M. Allen

发表

Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs

R. Dowell, Joseph F Cardiello, Gilson J Sanchez, 2019, Transcription.

Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications.

Jeremy R. Jacobsen, A. Shilatifard, Christopher C. Ebmeier, 2017, Cell reports.

Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease

Robin D. Dowell, Sara L. Sawyer, Mary A. Allen, 2019, PSB.

RNA Pol II transcription model and interpretation of GRO-seq data

R. Dowell, Joseph Azofeifa, M. Lladser, 2016, Journal of Mathematical Biology.

Detecting Differential Transcription Factor Activity from ATAC-Seq Data

Ignacio J. Tripodi, R. Dowell, M. Allen, 2018, bioRxiv.

Extracellular matrix stiffness controls cardiac valve myofibroblast activation through epigenetic remodeling

Brian A. Aguado, L. Leinwand, K. Anseth, 2022, Bioengineering & translational medicine.

Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties

G. Besra, C. Lowry, R. Dowell, 2019, Psychopharmacology.

RNA Pol II transcription model and interpretation of GRO-seq data

R. Dowell, Joseph Azofeifa, M. Lladser, 2016, Journal of Mathematical Biology.

Characterization of Global Gene Expression, Regulation of Metal Ions, and Infection Outcomes in Immune-Competent 129S6 Mouse Macrophages

A. Palmer, R. Dowell, M. Allen, 2021, Infection and immunity.

Infection of immune competent macrophages expressing functional Slc11a1 alters global gene expression, regulation of metal ions, and infection outcomes

A. Palmer, R. Dowell, M. Allen, 2021, bioRxiv.

Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries

Jacob T. Stanley, Rutendo F. Sigauke, R. Dowell, 2021, BMC Genomics.

Nuclear mechanosensing drives chromatin remodelling in persistently activated fibroblasts

Brian A. Aguado, L. Leinwand, K. Anseth, 2021, Nature Biomedical Engineering.

Genes involved in pre-mRNA 3′-end formation and transcription termination revealed by a lin-15 operon Muv suppressor screen

Min Han, M. Allen, M. Macmorris, 2008, Proceedings of the National Academy of Sciences.

Heat Shock in C. elegans Induces Downstream of Gene Transcription andAccumulation of Double-Stranded RNA

C. Link, R. Dowell, Joseph M Cabral, 2018, bioRxiv.

Myonuclear maturation dynamics in aged and adult regenerating mouse skeletal muscle

Jesse V. Kurland, R. