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Alan P Boyle - Publications

Affiliations: 
University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Computational Biology, Genomics, Human Genetics
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47 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
2023 McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, et al. Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants. Cell Genomics. 3: 100404. PMID 37868037 DOI: 10.1016/j.xgen.2023.100404  0.707
2023 Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu YC, et al. Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1. Nature Structural & Molecular Biology. PMID 37460896 DOI: 10.1038/s41594-023-01033-4  0.653
2023 Holmes MJ, Mahjour B, Castro CP, Farnum GA, Diehl AG, Boyle AP. LRphase: an efficient method for assigning haplotype identity to long reads. Biorxiv : the Preprint Server For Biology. PMID 36712073 DOI: 10.1101/2023.01.18.524565  0.3
2022 Nishizaki SS, Boyle AP. SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. Bmc Bioinformatics. 23: 317. PMID 35927613 DOI: 10.1186/s12859-022-04865-x  0.304
2022 Qin T, Lee C, Li S, Cavalcante RG, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. Genome Biology. 23: 105. PMID 35473573 DOI: 10.1186/s13059-022-02668-0  0.331
2021 Dong S, Boyle AP. Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome. Nucleic Acids Research. PMID 34648033 DOI: 10.1093/nar/gkab924  0.335
2021 McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nature Communications. 12: 3586. PMID 34117247 DOI: 10.1038/s41467-021-23918-y  0.344
2020 Tsuzuki M, Sethuraman S, Coke AN, Rothi MH, Boyle AP, Wierzbicki AT. Broad noncoding transcription suggests genome surveillance by RNA polymerase V. Proceedings of the National Academy of Sciences of the United States of America. PMID 33199612 DOI: 10.1073/pnas.2014419117  0.31
2020 Diehl AG, Boyle AP. MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony. Bmc Bioinformatics. 21: 416. PMID 32962625 DOI: 10.1186/s12859-020-03742-9  0.304
2020 Ouyang N, Boyle AP. TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence. Genome Research. PMID 32660981 DOI: 10.1101/Gr.258228.119  0.459
2020 Diehl AG, Ouyang N, Boyle AP. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nature Communications. 11: 1796. PMID 32286261 DOI: 10.1038/S41467-020-15520-5  0.463
2020 Lee CT, Cavalcante RG, Lee C, Qin T, Patil S, Wang S, Tsai ZTY, Boyle AP, Sartor MA. Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. Nar Genomics and Bioinformatics. 2: lqaa006. PMID 32051932 DOI: 10.1093/nargab/lqaa006  0.333
2019 Nishizaki SS, Ng N, Dong S, Porter RS, Morterud C, Williams C, Asman C, Switzenberg JA, Boyle AP. Predicting the effects of SNPs on transcription factor binding affinity. Bioinformatics (Oxford, England). PMID 31373606 DOI: 10.1093/Bioinformatics/Btz612  0.34
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  0.468
2019 Dong S, Boyle AP. Predicting functional variants in enhancer and promoter elements using RegulomeDB. Human Mutation. PMID 31228310 DOI: 10.1002/Humu.23791  0.422
2019 Shigaki D, Adato O, Adhikar AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DP, Schubach M, Xiong C, Yan Z, Boyle AP, et al. Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay. Human Mutation. PMID 31106481 DOI: 10.1002/Humu.23797  0.417
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  0.506
2018 Diehl AG, Boyle AP. Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. Nucleic Acids Research. 46: 1878-1894. PMID 29361190 DOI: 10.1093/Nar/Gky018  0.48
2017 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, ... ... Boyle AP, et al. Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. American Journal of Human Genetics. PMID 29290336 DOI: 10.1016/J.Ajhg.2017.12.003  0.401
2017 Spadafore M, Najarian K, Boyle AP. A proximity-based graph clustering method for the identification and application of transcription factor clusters. Bmc Bioinformatics. 18: 530. PMID 29187152 DOI: 10.1186/S12859-017-1935-Y  0.376
2017 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, ... ... Boyle AP, et al. Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. Nature Communications. 8: 15481. PMID 28541271 DOI: 10.1038/Ncomms15481  0.352
2017 Nishizaki SS, Boyle AP. Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms. Trends in Genetics : Tig. 33: 34-45. PMID 27939749 DOI: 10.1016/J.Tig.2016.10.008  0.371
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  0.737
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  0.731
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  0.69
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  0.694
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  0.807
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  0.807
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  0.768
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  0.5
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  0.76
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  0.805
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  0.414
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  0.752
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  0.658
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  0.761
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  0.77
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  0.775
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  0.657
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  0.779
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  0.458
2010 Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SCJ, Boyle AP, Scott LJ, Program NCS, Margulies EH, Boehnke M, Furey TS, Crawford GE, et al. Erratum: Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci (Cell Metabolism (2010) 12 (443-455)) Cell Metabolism. 12. DOI: 10.1016/J.Cmet.2010.11.013  0.721
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  0.706
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  0.719
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  0.735
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  0.775
2003 Boyle AP, Boyle JA. Visualization of aligned genomic open reading frame data Biochemistry and Molecular Biology Education. 31: 64-68. DOI: 10.1002/Bmb.2003.494031010144  0.42
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