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Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology.

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.

Nat Commun. 2019 Sep 6;10(1):4064. doi: 10.1038/s41467-019-11953-9.


AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature.

Birgmeier J, Deisseroth CA, Hayward LE, Galhardo LMT, Tierno AP, Jagadeesh KA, Stenson PD, Cooper DN, Bernstein JA, Haeussler M, Bejerano G.

Genet Med. 2019 Aug 30. doi: 10.1038/s41436-019-0643-6. [Epub ahead of print]


Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

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, Zastrow DB, Reuter CM, Fisk DG, Grove ME, Davidson JM, Hartley T, Joshi R, Strober BJ, Utiramerur S; Undiagnosed Diseases Network; Care4Rare Canada Consortium, Lind L, Ingelsson E, Battle A, Bejerano G, Bernstein JA, Ashley EA, Boycott KM, Merker JD, Wheeler MT, Montgomery SB.

Nat Med. 2019 Jun;25(6):911-919. doi: 10.1038/s41591-019-0457-8. Epub 2019 Jun 3.


CRISPR/Cas9 Genome Engineering in Engraftable Human Brain-Derived Neural Stem Cells.

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, Porteus MH.

iScience. 2019 May 31;15:524-535. doi: 10.1016/j.isci.2019.04.036. Epub 2019 May 4.


S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing.

Jagadeesh KA, Paggi JM, Ye JS, Stenson PD, Cooper DN, Bernstein JA, Bejerano G.

Nat Genet. 2019 Apr;51(4):755-763. doi: 10.1038/s41588-019-0348-4. Epub 2019 Feb 25.


ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis.

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; Undiagnosed Diseases Network, Martinez-Agosto JA, Shashi V, Beggs AH, Wheeler MT, Bernstein JA, Bejerano G.

Genet Med. 2019 Jul;21(7):1585-1593. doi: 10.1038/s41436-018-0381-1. Epub 2018 Dec 5.


A sequence-based, deep learning model accurately predicts RNA splicing branchpoints.

Paggi JM, Bejerano G.

RNA. 2018 Dec;24(12):1647-1658. doi: 10.1261/rna.066290.118. Epub 2018 Sep 17.


Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals.

Berger MJ, Wenger AM, Guturu H, Bejerano G.

Nucleic Acids Res. 2018 Oct 12;46(18):9299-9308. doi: 10.1093/nar/gky741.


An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease.

Chen HI, Jagadeesh KA, Birgmeier J, Wenger AM, Guturu H, Schelley S, Bernstein JA, Bejerano G.

Eur J Hum Genet. 2018 Dec;26(12):1810-1818. doi: 10.1038/s41431-018-0221-4. Epub 2018 Aug 7.


Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization.

Jagadeesh KA, Birgmeier J, Guturu H, Deisseroth CA, Wenger AM, Bernstein JA, Bejerano G.

Genet Med. 2019 Feb;21(2):464-470. doi: 10.1038/s41436-018-0072-y. Epub 2018 Jul 12.


Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome.

Birgmeier J, Esplin ED, Jagadeesh KA, Guturu H, Wenger AM, Chaib H, Buckingham JA, Bejerano G, Bernstein JA.

Am J Med Genet A. 2018 Apr;176(4):1030-1036. doi: 10.1002/ajmg.a.38636.


A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human.

Madelaine R, Notwell JH, Skariah G, Halluin C, Chen CC, Bejerano G, Mourrain P.

Nucleic Acids Res. 2018 Apr 20;46(7):3517-3531. doi: 10.1093/nar/gky166.


Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly.

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, Jacquinet A, Ygberg S, Bernstein JA, Wenger AM, Guturu H, Bejerano G, Gomez-Ospina N, Lehman A, Alfei E, Pantaleoni C, Conti V, Guerrini R, Moog U, Graham JM Jr, Hevner R, Dobyns WB, O'Driscoll M, Mirzaa GM.

Brain. 2017 Oct 1;140(10):2610-2622. doi: 10.1093/brain/awx203.


