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Scientific Reports|June 29, 2019
The ENCODE Blacklist: Identification of Problematic Regions of the GenomeHaley M Amemiya, Anshul Kundaje, Alan P BoyleMicrobiology Resource Announcements|July 31, 2025
Draft de novo genome construction of Scytonema sp. PRP1: identified from single-cell sequencing library preparationPreston Parana, Camille Mumm, Michael J McConnell, et al.Bioinformatics (Oxford, England)|September 12, 2008
F-Seq: a feature density estimator for high-throughput sequence tagsAlan P Boyle, Justin Guinney, Gregory E Crawford, et al.Bioinformatics (Oxford, England)|June 3, 2015
Mango: a bias-correcting ChIA-PET analysis pipelineDouglas H Phanstiel, Alan P Boyle, Nastaran Heidari, et al.Genome Research|September 8, 2012
Linking disease associations with regulatory information in the human genomeMarc A Schaub, Alan P Boyle, Anshul Kundaje, et al.Bioinformatics (Oxford, England)|June 7, 2014
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figuresDouglas H Phanstiel, Alan P Boyle, Carlos L Araya, et al.Genome Biology|February 17, 2010
Evidence-ranked motif identificationStoyan Georgiev, Alan P Boyle, Karthik Jayasurya, et al.Cell|November 19, 2013
Dynamic trans-acting factor colocalization in human cellsDan Xie, Alan P Boyle, Linfeng Wu, et al.Investigative Ophthalmology & Visual Science|April 28, 2006
Extraocular muscle morphogenesis and gene expression are regulated by Pitx2 gene doseAdam G Diehl, Sepideh Zareparsi, Min Qian, et al.Bioinformatics (Oxford, England)|June 12, 2026
SEMPLR: an R package for transcription factor binding predictionGrace E Kenney, Rintsen N Sherpa, Jeremy D Burgess, et al.Pageof 8