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2020 – today
- 2022
[j9]Sierra S. Nishizaki
, Alan P. Boyle:
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. BMC Bioinform. 23(1): 317 (2022)- 2020
- [j8]Sierra S. Nishizaki, Natalie Ng, Shengcheng Dong, Robert S. Porter, Cody Morterud, Colten Williams, Courtney Asman, Jessica A Switzenberg, Alan P. Boyle:
Predicting the effects of SNPs on transcription factor binding affinity. Bioinform. 36(2): 364-372 (2020) - [j7]Adam Diehl, Alan P. Boyle:
MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony. BMC Bioinform. 21(1): 416 (2020)
2010 – 2019
- 2019
- [j6]Adam Diehl, Alan P. Boyle:
CGIMP: Real-time exploration and covariate projection for self-organizing map datasets. J. Open Source Softw. 4(39): 1520 (2019) - 2017
- [j5]Maxwell T. Spadafore, Kayvan Najarian, Alan P. Boyle:
A proximity-based graph clustering method for the identification and application of transcription factor clusters. BMC Bioinform. 18(1): 530:1-530:14 (2017) - 2015
- [j4]Douglas H. Phanstiel, Alan P. Boyle, Nastaran Heidari, Michael P. Snyder:
Mango: a bias-correcting ChIA-PET analysis pipeline. Bioinform. 31(19): 3092-3098 (2015) - 2014
- [j3]Douglas H. Phanstiel, Alan P. Boyle, Carlos L. Araya, Michael P. Snyder:
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinform. 30(19): 2808-2810 (2014) - [j2]Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder:
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512(7515): 453-456 (2014)
2000 – 2009
- 2008
- [j1]Alan P. Boyle, Justin Guinney, Gregory E. Crawford, Terrence S. Furey:
F-Seq: a feature density estimator for high-throughput sequence tags. Bioinform. 24(21): 2537-2538 (2008)
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