Alan P Boyle - Publications

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

27/72 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 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  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.2010.11.013  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
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  0.72
Low-probability matches
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/s41586-020-2449-8  0.04
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  0.04
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  0.04
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  0.04
1984 Tait BD, Boyle A, Solty S, Cunningham T, Mandel T, Martin FI, Doran T. DR4 related antisera pattern differences in insulin dependent diabetes mellitus and rheumatoid arthritis. Tissue Antigens. 24: 228-33. PMID 6334907 DOI: 10.1111/j.1399-0039.1984.tb02131.x  0.04
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  0.01
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  0.01
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/s41586-020-2493-4  0.01
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  0.01
2019 Diehl AG, Boyle AP. CGIMP: Real-time exploration and covariate projection for self-organizing map datasets. Journal of Open Source Software. 4. PMID 32500114 DOI: 10.21105/joss.01520  0.01
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  0.01
2019 Dong S, Boyle AP. Predicting functional variants in enhancer and promoter elements using RegulomeDB. Human Mutation. PMID 31228310 DOI: 10.1002/humu.23791  0.01
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  0.01
2019 Boyle A. Litigating Climate Change under Part XII of the LOSC The International Journal of Marine and Coastal Law. 34: 458-481. DOI: 10.1163/15718085-13431097  0.01
2019 Boyle A. United Nations Convention on the Law of the Sea: A Commentary, edited by Alexander Proelss [C.H. Beck/Hart/Nomos, Munich, Oxford and Baden-Baden, 2017, 1800pp, ISBN 9781849461924, £495.00 (h/bk)] International and Comparative Law Quarterly. 68: 771-772. DOI: 10.1017/S0020589319000198  0.01
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  0.01
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  0.01
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  0.01
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  0.01
2017 Bhow A, Henroid D, Booth P, Boyle A, Tabrizi L, Badri R, Blakenship S, Burke S, Fujii M, Hu S, Smith S. Glycemic Control with Different Foodservice Models: On Demand Room Service and Batch Set-time Models in an Urban Academic Medical Center Journal of the Academy of Nutrition and Dietetics. 117: A46. DOI: 10.1016/j.jand.2017.06.124  0.01
2016 Diehl AG, Boyle AP. Deciphering ENCODE. Trends in Genetics : Tig. 32: 238-249. PMID 26962025 DOI: 10.1016/j.tig.2016.02.002  0.01
2016 Nolze G, Winkelmann A, Boyle AP. Pattern matching approach to pseudosymmetry problems in electron backscatter diffraction. Ultramicroscopy. 160: 146-154. PMID 26517547 DOI: 10.1016/j.ultramic.2015.10.010  0.01
2015 Boyle A. Transboundary air pollution: A tale of two paradigms Transboundary Pollution: Evolving Issues of International Law and Policy. 233-259. DOI: 10.4337/9781784715793.00018  0.01
2012 . An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247  0.01
2011 Boyle A. The cold call: How to face an interview. The Journal of the Acoustical Society of America. 129: 2518-2518. DOI: 10.1121/1.3588327  0.01
2011 Boyle A. A veteran reporter’s perspective on science. The Journal of the Acoustical Society of America. 129: 2517-2517. DOI: 10.1121/1.3588322  0.01
2011 Williams M, Williams P, Boyle A. Using internet-based problem-solving activities to enhance students' understanding of 3-dimensional spatial relationships Planet. 24: 68-75. DOI: 10.11120/plan.2011.00240068  0.01
