Alan P Boyle - Publications

Affiliations: 
University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Computational Biology, Genomics, Human Genetics

25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Scientific Reports. 9: 9354. PMID 31249361 DOI: 10.1038/s41598-019-45839-z  0.4
2018 Varshney A, VanRenterghem H, Orchard P, Boyle AP, Stitzel ML, Ucar D, Parker SCJ. Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics. PMID 30593493 DOI: 10.1534/genetics.118.301525  0.4
2015 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, et al. Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. PMID 26560031 DOI: 10.1038/nature16075  0.4
2015 Phanstiel DH, Boyle AP, Heidari N, Snyder MP. Mango: A bias correcting ChIA-PET analysis pipeline. Bioinformatics (Oxford, England). PMID 26034063 DOI: 10.1093/bioinformatics/btv336  0.72
2014 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, et al. Principles of regulatory information conservation between mouse and human. Nature. 515: 371-5. PMID 25409826 DOI: 10.1038/nature13985  0.72
2014 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, ... ... Boyle AP, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/nature13992  0.72
2014 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, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/nature13668  0.72
2014 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, et al. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 512: 400-5. PMID 25164749 DOI: 10.1038/nature13497  0.72
2014 Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinformatics (Oxford, England). 30: 2808-10. PMID 24903420 DOI: 10.1093/bioinformatics/btu379  0.72
2013 Xie D, Boyle AP, Wu L, Zhai J, Kawli T, Snyder M. Dynamic trans-acting factor colocalization in human cells. Cell. 155: 713-24. PMID 24243024 DOI: 10.1016/j.cell.2013.09.043  0.4
2013 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, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/science.1242510  0.4
2012 Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Research. 22: 1790-7. PMID 22955989 DOI: 10.1101/gr.137323.112  0.72
2012 Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Research. 22: 1748-59. PMID 22955986 DOI: 10.1101/gr.136127.111  0.72
2012 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, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/nature11245  0.72
2012 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, ... ... Boyle AP, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/j.cell.2012.02.009  0.72
2011 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, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/gr.121541.111  0.72
2011 Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Research. 21: 456-64. PMID 21106903 DOI: 10.1101/gr.112656.110  0.72
2010 Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metabolism. 12: 443-55. PMID 21035756 DOI: 10.1016/j.cmet.2010.09.012  0.72
2010 Babbitt CC, Fedrigo O, Pfefferle AD, Boyle AP, Horvath JE, Furey TS, Wray GA. Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biology and Evolution. 2: 67-79. PMID 20333225 DOI: 10.1093/gbe/evq002  0.72
2010 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, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science (New York, N.Y.). 328: 235-9. PMID 20299549 DOI: 10.1126/science.1184655  0.72
2010 Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U. Evidence-ranked motif identification. Genome Biology. 11: R19. PMID 20156354 DOI: 10.1186/gb-2010-11-2-r19  0.72
2009 Boyle AP, Furey TS. High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics. 1: 319-329. PMID 20514362 DOI: 10.2217/epi.09.29  0.72
2009 Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M. DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Nucleic Acids Research. 37: 7381-93. PMID 19820107 DOI: 10.1093/nar/gkp833  0.72
2008 Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (Oxford, England). 24: 2537-8. PMID 18784119 DOI: 10.1093/bioinformatics/btn480  0.72
2008 Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 132: 311-22. PMID 18243105 DOI: 10.1016/j.cell.2007.12.014  0.72
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