Deriving genomic diagnoses without revealing patient genomes.

Jagadeesh KA, Wu DJ, Birgmeier JA, Boneh D, Bejerano G.

Science. 2017 Aug 18;357(6352):692-695. doi: 10.1126/science.aam9710.


MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis.

Madelaine R, Sloan SA, Huber N, Notwell JH, Leung LC, Skariah G, Halluin C, Paşca SP, Bejerano G, Krasnow MA, Barres BA, Mourrain P.

Cell Rep. 2017 Aug 15;20(7):1533-1542. doi: 10.1016/j.celrep.2017.07.051.


M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.

Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G.

Nat Genet. 2016 Dec;48(12):1581-1586. doi: 10.1038/ng.3703. Epub 2016 Oct 24.


Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene.

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; DDD Study, Bejerano G, Bernstein JA, Chitayat D.

J Med Genet. 2017 Mar;54(3):157-165. doi: 10.1136/jmedgenet-2016-104143. Epub 2016 Oct 13.


Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers.

Wenger AM, Guturu H, Bernstein JA, Bejerano G.

Genet Med. 2017 Feb;19(2):209-214. doi: 10.1038/gim.2016.88. Epub 2016 Jul 21.


TBR1 regulates autism risk genes in the developing neocortex.

Notwell JH, Heavner WE, Darbandi SF, Katzman S, McKenna WL, Ortiz-Londono CF, Tastad D, Eckler MJ, Rubenstein JL, McConnell SK, Chen B, Bejerano G.

Genome Res. 2016 Aug;26(8):1013-22. doi: 10.1101/gr.203612.115. Epub 2016 Jun 20.


Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories.

Guturu H, Chinchali S, Clarke SL, Bejerano G.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004711. doi: 10.1371/journal.pcbi.1004711. eCollection 2016 Feb.


"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.

Marcovitz A, Jia R, Bejerano G.

Mol Biol Evol. 2016 May;33(5):1358-69. doi: 10.1093/molbev/msw001. Epub 2016 Jan 6.


Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network.

Tuteja G, Chung T, Bejerano G.

Placenta. 2016 Jan;37:45-55. doi: 10.1016/j.placenta.2015.11.001. Epub 2015 Nov 6.


Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales.

Braun BA, Marcovitz A, Camp JG, Jia R, Bejerano G.

Proc Natl Acad Sci U S A. 2015 Jun 30;112(26):8036-40. doi: 10.1073/pnas.1501844112. Epub 2015 Jun 15.


Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci.

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.

PLoS Genet. 2015 May 28;11(5):e1005202. doi: 10.1371/journal.pgen.1005202. eCollection 2015 May.


A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.

Notwell JH, Chung T, Heavner W, Bejerano G.

Nat Commun. 2015 Mar 25;6:6644. doi: 10.1038/ncomms7644.


Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.

Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF.

Genome Res. 2014 Sep;24(9):1504-16. doi: 10.1101/gr.165845.113. Epub 2014 Jun 24.


Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data.

Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G.

PLoS Comput Biol. 2014 Jan 30;10(1):e1003449. doi: 10.1371/journal.pcbi.1003449. eCollection 2014 Jan.


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.

Reno PL, McLean CY, Hines JE, Capellini TD, Bejerano G, Kingsley DM.

PLoS One. 2013 Dec 19;8(12):e84258. doi: 10.1371/journal.pone.0084258. eCollection 2013.


Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

Guturu H, Doxey AC, Wenger AM, Bejerano G.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130029. doi: 10.1098/rstb.2013.0029. Print 2013 Dec 19.


The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.

Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G.

PLoS Genet. 2013 Aug;9(8):e1003728. doi: 10.1371/journal.pgen.1003728. Epub 2013 Aug 29.


Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.

Hiller M, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G.

Nucleic Acids Res. 2013 Aug;41(15):e151. doi: 10.1093/nar/gkt557. Epub 2013 Jun 27.


Enhancers: five essential questions.

Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G.

Nat Rev Genet. 2013 Apr;14(4):288-95. doi: 10.1038/nrg3458. Review.


