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Items: 22

1.

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.

2.

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.

PMID:
30087448
3.

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. 2018 Jul 12. doi: 10.1038/s41436-018-0072-y. [Epub ahead of print]

PMID:
29997393
4.

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.

PMID:
29575631
5.

Variant Review with the Integrative Genomics Viewer.

Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP.

Cancer Res. 2017 Nov 1;77(21):e31-e34. doi: 10.1158/0008-5472.CAN-17-0337.

6.

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.

7.

Long-read genome sequencing identifies causal structural variation in a Mendelian disease.

Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, Waggott D, Utiramerur S, Hou Y, Smith KS, Montgomery SB, Wheeler M, Buchan JG, Lambert CC, Eng KS, Hickey L, Korlach J, Ford J, Ashley EA.

Genet Med. 2018 Jan;20(1):159-163. doi: 10.1038/gim.2017.86. Epub 2017 Jun 22.

8.

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.

PMID:
27776117
9.

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.

10.

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.

PMID:
27441994
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

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