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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