publication
Genome Res. 2018 Feb 15. doi: 10.1101/gr.225755.117.Azofeifa JG1,2, Allen MA2, Hendrix JR1,3, Read T2,4, Rubin JD4, Dowell RD1,2,3AbstractTranscription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in
IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1070-1081. doi: 10.1109/TCBB.2016.2520919. Epub 2016 Jan 26.An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.Azofeifa JG, Allen MA, Lladser ME, Dowell RD.
Cell Rep. 2017 Aug 1;20(5):1173-1186. doi: 10.1016/j.celrep.2017.07.021.Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications.Ebmeier CC1, Erickson B2, Allen BL3, Allen MA4, Kim H2, Fong N2, Jacobsen JR5, Liang K6,
J Math Biol. 2017 Jan;74(1-2):77-97. doi: 10.1007/s00285-016-1014-4. Epub 2016 May 3.RNA Pol II transcription model and interpretation of GRO-seq data.Lladser ME1, Azofeifa JG2, Allen MA3, Dowell RD4.Author information AbstractA mixture model
FStitch: A fast and simple algorithm for detecting nascent RNA transcripts.Azofiefa J, Allen M, Lladser M, Dowell R.Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB ’14). 2014
Elife. 2014 May 27;3:e02200. doi: 10.7554/eLife.02200.Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.Allen MA1, Andrysik Z2, Dengler VL2, Mellert HS2, Guarnieri A2, Freeman JA2,
Account Res. 2013;20(5-6):339-48. doi: 10.1080/08989621.2013.822249.Retrospective reflections of a whistleblower: opinions on misconduct responses.Allen M1, Dowell R.Author information AbstractAlmost 10 years ago, when I was in my fourth year
Cell. 2013 Jun 6;153(6):1327-39. doi: 10.1016/j.cell.2013.04.048.HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia.Galbraith MD1, Allen MA, Bensard CL, Wang X, Schwinn MK, Qin B, Long HW, Daniels DL, Hahn WC, Dowell
J Clin Invest. 2011 May;121(5):1768-81. doi: 10.1172/JCI46307. Epub 2011 Apr 25.Basal cell carcinomas in mice arise from hair follicle stem cells and multiple epithelial progenitor populations.Grachtchouk M1, Pero J, Yang SH, Ermilov AN, Michael LE
Allen MA, Hillier LW, Waterston RH, Blumenthal T.Genome research. 2011; 21(2):255-64.PMID:21177958PMCID:PMC3032929