Gil Bejerano, Professor - Publications

Affiliations: 
CS Stanford University, Palo Alto, CA 
Area:
Computational Biology

53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Wenger AM, Guturu H, Bernstein JA, Bejerano G. Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 27441994 DOI: 10.1038/gim.2016.88  0.4
2016 Guturu H, Chinchali S, Clarke SL, Bejerano G. Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. Plos Computational Biology. 12: e1004711. PMID 26845687 DOI: 10.1371/journal.pcbi.1004711  0.72
2015 Tuteja G, Chung T, Bejerano G. Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. Placenta. PMID 26604129 DOI: 10.1016/j.placenta.2015.11.001  0.72
2015 Braun BA, Marcovitz A, Camp JG, Jia R, Bejerano G. Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales. Proceedings of the National Academy of Sciences of the United States of America. 112: 8036-40. PMID 26080416 DOI: 10.1073/pnas.1501844112  0.72
2015 Sazonova O, Zhao Y, Nürnberg S, Miller C, Pjanic M, Castano VG, Kim JB, Salfati EL, Kundaje AB, Bejerano G, Assimes T, Yang X, Quertermous T. Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. Plos Genetics. 11: e1005202. PMID 26020271 DOI: 10.1371/journal.pgen.1005202  0.72
2015 Notwell JH, Chung T, Heavner W, Bejerano G. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nature Communications. 6: 6644. PMID 25806706 DOI: 10.1038/ncomms7644  0.72
2014 Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Research. 24: 1504-16. PMID 24963153 DOI: 10.1101/gr.165845.113  0.72
2014 Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G. Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. Plos Computational Biology. 10: e1003449. PMID 24499934 DOI: 10.1371/journal.pcbi.1003449  0.72
2013 Reno PL, McLean CY, Hines JE, Capellini TD, Bejerano G, Kingsley DM. A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. Plos One. 8: e84258. PMID 24367647 DOI: 10.1371/journal.pone.0084258  0.72
2013 Guturu H, Doxey AC, Wenger AM, Bejerano G. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20130029. PMID 24218641 DOI: 10.1098/rstb.2013.0029  0.72
2013 Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G. The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. Plos Genetics. 9: e1003728. PMID 24009522 DOI: 10.1371/journal.pgen.1003728  0.72
2013 Hiller M, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Research. 41: e151. PMID 23814184 DOI: 10.1093/nar/gkt557  0.72
2013 Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nature Reviews. Genetics. 14: 288-95. PMID 23503198 DOI: 10.1038/nrg3458  0.72
2013 Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G. PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Research. 23: 889-904. PMID 23382538 DOI: 10.1101/gr.139071.112  0.72
2013 Losos JB, Arnold SJ, Bejerano G, Brodie ED, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL. Evolutionary biology for the 21st century. Plos Biology. 11: e1001466. PMID 23319892 DOI: 10.1371/journal.pbio.1001466  0.72
2012 Tuteja G, Cheng E, Papadakis H, Bejerano G. PESNPdb: a comprehensive database of SNPs studied in association with pre-eclampsia. Placenta. 33: 1055-7. PMID 23084601 DOI: 10.1016/j.placenta.2012.09.016  0.72
2012 Hiller M, Schaar BT, Bejerano G. Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Research. 40: 11463-76. PMID 23042682 DOI: 10.1093/nar/gks905  0.72
2012 Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G. A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species. Cell Reports. 2: 817-23. PMID 23022484 DOI: 10.1016/j.celrep.2012.08.032  0.72
2012 Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes. Plos Genetics. 8: e1002852. PMID 22876195 DOI: 10.1371/journal.pgen.1002852  0.72
2012 Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A. A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Human Mutation. 33: 1063-6. PMID 22495965 DOI: 10.1002/humu.22097  0.72
2012 Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, et al. Coding exons function as tissue-specific enhancers of nearby genes. Genome Research. 22: 1059-68. PMID 22442009 DOI: 10.1101/gr.133546.111  0.72
2011 Capellini TD, Handschuh K, Quintana L, Ferretti E, Di Giacomo G, Fantini S, Vaccari G, Clarke SL, Wenger AM, Bejerano G, Sharpe J, Zappavigna V, Selleri L. Control of pelvic girdle development by genes of the Pbx family and Emx2. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 240: 1173-89. PMID 21455939 DOI: 10.1002/dvdy.22617  0.72
2011 McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 471: 216-9. PMID 21390129 DOI: 10.1038/nature09774  0.72
2011 Fan X, Ren P, Dhal S, Bejerano G, Goodman SB, Druzin ML, Gambhir SS, Nayak NR. Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging. Plos One. 6: e16348. PMID 21283713 DOI: 10.1371/journal.pone.0016348  0.72
