific DNA alterations in HARs that are responsible for variation in gene expression.

We are also developing methods for characterizing microbial communities from metagenomic data, the pool of DNA from different microorganisms in a sample. We designed PhylOTU, the first computational tool for estimating the taxonomic composition of metagenomic samples from short, next-generation sequencing reads. Our current emphasis is to extend this approach to measure the functional composition of microbial communities. The goal of this project is to relate DNA based measurements of microbial communities from the human gut and other body sites to patient health status through niche modeling.

Current Lab Focus

  • Can we identify more HARs using archaic hominin genomes (e.g., Neanderthal) and many human genomes?
  • When do mutations in HARs and other regulatory sequences have a functional impact?
  • Is the functional profile of a metagenomic community more informative about host health status than the taxonomic profile?

Joined Gladstone

2008

Why Gladstone?

We are excited about bringing computational biology to Gladstone and incorporating world-class experimental biology into our research program.

Key Achievements

  • Discovered HARs by comparing the human genome to the genomes of chimpanzee and other mammals.
  • Characterized the role of biased gene conversion, a non-adaptive recombination associated process, in shaping the fastest evolving regions of the human genome.
  • Solved the problem of clustering short metegnomic sequencing reads into taxonomic groups by leveraging sequenced genomes and phylogenetic triangulation.

Education

Pomona College (BA, Summa Cum Laude), Anthropology and Mathematics (1995)
University of California, Berkeley (MA, PhD), Biostatistics (2000, 2003)

Affiliations

American Society of Human Genetics
American Statistical Association
International Society for Computational Biology

Awards

  • Sophomore Math Prize, Pomona College (1993)
  • Valedictorian, High Scholarship Prize (4.0 GPA), Math Prize, Anthropology Prize, Phi Beta Kappa Award, Pomona College (1995)
  • Thomas J. Watson Fellowship, Watson Foundation (1996)
  • Berkeley Fellowship, University of California, Berkeley (1998)
  • Evelyn Fix Memorial Prize, Chin Long Chiang Biostatistics Student of the Year, University of California, Berkeley (2003)
  • Faculty Development Award, University of California, Davis (2007)
  • Sloan Research Fellowship, Alfred P. Sloan Foundation (2008)
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Featured Publications

Katie Pollard, PhDLindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 27; 478(7370):476-82. View in: PubMed
Katie Pollard, PhDCapra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol. 2011; 3:516-27. View in: PubMed