2010 Boyle AP, Prior DJ, Heath AE. Using portfolio assessment to engage Level 1 Geoscience students in their subject and to develop their learning skills Planet. 23: 12-15. DOI: 10.11120/PLAN.2010.00230012  0.01
2007 Boyle AP. Using Alignment and Reflection to Improve Student Learning Elements. 3: 113-117. DOI: 10.2113/GSELEMENTS.3.2.113  0.01
2007 Boyle A, Maguire S, Martin A, Milsom C, Nash R, Rawlinson S, Turner A, Wurthmann S, Conchie S. Fieldwork is Good: the Student Perception and the Affective Domain Journal of Geography in Higher Education. 31: 299-317. DOI: 10.1080/03098260601063628  0.01
2006 Boyle A, Potts G, Williams M, Williams P. Preliminary report on studio teaching in Earth sciences: a way to improve students’ problem-solving abilities? Planet. 17: 34-36. DOI: 10.11120/PLAN.2006.00170034  0.01
2006 Truscott JB, Boyle A, Burkill S, Libarkin J, Lonsdale J. The concept of time: can it be fully realised and taught? Planet. 17: 21-23. DOI: 10.11120/PLAN.2006.00170021  0.01
2006 Boyle A. Further Development of the 1982 Convention on the Law of the Sea: Mechanisms for Change The Law of the Sea: Progress and Prospects. DOI: 10.1093/acprof:oso/9780199299614.003.0003  0.01
2005 Ohfuji H, Boyle AP, Prior DJ, Rickard D. Structure of framboidal pyrite: An electron backscatter diffraction study American Mineralogist. 90: 1693-1704. DOI: 10.2138/am.2005.1829  0.01
2002 Cantwell L, Boyle A, Diviney M, Hepner J, Kanaan C, Oliver D, Abud D, Holdsworth R, Tait B. Identification of two new Cw alleles - implications for epitope recognition Human Immunology. 63: S37. DOI: 10.1016/S0198-8859(02)00540-2  0.01
2000 Gill K, Boyle A, Lake K, Desaulniers N. Alcohol-induced locomotor activation in C57BL/6J, A/J, and AXB/BXA recombinant inbred mice: strain distribution patterns and quantitative trait loci analysis. Psychopharmacology. 150: 412-21. PMID 10958083 DOI: 10.1007/s002130000458  0.01
1999 Tanvir NR, Boyle A. Photometry of 40 Large Magellanic Cloud Cepheids Monthly Notices of the Royal Astronomical Society. 304: 957-960. DOI: 10.1046/J.1365-8711.1999.02387.X  0.01
1997 Allanson DR, Rowe WB, Chen X, Boyle A. Automatic dwell control in computer numerical control plunge grinding Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture. 211: 565-575. DOI: 10.1243/0954405971516518  0.01
1997 Boyle A, Bryon D, Paul C. Computer-based learning and assessment: A palaeontological case study with outcomes and implications Computers & Geosciences. 23: 573-580. DOI: 10.1016/S0098-3004(97)00025-3  0.01
1994 Keller SA, Jones JM, Boyle A, Barrow LL, Killen PD, Green DG, Kapousta NV, Hitchcock PF, Swank RT, Meisler MH. Kidney and retinal defects (Krd), a transgene-induced mutation with a deletion of mouse chromosome 19 that includes the Pax2 locus. Genomics. 23: 309-20. PMID 7835879 DOI: 10.1006/geno.1994.1506  0.01
1994 Boyle A. Polymer chain packing analysis using molecular modeling Journal of Molecular Graphics. 12: 219-225. PMID 7819163 DOI: 10.1016/0263-7855(94)80091-X  0.01
1991 Grifo JA, Boyle A, Fischer E, Lavy G, DeCherney AH, Ward DC, Sanyal MK. Preembryo biopsy and analysis of blastomeres by in situ hybridization. American Journal of Obstetrics and Gynecology. 163: 2013-9. PMID 2256514 DOI: 10.1016/0002-9378(90)90789-A  0.01
1991 Boyle AP. Simultaneous solution of geobarometers and geothermometers using a microcomputer spreadsheet Computers and Geosciences. 17: 1473-1479. DOI: 10.1016/0098-3004(91)90008-2  0.01
1988 Rowe W, Pettit J, Boyle A, Moruzzi J. Avoidance of Thermal Damage in Grinding and Prediction of the Damage Threshold Cirp Annals. 37: 327-330. DOI: 10.1016/S0007-8506(07)61646-1  0.01
1987 Boyle AP, McCarthy PM, Stewart D. Geochemical control of saxicolous lichen communities on the creggaun gabbro, Letterfrack, Co. Galway, Western ireland The Lichenologist. 19: 307-317. DOI: 10.1017/S0024282987000276  0.01
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