Publication

Genome Res. 2018 Feb 15. doi: 10.1101/gr.225755.117. Azofeifa JG 1, 2 , Allen MA 2 , Hendrix JR 1, 3 , Read T 2, 4 , Rubin JD 4 , Dowell RD 1, 2,3 Abstract Transcription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in coordination...

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 . Abstract We present a fast and simple algorithm to detect nascent RNA transcription in...

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 CC 1 , Erickson B 2 , Allen BL 3 , Allen MA 4 , Kim H 2 , Fong N 2 , Jacobsen JR 5 , Liang K 6 , Shilatifard A 6...

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 ME 1 , Azofeifa JG 2 , Allen MA 3 , Dowell RD 4 . Author information Abstract A mixture model and statistical method is proposed to interpret...

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 September; pdf

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 MA 1 , Andrysik Z 2 , Dengler VL 2 , Mellert HS 2 , Guarnieri A 2 , Freeman JA 2 , Sullivan KD 2 , Galbraith MD 2...

Account Res. 2013;20(5-6):339-48. doi: 10.1080/08989621.2013.822249. Retrospective reflections of a whistleblower: opinions on misconduct responses. Allen M 1 , Dowell R . Author information Abstract Almost 10 years ago, when I was in my fourth year of graduate school, my fellow graduate students discovered that our thesis advisor had engaged in...

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 MD 1 , Allen MA , Bensard CL , Wang X , Schwinn MK , Qin B , Long HW , Daniels DL , Hahn WC , Dowell RD , Espinosa JM...

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 M 1 , Pero J , Yang SH , Ermilov AN , Michael LE , Wang A , Wilbert D , Patel...

Allen MA, Hillier LW, Waterston RH, Blumenthal T. Genome research. 2011; 21(2):255-64. PMID: 21177958 PMCID: PMC3032929