Cancer Institute A national cancer institute
designated cancer center
Email this profile
Portrait View Larger

Gill Bejerano

Academic Appointments

  • Associate Professor of Developmental Biology, of Computer Science and of Pediatrics (Genetics)

Key Documents

Contact Information

  • Academic Offices
    Alternate Contact
    Kathy Fisher Admininstrative Associate Tel Work 650-725-6792


The Bejerano Lab studies genome function in human and related species. We are deeply interested in the following broad questions: Mapping genome sequence (variation) to phenotype (differences) and extracting specific genetic insights from deep sequencing measurements. We take a particular interest in gene cis regulation. We use our joint affiliation to apply a combination of computational and experimental approaches. We collect large scale experimental data; write computational analysis tools; run them massively to discover the most exciting testable hypotheses; which we proceed to experimentally validate. We work in small teams, in house or with close collaborators of experimentalists and computational tool users who interact directly with our computational tool builders. Please see our research tab for more.

Academic Appointments

Administrative Appointments

  • Technical Advisory Board, Numenta (2008 - present)
  • Member, Editorial Board, Gene (2007 - 2008)

Honors and Awards

  • New Faculty Fellow, Microsoft Research (2009)
  • Fellow, David & Lucile Packard Foundation (2008-2013)
  • Research Grant Award, Okawa Foundation (2008)
  • Searle Scholar, Searle Scholars Program (2008-2011)
  • Young Investigator Award, Human Frontier Science Program (2008-2011)
  • Alfred P. Sloan Fellow, Alfred P. Sloan Foundation (2008-2010)
View All 15honors and awards of Gill Bejerano

Professional Education

Ph.D.: Hebrew University, Computer Science (2004)
B.Sc.: Hebrew University, Physics, Mathematics, Computer Science (summa cum laude) (1997)

Research & Scholarship

Current Research and Scholarly Interests

The Bejerano Lab is currently focused on the following topics:

1. Genotype - Phenotype relationships in humans.
We are developing novel methods for linking human whole genome variation with human disease and trait variation. We apply these methods to multiple datasets in the contexts of prematurity, autism, heart disease and more [20, 29, 32, 34, 36, 38, 39, 43].

2. Genotype - Phenotype relationships between mammals.
We develop novel methods to link trait evolution in the mammalian tree to whole genome evolution in over a hundred species. Application of these methods allow us to shed new light on human genome function, on human disease and on human evolution [29, 34, 35]. See our "Forward Genomics" web server.

3. Extracting genetic knowledge from high throughput genomic assays.
High throughput genomic assays are most often used to make biochemical discoveries. We develop methods to extract genetic and developmental knowledge from these assays [27, 28, 31]. Through joint work with Sue McConnell we take special interest in the developing neocortex [29, 41]. Also see our popular GREAT web server for the cis-regulatory interpretation of high throughput genomic datasets.

4. Vertebrate transcription regulation.
Much of our work relies on our strong foundations in the study of vertebrate gene regulation [9-11, 14, 15, 18, 22, 25, 27, 29-33, 35, 38-42]. See our PRISM resource of predicted transcription factor functions and COMPLEX resource for predicted transcription factor dimers and complexes. Also see our zCNE resource of conserved non-coding (likely gene regulatory) sequences in the zebrafish genome.

5. Vertebrate genome evolution.
We are extremely well versed in human and vertebrate genome evolution [9-11, 14, 17, 18, 22, 23, 25, 26, 29, 33-35, 37, 39, 40]. Notably, we discovered ultraconservation and correctly postulated that many of these elements are developmental enhancers. We also showed that mammalian ultraconserved elements evolve under extreme purifying selection, and that they are almost never lost during mammalian evolution [9, 23, 25]. We also discovered the first developmental enhancers conserved between human and protostomes [33], attempted to group human conserved non-coding DNA into paralog families [10], and studied the co-option of mobile elements into cis-regulatory roles [18, 22, 26, 41].

6. Evolutionary Developmental Biology ("evo devo").
We have done work in the field of evolutionary developmental biology [29, 33-35, 43], including a first survey of developmental enhancers (including a penile spine/vibrissae enhancer) uniquely lost in humans [29], fueled by our deep interest in phenotype - genotype relationships.

[For links to the references and more, pleae see our lab's website]




Prior Year Coursescourses of Gill Bejerano

Postdoctoral Advisees

Whitney HeavnerAmir Marcovitz

Graduate and Fellowship Program Affiliations



Publication tag cloud

Publication Topics

View All 63

Stanford Medicine Resources:

Footer Links: