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Items: 31

1.

Williams-Beuren syndrome in diverse populations.

Kruszka P, Porras AR, de Souza DH, Moresco A, Huckstadt V, Gill AD, Boyle AP, Hu T, Addissie YA, Mok GTK, Tekendo-Ngongang C, Fieggen K, Prijoles EJ, Tanpaiboon P, Honey E, Luk HM, Lo IFM, Thong MK, Muthukumarasamy P, Jones KL, Belhassan K, Ouldim K, El Bouchikhi I, Bouguenouch L, Shukla A, Girisha KM, Sirisena ND, Dissanayake VHW, Paththinige CS, Mishra R, Kisling MS, Ferreira CR, de Herreros MB, Lee NC, Jamuar SS, Lai A, Tan ES, Ying Lim J, Wen-Min CB, Gupta N, Lotz-Esquivel S, Badilla-Porras R, Hussen DF, El Ruby MO, Ashaat EA, Patil SJ, Dowsett L, Eaton A, Innes AM, Shotelersuk V, Badoe Ë, Wonkam A, Obregon MG, Chung BHY, Trubnykova M, La Serna J, Gallardo Jugo BE, Chávez Pastor M, Abarca Barriga HH, Megarbane A, Kozel BA, van Haelst MM, Stevenson RE, Summar M, Adeyemo AA, Morris CA, Moretti-Ferreira D, Linguraru MG, Muenke M.

Am J Med Genet A. 2018 May;176(5):1128-1136. doi: 10.1002/ajmg.a.38672.

PMID:
29681090
2.

Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.

Diehl AG, Boyle AP.

Nucleic Acids Res. 2018 Feb 28;46(4):1878-1894. doi: 10.1093/nar/gky018.

3.

Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.

Nielsen JB, Fritsche LG, Zhou W, Teslovich TM, Holmen OL, Gustafsson S, Gabrielsen ME, Schmidt EM, Beaumont R, Wolford BN, Lin M, Brummett CM, Preuss MH, Refsgaard L, Bottinger EP, Graham SE, Surakka I, Chu Y, Skogholt AH, Dalen H, Boyle AP, Oral H, Herron TJ, Kitzman J, Jalife J, Svendsen JH, Olesen MS, Njølstad I, Løchen ML, Baras A, Gottesman O, Marcketta A, O'Dushlaine C, Ritchie MD, Wilsgaard T, Loos RJF, Frayling TM, Boehnke M, Ingelsson E, Carey DJ, Dewey FE, Kang HM, Abecasis GR, Hveem K, Willer CJ.

Am J Hum Genet. 2018 Jan 4;102(1):103-115. doi: 10.1016/j.ajhg.2017.12.003. Epub 2017 Dec 28.

4.

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

Spadafore M, Najarian K, Boyle AP.

BMC Bioinformatics. 2017 Nov 29;18(1):530. doi: 10.1186/s12859-017-1935-y.

5.

Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve.

Yang B, Zhou W, Jiao J, Nielsen JB, Mathis MR, Heydarpour M, Lettre G, Folkersen L, Prakash S, Schurmann C, Fritsche L, Farnum GA, Lin M, Othman M, Hornsby W, Driscoll A, Levasseur A, Thomas M, Farhat L, Dubé MP, Isselbacher EM, Franco-Cereceda A, Guo DC, Bottinger EP, Deeb GM, Booher A, Kheterpal S, Chen YE, Kang HM, Kitzman J, Cordell HJ, Keavney BD, Goodship JA, Ganesh SK, Abecasis G, Eagle KA, Boyle AP, Loos RJF, Eriksson P, Tardif JC, Brummett CM, Milewicz DM, Body SC, Willer CJ.

Nat Commun. 2017 May 25;8:15481. doi: 10.1038/ncomms15481.

6.

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.

Nishizaki SS, Boyle AP.

Trends Genet. 2017 Jan;33(1):34-45. doi: 10.1016/j.tig.2016.10.008. Epub 2016 Dec 6. Review.

7.

Deciphering ENCODE.

Diehl AG, Boyle AP.