PRISM offers a comprehensive genomic approach to transcription factor function prediction.

Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G.

Genome Res. 2013 May;23(5):889-904. doi: 10.1101/gr.139071.112. Epub 2013 Feb 4.


Evolutionary biology for the 21st century.

Losos JB, Arnold SJ, Bejerano G, Brodie ED 3rd, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL.

PLoS Biol. 2013;11(1):e1001466. doi: 10.1371/journal.pbio.1001466. Epub 2013 Jan 8. No abstract available.


PESNPdb: a comprehensive database of SNPs studied in association with pre-eclampsia.

Tuteja G, Cheng E, Papadakis H, Bejerano G.

Placenta. 2012 Dec;33(12):1055-7. doi: 10.1016/j.placenta.2012.09.016. Epub 2012 Oct 18.


Hundreds of conserved non-coding genomic regions are independently lost in mammals.

Hiller M, Schaar BT, Bejerano G.

Nucleic Acids Res. 2012 Dec;40(22):11463-76. doi: 10.1093/nar/gks905. Epub 2012 Oct 5.


A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species.

Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G.

Cell Rep. 2012 Oct 25;2(4):817-23. doi: 10.1016/j.celrep.2012.08.032. Epub 2012 Sep 27.


Human developmental enhancers conserved between deuterostomes and protostomes.

Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G.

PLoS Genet. 2012;8(8):e1002852. doi: 10.1371/journal.pgen.1002852. Epub 2012 Aug 2.


A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb.

Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A.

Hum Mutat. 2012 Jul;33(7):1063-6. doi: 10.1002/humu.22097. Epub 2012 May 11.


Coding exons function as tissue-specific enhancers of nearby genes.

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, Lomvardas S, Ahituv N.

Genome Res. 2012 Jun;22(6):1059-68. doi: 10.1101/gr.133546.111. Epub 2012 Mar 22.


Control of pelvic girdle development by genes of the Pbx family and Emx2.

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.

Dev Dyn. 2011 May;240(5):1173-89. doi: 10.1002/dvdy.22617. Epub 2011 Mar 31.


Human-specific loss of regulatory DNA and the evolution of human-specific traits.

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.

Nature. 2011 Mar 10;471(7337):216-9. doi: 10.1038/nature09774.


Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging.

Fan X, Ren P, Dhal S, Bejerano G, Goodman SB, Druzin ML, Gambhir SS, Nayak NR.

PLoS One. 2011 Jan 21;6(1):e16348. doi: 10.1371/journal.pone.0016348.


GREAT improves functional interpretation of cis-regulatory regions.

McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.


Endangered species hold clues to human evolution.

Lowe CB, Bejerano G, Salama SR, Haussler D.

J Hered. 2010 Jul-Aug;101(4):437-47. doi: 10.1093/jhered/esq016. Epub 2010 Mar 23.


Establishment of a national program for quality control of nuclear medicine instrumentation.

Coca Perez MA, Torres Aroche LA, Bejerano GL, Mayor RF, Corona CV, López A.

J Nucl Med Technol. 2008 Dec;36(4):203-6. doi: 10.2967/jnmt.108.053504. Epub 2008 Nov 13.


Dispensability of mammalian DNA.

McLean C, Bejerano G.

Genome Res. 2008 Nov;18(11):1743-51. doi: 10.1101/gr.080184.108. Epub 2008 Oct 2.


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.


Human genome ultraconserved elements are ultraselected.

Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D.

Science. 2007 Aug 17;317(5840):915.


A protocol for the calibration of gamma cameras to estimate internal contamination in emergency situations.

Dantas BM, Lucena EA, Dantas AL, Araújo F, Rebelo AM, Terán M, Paolino A, Hermida JC, Rojo AM, Puerta JA, Morales J, Bejerano GM, Alfaro M, Ruiz MA, Videla R, Piñones O, González S, Navarro T, Melo D, Cruz-Suárez R.

Radiat Prot Dosimetry. 2007;127(1-4):253-7. Epub 2007 Jun 11.


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