Gill Bejerano - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
Developmental Biology, Computer Science

69 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
2023 Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Molecular Biology and Evolution. 40. PMID 37739926 DOI: 10.1093/molbev/msad188  0.336
2023 Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages. Biorxiv : the Preprint Server For Biology. PMID 36778215 DOI: 10.1101/2023.01.30.526059  0.336
2022 Schull JK, Turakhia Y, Hemker JA, Dally WJ, Bejerano G. Champagne: Automated whole-genome phylogenomic character matrix method using large genomic indels for homoplasy-free inference. Genome Biology and Evolution. PMID 35171243 DOI: 10.1093/gbe/evac013  0.32
2021 Yoo B, Birgmeier J, Bernstein JA, Bejerano G. InpherNet accelerates monogenic disease diagnosis using patients' candidate genes' neighbors. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 34230641 DOI: 10.1038/s41436-021-01238-2  0.311
2020 Heavner WE, Ji S, Notwell JH, Dyer ES, Tseng AM, Birgmeier J, Yoo B, Bejerano G, McConnell SK. Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes. Proceedings of the National Academy of Sciences of the United States of America. PMID 32948690 DOI: 10.1073/Pnas.2008013117  0.342
2020 Turakhia Y, Chen HI, Marcovitz A, Bejerano G. A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. Nucleic Acids Research. PMID 32614390 DOI: 10.1093/Nar/Gkaa550  0.477
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  0.344
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  0.427
2019 Tanigawa Y, Li J, Justesen JM, Horn H, Aguirre M, DeBoever C, Chang C, Narasimhan B, Lage K, Hastie T, Park CY, Bejerano G, Ingelsson E, Rivas MA. Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology. Nature Communications. 10: 4064. PMID 31492854 DOI: 10.1038/S41467-019-11953-9  0.401
2019 Birgmeier J, Deisseroth CA, Hayward LE, Galhardo LMT, Tierno AP, Jagadeesh KA, Stenson PD, Cooper DN, Bernstein JA, Haeussler M, Bejerano G. AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 31467448 DOI: 10.1038/S41436-019-0643-6  0.332
2019 Frésard L, Smail C, Ferraro NM, Teran NA, Li X, Smith KS, Bonner D, Kernohan KD, Marwaha S, Zappala Z, Balliu B, Davis JR, Liu B, Prybol CJ, Kohler JN, ... ... Bejerano G, et al. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nature Medicine. PMID 31160820 DOI: 10.1038/S41591-019-0457-8  0.374
2019 Dever DP, Scharenberg SG, Camarena J, Kildebeck EJ, Clark JT, Martin RM, Bak RO, Tang Y, Dohse M, Birgmeier JA, Jagadeesh KA, Bejerano G, Tsukamoto A, Gomez-Ospina N, Uchida N, et al. CRISPR/Cas9 Genome Engineering in Engraftable Human Brain-Derived Neural Stem Cells. Iscience. 15: 524-535. PMID 31132746 DOI: 10.1016/J.Isci.2019.04.036  0.313
2019 Jagadeesh KA, Paggi JM, Ye JS, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nature Genetics. PMID 30804562 DOI: 10.1038/S41588-019-0348-4  0.349
2019 Turakhia Y, Bejerano G, Dally WJ. Darwin: A Genomics Coprocessor Ieee Micro. 39: 29-37. DOI: 10.1109/Mm.2019.2910009  0.383
2018 Deisseroth CA, Birgmeier J, Bodle EE, Kohler JN, Matalon DR, Nazarenko Y, Genetti CA, Brownstein CA, Schmitz-Abe K, Schoch K, Cope H, Signer R, Martinez-Agosto JA, Shashi V, ... ... Bejerano G, et al. ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 30514889 DOI: 10.1038/S41436-018-0381-1  0.38
2018 Paggi JM, Bejerano G. A sequence-based, deep learning model accurately predicts RNA splicing branchpoints. Rna (New York, N.Y.). 24: 1647-1658. PMID 30224349 DOI: 10.1261/Rna.066290.118  0.41
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  0.357
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  0.434
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  0.39
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  0.316
2018 Madelaine R, Notwell JH, Skariah G, Halluin C, Chen CC, Bejerano G, Mourrain P. A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human. Nucleic Acids Research. PMID 29518216 DOI: 10.1093/Nar/Gky166  0.387
2017 Jagadeesh KA, Wu DJ, Birgmeier JA, Boneh D, Bejerano G. Deriving genomic diagnoses without revealing patient genomes. Science (New York, N.Y.). 357: 692-695. PMID 28818945 DOI: 10.1126/Science.Aam9710  0.432
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  0.37
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  0.303
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  0.387
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  0.408
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  0.472
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  0.309
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  0.38
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  0.419
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  0.373
2015 Tuteja G, Bejerano G. Assaying the enhancer landscape during early placental development to identify a trophoblast invasion transcriptional code and gene-enhancer network Placenta. 36: A8. DOI: 10.1016/J.Placenta.2015.07.209  0.313
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  0.35
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  0.429
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  0.42
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  0.332
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  0.45
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  0.461
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  0.409
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  0.395
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  0.382
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  0.44
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  0.415
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  0.444
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  0.452
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  0.378
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  0.438
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  0.354
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  0.422
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  0.309
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  0.467
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  0.425
2008 McLean C, Bejerano G. Dispensability of mammalian DNA. Genome Research. 18: 1743-51. PMID 18832441 DOI: 10.1101/Gr.080184.108  0.378
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: 10.1007/978-1-59745-514-5_2  0.424
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  0.455
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  0.462
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  0.44
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  0.462
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  0.376
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  0.5
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  0.458
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  0.465
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  0.466
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  0.478
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  0.325
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  0.493
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  0.353
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 DOI: 10.1093/Bioinformatics/17.1.23  0.319
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 DOI: 10.1093/Nar/29.1.277  0.312
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