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Gil Bejerano, Professor - Publications

Affiliations: 
CS Stanford University, Palo Alto, CA 
Area:
Computational Biology
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36 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
2020 Birgmeier J, Haeussler M, Deisseroth CA, Steinberg EH, Jagadeesh KA, Ratner AJ, Guturu H, Wenger AM, Diekhans ME, Stenson PD, Cooper DN, Ré C, Beggs AH, Bernstein JA, Bejerano G. AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature. Science Translational Medicine. 12. PMID 32434849 DOI: 10.1126/Scitranslmed.Aau9113  0.649
2019 Marcovitz A, Turakhia Y, Chen HI, Gloudemans M, Braun BA, Wang H, Bejerano G. A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales. Proceedings of the National Academy of Sciences of the United States of America. PMID 31570615 DOI: 10.1073/Pnas.1818532116  0.303
2018 Berger MJ, Wenger AM, Guturu H, Bejerano G. Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals. Nucleic Acids Research. PMID 30137416 DOI: 10.1093/Nar/Gky741  0.665
2018 Chen HI, Jagadeesh KA, Birgmeier J, Wenger AM, Guturu H, Schelley S, Bernstein JA, Bejerano G. An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease. European Journal of Human Genetics : Ejhg. PMID 30087448 DOI: 10.1038/S41431-018-0221-4  0.691
2018 Jagadeesh KA, Birgmeier J, Guturu H, Deisseroth CA, Wenger AM, Bernstein JA, Bejerano G. Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 29997393 DOI: 10.1038/S41436-018-0072-Y  0.66
2018 Birgmeier J, Esplin ED, Jagadeesh KA, Guturu H, Wenger AM, Chaib H, Buckingham JA, Bejerano G, Bernstein JA. Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome. American Journal of Medical Genetics. Part A. 176: 1030-1036. PMID 29575631 DOI: 10.1002/Ajmg.A.38636  0.641
2017 Alcantara D, Timms AE, Gripp K, Baker L, Park K, Collins S, Cheng C, Stewart F, Mehta SG, Saggar A, Sztriha L, Zombor M, Caluseriu O, Mesterman R, Van Allen MI, ... ... Bejerano G, et al. Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly. Brain : a Journal of Neurology. 140: 2610-2622. PMID 28969385 DOI: 10.1093/Brain/Awx203  0.638
2016 Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nature Genetics. PMID 27776117 DOI: 10.1038/Ng.3703  0.651
2016 Balasubramanian M, Lord H, Levesque S, Guturu H, Thuriot F, Sillon G, Wenger AM, Sureka DL, Lester T, Johnson DS, Bowen J, Calhoun AR, Viskochil DH, Bejerano G, et al. Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene. Journal of Medical Genetics. PMID 27738187 DOI: 10.1136/Jmedgenet-2016-104143  0.62
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  0.626
2016 Notwell JH, Heavner WE, Fazel Darbandi S, Katzman S, McKenna WL, Ortiz-Londono CF, Tastad D, Eckler MJ, Rubenstein JL, McConnell SK, Chen B, Bejerano G. TBR1 regulates autism risk genes in the developing neocortex. Genome Research. PMID 27325115 DOI: 10.1101/Gr.203612.115  0.302
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  0.31
2016 Marcovitz A, Jia R, Bejerano G. "Reverse genomics" predicts function of human conserved non-coding elements. Molecular Biology and Evolution. PMID 26744417 DOI: 10.1093/Molbev/Msw001  0.314
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  0.318
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  0.657
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  0.698
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  0.648
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  0.697
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  0.666
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  0.681
2013 Tuteja G, Wenger A, Moreira KB, Chung T, Bejerano G. Genomic approaches for the identification of genes and enhancers regulating placenta development Placenta. 34: A69-A70. DOI: 10.1016/J.Placenta.2013.06.210  0.67
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  0.691
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  0.683
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  0.69
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  0.662
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  0.669
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  0.698
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  0.304
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  0.364
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  0.329
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  0.322
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/Cmb.2004.11.867  0.508
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  0.323
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  0.666
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  0.563
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  0.53
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