Gill Bejerano

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)
• Tomorrow's Principal Investigator, Genome Technology Magazine (2008)
• Junior Faculty Grant, Edward Mallinckrodt, Jr. Foundation (2007-2010)
• Best paper by a young scientist award., RECOMB conference (2003)
• Levi Eshkol graduate studies fellowship., Hebrew University (1999-2002)
• Best paper by a young scientist award., RECOMB conference (1999)
• Rachel & Salim Banin scholarship., Hebrew University (1999)
• Rector Prize & Dean’s list for graduate studies achievements., Hebrew University (1997-1999)
• Intel award for achievements., Hebrew University (1996)
• Rector Prize & Dean’s list for undergraduate achievements., Hebrew University (1993-1996)

Professional Education

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

Postdoctoral Advisees

• Michael Hiller

Graduate & Fellowship Program Affiliations

• Developmental Biology

Web Site Links

• Bejerano Lab

Industry Relationships

Stanford is committed to ethical and transparent interactions with our industry partners. It is our policy to disclose payments of $5,000 or more, equity valued at $5,000 or more in a publicly traded company, or any equity in a privately held company, to physicians and scientists employed by Stanford University from companies or other commercial entities with which they interact as part of their professional activities. 

• Consulting: Numenta

Research Interests

The over-arching goal of the Bejerano lab is to bring Vertebrate Development and Genomics closer together.

Research in the lab sits at the intersection of highly cross-fertilizing fields: evolutionary developmental biology (evo-devo), comparative and functional genomics of extant species, and paleo-genomics (the reconstruction and study of ancestral genomes). Our focus is the functional landscape of vertebrate genomes, and in particular that of the Human Genome.

Recent research has highlighted many thousands of genomic regions that have never been studied before. These regions appear to enact the exquisite gene transcriptional control required during vertebrate development.
The Bejerano Lab focuses on mapping the individual and synergistic functions of these regions; tracing their evolutionary histories, thought to be the major contributor to morphological diversity among metazoans; and understanding the roles these novel regions play in contributing to human disease.

Our computational approaches rely heavily on machine learning, probabilistic and statistical reasoning, and aim to glean novel biological insights. Accordingly, projects range from the pursuit of novel biological knowledge through to the design and implementation of the tools that facilitate these studies.

