Google Scholar

* Indicates co-first authors

[1] Transcription factor co-binding patterns drive conserved regulatory outcomes.
Diehl AG, Boyle AP. bioRxiv 2017.
BibTeX  DOI  arXiv  Web

[2] 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. Nature communications 2017, 8:15481. PMID: 28541271.
BibTeX  DOI  Web  PDF

[3] Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.
Nishizaki SS, Boyle AP. Trends in Genetics 2017, 33:34--45. PMID: 27939749.
BibTeX  DOI  Web  PDF

[4] Deciphering ENCODE.
Diehl AG, Boyle AP. Trends in Genetics 2016, 32(4):238--249. PMID: 26962025.
BibTeX  DOI  Web  PDF

[5] Mango: A bias correcting ChIA-PET analysis pipeline.
Phanstiel DH, Boyle AP, Heidari N, Snyder MP. Bioinformatics 2015. PMID: 26034063.
BibTeX  DOI  Web  PDF

[6] 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, 515(7527):371--375. PMID: 25409826.
BibTeX  DOI  Web  PDF

[7] 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, 515(7527):355--364. PMID: 25409824.
BibTeX  DOI  Web  PDF

[8] 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, 512(7515):453--456. PMID: 25164757.
BibTeX  DOI  Web  PDF

[9] 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, 512(7515):400--405. PMID: 25164749.
BibTeX  DOI  Web  PDF

[10] Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.
Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Bioinformatics 2014. PMID: 24903420.
BibTeX  DOI  Web  PDF

[11] Dynamic trans-acting factor colocalization in human cells.
*Xie D, *Boyle AP, *Wu L, Kawli T, Zhai J, Snyder M. Cell 2013, 155(3):713--724. PMID: 24243024.
BibTeX  DOI  PubMed  PDF

[12] 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, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Science 2013, 342(6159):750--752. PMID: 24136358.
BibTeX  DOI  PubMed  PDF

[13] 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 Research 2012, 22(9):1790--1797. PMID: 22955989.
BibTeX  DOI  PubMed  PDF

[14] Linking disease associations with regulatory information in the human genome.
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Genome Research 2012, 22(9):1748--1759. PMID: 22955986.
BibTeX  DOI  PubMed  PDF

[15] An integrated encyclopedia of DNA elements in the human genome.
The ENCODE Project Consortium. Nature 2012, 489(7414):57--74. PMID: 22955616.
BibTeX  DOI  PubMed  PDF

[16] 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 J, 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, 489(7414):91--100. PMID: 22955619.
BibTeX  DOI  PubMed  PDF

[17] Personal omics profiling reveals dynamic molecular and medical phenotypes.
*Chen R, *Mias GI, *Li-Pook-Than J, *Jiang L, Lam HYK, 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, 148(6):1293--1307. PMID: 22424236.
BibTeX  DOI  PubMed  PDF

[18] 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 B, *Sheffield NC, Graff 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 Research 2011, 21(10):1757--1767. PMID: 21750106.
BibTeX  DOI  PubMed  PDF

[19] A user's guide to the encyclopedia of DNA elements (ENCODE).
The ENCODE Project Consortium. PLoS Biology 2011, 9(4):e1001046. PMID: 21526222.
BibTeX  DOI  PubMed  PDF

[20] High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee B, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. Genome Research 2011, 21:456--464. PMID: 21106903.
BibTeX  DOI  PubMed  PDF

[21] 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 SCJ, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS. Cell Metabolism 2010, 12(5):443--455. PMID: 21035756.
BibTeX  DOI  PubMed  PDF

[22] Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell R, Lee B, 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, 328(5975):235--239. PMID: 20299549.
BibTeX  DOI  PubMed  PDF  Faculty Of 1000

[23] Evidence-ranked motif identification.
Georgiev S, Boyle AP, Jayasurya K, Mukherjee S, Ohler U. Genome Biology 2010, 11(2):R19. PMID: 20156354.
BibTeX  DOI  PubMed  PDF

[24] 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 Biology and Evolution 2010, 2:67--79. PMID: 20333225.
BibTeX  DOI  PubMed  PDF

[25] 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 Research 2009, 37(22):7381--7393. PMID: 19820107.
BibTeX  DOI  PubMed  PDF

[26] High-resolution mapping studies of chromatin and gene regulatory elements.
Boyle AP, Furey TS. Epigenomics 2009, 1(2):319--329. PMID: 20514362.
BibTeX  DOI  PubMed  PDF

[27] F-Seq: a feature density estimator for high-throughput sequence tags.
Boyle AP, Guinney J, Crawford GE, Furey TS. Bioinformatics 2008, 24(21):2537--2538. PMID: 18784119.
BibTeX  DOI  PubMed  PDF

[28] 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, 132(2):311--322. PMID: 18243105.
BibTeX  DOI  PubMed  PDF

[29] Global analysis of microbial translation initiation regions.
Boyle AP, Boyle JA. In Journal of the Mississippi Academy of Sciences, Volume 48 2003:138--150.
BibTeX  Web  PDF

[30] Visualization of aligned genomic open reading frame data.
Boyle AP, Boyle JA. Biochemistry and Molecular Biology Education 2003, 31:64--68.
BibTeX  Web  PDF

[31] Interactive clustering for exploration of genomic data.
Wan X, Boyle JA, Bridges SM, Boyle AP. In Proceedings of the Artificial Neural Networks in Engineering Conference, Volume 12, St. Louis, MO 2002:753--758.
BibTeX  PDF