Trends Genet. 2016 Apr;32(4):238-249. doi: 10.1016/j.tig.2016.02.002. Epub 2016 Mar 5. Review.

PMID:
26962025
8.

Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M.

Nature. 2015 Dec 3;528(7580):152. doi: 10.1038/nature16075. Epub 2015 Nov 11. No abstract available.

PMID:
26560031
9.

Pattern matching approach to pseudosymmetry problems in electron backscatter diffraction.

Nolze G, Winkelmann A, Boyle AP.

Ultramicroscopy. 2016 Jan;160:146-154. doi: 10.1016/j.ultramic.2015.10.010. Epub 2015 Oct 23.

PMID:
26517547
10.

Mango: a bias-correcting ChIA-PET analysis pipeline.

Phanstiel DH, Boyle AP, Heidari N, Snyder MP.

Bioinformatics. 2015 Oct 1;31(19):3092-8. doi: 10.1093/bioinformatics/btv336. Epub 2015 Jun 1.

11.

Principles of regulatory information conservation between mouse and human.

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.

Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985.

12.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

13.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

14.

Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M.

Nature. 2014 Aug 28;512(7515):400-5. doi: 10.1038/nature13497. Erratum in: Nature. 2015 Dec 3;528(7580):152.

15.

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.

Phanstiel DH, Boyle AP, Araya CL, Snyder MP.

Bioinformatics. 2014 Oct;30(19):2808-10. doi: 10.1093/bioinformatics/btu379. Epub 2014 Jun 5.

16.

Dynamic trans-acting factor colocalization in human cells.

Xie D, Boyle AP, Wu L, Zhai J, Kawli T, Snyder M.

Cell. 2013 Oct 24;155(3):713-24. doi: 10.1016/j.cell.2013.09.043. Epub 2013 Oct 24.

17.

Extensive variation in chromatin states across humans.

Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M.

Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17.

18.

Annotation of functional variation in personal genomes using RegulomeDB.

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M.

Genome Res. 2012 Sep;22(9):1790-7. doi: 10.1101/gr.137323.112.

19.

Linking disease associations with regulatory information in the human genome.

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M.

Genome Res. 2012 Sep;22(9):1748-59. doi: 10.1101/gr.136127.111.

20.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

21.

Personal omics profiling reveals dynamic molecular and medical phenotypes.

Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M.

Cell. 2012 Mar 16;148(6):1293-307. doi: 10.1016/j.cell.2012.02.009.

22.

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12.

23.

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS.

Genome Res. 2011 Mar;21(3):456-64. doi: 10.1101/gr.112656.110. Epub 2010 Nov 24.

24.

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.

Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ; NISC Comparative Sequencing Program, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS.

Cell Metab. 2010 Nov 3;12(5):443-55. doi: 10.1016/j.cmet.2010.09.012. Erratum in: Cell Metab. 2010 Dec 1;12(6):683.

25.

High-resolution mapping studies of chromatin and gene regulatory elements.

Boyle AP, Furey TS.

Epigenomics. 2009 Dec 1;1(2):319-329.

26.

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.

Babbitt CC, Fedrigo O, Pfefferle AD, Boyle AP, Horvath JE, Furey TS, Wray GA.

Genome Biol Evol. 2010 Jan 18;2:67-79. doi: 10.1093/gbe/evq002.

27.

Heritable individual-specific and allele-specific chromatin signatures in humans.

McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E.

Science. 2010 Apr 9;328(5975):235-9. doi: 10.1126/science.1184655. Epub 2010 Mar 18.

28.

Evidence-ranked motif identification.

Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U.

Genome Biol. 2010;11(2):R19. doi: 10.1186/gb-2010-11-2-r19. Epub 2010 Feb 15.

29.

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.

Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M.

Nucleic Acids Res. 2009 Dec;37(22):7381-93. doi: 10.1093/nar/gkp833.

30.

F-Seq: a feature density estimator for high-throughput sequence tags.

Boyle AP, Guinney J, Crawford GE, Furey TS.

Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10.

31.

High-resolution mapping and characterization of open chromatin across the genome.

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE.

Cell. 2008 Jan 25;132(2):311-22. doi: 10.1016/j.cell.2007.12.014.

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