Publications

• Dispensability of mammalian DNA. McLean C,  Bejerano G.  Genome Res.  2008; 18 (11): 1743-51
• Human genome ultraconserved elements are ultraselected. Katzman S,  Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D.  Science.  2007; 317 (5840): 915
• Thousands of human mobile element fragments undergo strong purifying selection near developmental genes C.B. Lowe,  G. Bejerano, D. Haussler.  Proc. Nat’l Acad. Sci. USA.  2007; 104 (19): 8005-8010
• Comparative genomic analysis using the UCSC genome browser. Karolchik D,  Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ.  Methods Mol Biol.  2007; 395 17-34
• The UCSC genome browser database: update 2007 UCSC Genomics Group,  Nucleic Acids Research.  2007; 35 D668-73
• Forces Shaping the Fastest Evolving Regions in the Human Genome K.S. Pollard, S.R. Salama, B. King, A.D. Kern, T. Dreszer, S. Katzman,  A.Siepel, J.S. Pedersen, G. Bejerano, R. Baertsch, K.R. Rosenbloom, J. Kent and D. Haussler.  PLoS Genetics.  2006; 2 (10): e168
• Branch and bound computation of exact P-values G. Bejerano,  Bioinformatics.  2006; 22 (17): 2158-2159
• A Distal Enhancer and an Ultraconserved Exon are Derived From a Novel Retroposon G. Bejerano,  C.B. Lowe, N. Ahituv, B. King, A. Siepel, S.R. Salama, E.M. Rubin, W.J. Kent, D. Haussler.  Nature.  2006; 441 (7089): 87-90
• The UCSC Genome Browser Database: Update 2006 UCSC Genomics Group,  Nucleic Acids Res..  2006; 34 D590-D598
• Identification and classification of conserved RNA secondary structures in the human genome. Pedersen JS,  Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D.  PLoS Comput Biol.  2006; 2 (4): e33
• Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing E.A. Glazov, M. Pheasant, E.A. McGraw, G. Bejerano, J.S. Mattick,  Genome Research.  2005; 15 (6): 800-808
• Computational screening of conserved genomic DNA in search of functional non-coding elements G. Bejerano, A.C. Siepel, W.J. Kent, D. Haussler,  Nature Methods.  2005; 2 (7): 535-545
• Evolutionarily Conserved Elements in Vertebrate, Fly, Worm, and Yeast Genomes A. Siepel, G. Bejerano, J.S. Pedersen, A. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth,  L.W. Hillier, S. Richards, G.M. Weinstock, R.K. Wilson, R.A. Gibbs, W.J. Kent, W. Miller, D. Hausler.  Genome Research.  2005; 15 (8): 1034-1050
• Into the heart of darkness: large-scale clustering of human non-coding DNA G. Bejerano, D. Haussler, M. Blanchette,  Bioinformatics.  2004; 20 I40-I48
• Sequencing and comparative analysis of the chicken genome International Chicken Genome Sequencing Consortium,  Nature.  2004; 432 (7018): 695-716
• Ultraconserved elements in the human genome G. Bejerano, M. Pheasant, I.V. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, D. Haussler,  Science.  2004; 305 (5675): 1321-1325
• Extremely conserved non-coding sequences in the vertebrate genomes I.V. Makunin, S. Stephen, M. Pheasant, G. Bejerano, W.J. Kent, D. Haussler, J.S. Mattick,  Proceedings of 4th International Conference on Bioinformatics of Genome Regulation and Structure.  2004; BGRS
• Efficient exact p-value computation for small sample, sparse and surprising categorical data G. Bejerano, N. Friedman, N. Tishby,  J. Computational Biology.  2004; 11 (5675): 867-886
• Algorithms for variable length Markov chain modeling G. Bejerano,  Bioinformatics.  2004; 20 (5): 788-789
• Efficient exact p-value computation and applications to biosequence analysis G. Bejerano,  Proceedings of the 7th annual international conference on research in computational molecular biology.  2003; RECOMB
• Discriminative feature selection via multiclass variable memory Markov models N. Slonim, G. Bejerano, S. Fine, N. Tishby,  EURASIP J. Applied Signal Processing.  2003; 2 93-102
• A system for computer music generation by learning and improvisation in a particular style O. Lartillot, S. Dubnov, G. Assayag, G. Bejerano,  IEEE Computer J..  2003; 36 (10): 73-80
• Discriminative feature selection via multiclass variable memory Markov models N. Slonim, G. Bejerano, S. Fine, N. Tishby,  Proceedings of 19th International Conference on Machine Learning.  2002; ICML
• Automated modeling of musical style O. Lartillot, S. Dubnov, G. Assayag, G. Bejerano,  Proceedings of the International Computer Music Conference.  2001; ICMC
• A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites, 1st Workshop on Algorithms in Bioinformatics Y. Barash, G. Bejerano, N. Friedman,  Lecture Notes in Computer Science.  2001; WABI (2149): 278-293
• Unsupervised sequence segmentation by a mixture of switching variable memory Markov sources Y. Seldin, G. Bejerano, N. Tishby,  Proceedings of 18th International Conference on Machine Learning.  2001; IMCL
• A variable memory Markovian modeling approach to unsupervised sequence segmentation Y. Seldin, G. Bejerano, N. Tishby,  Proceedings of 33rd Symposium on the Interface of Computing Science and Statistics.  2001; INTERFACE
• Markovian domain fingerprinting: Statistical segmentation of protein sequences G. Bejerano,,  Y. Seldin, H. Margalit, N. Tishby.  Bioinformatics.  2001; 17 (10): 927-934
• Novel small RNA-encoding genes in Escherichia coli L. Argaman, R. Hershberg, J. Vogel, G. Bejerano, G. Wagner, H. Margalit, S. Altuvia,  Current Biology.  2001; 11 (12): 941-950
• Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bejerano G,  Yona G.  Bioinformatics.  2001; 17 (1): 23-43
• PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites R. Hershberg, G. Bejerano, A. Santos-Zavaleta, H. Margalit,  Nucleic Acids Research.  2001; 29 (1): 277
• Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Argaman L,  Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S.  Curr Biol.  2001; 11 (12): 941-50
• Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space A. Apostolico, G. Bejerano,  J. Computational Biology.  2000; 7 (3-4): 381-393
• Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space A. Apostolico, G. Bejerano,  Proceedings of the 4th annual international conference on research in computational molecular biology.  2000; RECOMB
• Modeling protein families using probabilistic suffix trees, Proceedings of the 3rd annual international conference on research in computational molecular biology G. Bejerano,  G. Yona.  RECOMB.  1999;