2010 McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology. 28: 495-501. PMID 20436461 DOI: 10.1038/nbt.1630  0.72
2010 Lowe CB, Bejerano G, Salama SR, Haussler D. Endangered species hold clues to human evolution. The Journal of Heredity. 101: 437-47. PMID 20332163 DOI: 10.1093/jhered/esq016  0.72
2008 McLean C, Bejerano G. Dispensability of mammalian DNA. Genome Research. 18: 1743-51. PMID 18832441 DOI: 10.1101/gr.080184.108  0.72
2007 Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC genome browser. Methods in Molecular Biology (Clifton, N.J.). 395: 17-34. PMID 17993665 DOI: 10.1385/1-59745-514-8:17  0.72
2007 Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science (New York, N.Y.). 317: 915. PMID 17702936 DOI: 10.1126/science.1142430  0.72
2007 Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proceedings of the National Academy of Sciences of the United States of America. 104: 8005-10. PMID 17463089 DOI: 10.1073/pnas.0611223104  0.72
2007 Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, ... ... Bejerano G, et al. The UCSC genome browser database: update 2007. Nucleic Acids Research. 35: D668-73. PMID 17142222 DOI: 10.1093/nar/gkl928  0.72
2006 Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. Plos Genetics. 2: e168. PMID 17040131 DOI: 10.1371/journal.pgen.0020168  0.72
2006 Bejerano G. Branch and bound computation of exact p-values. Bioinformatics (Oxford, England). 22: 2158-9. PMID 16895926 DOI: 10.1093/bioinformatics/btl357  0.72
2006 Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. Plos Computational Biology. 2: e33. PMID 16628248 DOI: 10.1371/journal.pcbi.0020033  0.72
2006 Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441: 87-90. PMID 16625209 DOI: 10.1038/nature04696  0.72
2006 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34: D590-8. PMID 16381938 DOI: 10.1093/nar/gkj144  0.72
2005 Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods. 2: 535-45. PMID 16170870 DOI: 10.1038/nmeth0705-535  0.72
2005 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research. 15: 1034-50. PMID 16024819 DOI: 10.1101/gr.3715005  0.72
2005 Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Research. 15: 800-8. PMID 15899965 DOI: 10.1101/gr.3545105  0.72
2004 Bejerano G, Friedman N, Tishby N. Efficient exact p-value computation for small sample, sparse, and surprising categorical data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 867-86. PMID 15700407 DOI: 10.1089/1066527042432224  0.72
2004 Bejerano G, Haussler D, Blanchette M. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (Oxford, England). 20: i40-8. PMID 15262779 DOI: 10.1093/bioinformatics/bth946  0.72
2004 Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science (New York, N.Y.). 304: 1321-5. PMID 15131266 DOI: 10.1126/science.1098119  0.72
2004 Bejerano G. Algorithms for variable length Markov chain modeling. Bioinformatics (Oxford, England). 20: 788-9. PMID 14751999 DOI: 10.1093/bioinformatics/btg489  0.72
2003 Zerquera JT, Alonso MP, Bejerano GL, López JO, Rodríguez NA. Assessment of the doses received by the Cuban population from 40K contained in the body: modelling based on a neural network. Radiation Protection Dosimetry. 104: 237-43. PMID 14565730  0.72
2003 Slonim N, Bejerano G, Fine S, Tishby N. Discriminative feature selection via multiclass variable memory Markov model Eurasip Journal On Applied Signal Processing. 2003: 93-102. DOI: 10.1155/S111086570321115X  0.72
2003 Dubnov S, Assayag G, Lartillot O, Bejerano G. Using machine-learning methods for musical style modeling Computer. 36: 73-80. DOI: 10.1109/MC.2003.1236474  0.72
2003 Bejerano G. Efficient exact p-value computation and applications to biosequence analysis Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 38-47.  0.72
2001 Bejerano G, Seldin Y, Margalit H, Tishby N. Markovian domain fingerprinting: statistical segmentation of protein sequences. Bioinformatics (Oxford, England). 17: 927-34. PMID 11673237  0.72
2001 Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology : Cb. 11: 941-50. PMID 11448770 DOI: 10.1016/S0960-9822(01)00270-6  0.72
2001 Bejerano G, Yona G. Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bioinformatics (Oxford, England). 17: 23-43. PMID 11222260  0.72
2001 Hershberg R, Bejerano G, Santos-Zavaleta A, Margalit H. PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Research. 29: 277. PMID 11125111  0.72
2000 Apostolico A, Bejerano G. Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 381-93. PMID 11108469 DOI: 10.1089/106652700750050844  0.72
1999 Bejerano G, Yona G. Modeling protein families using probabilistic suffix trees Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 15-24.  0.72
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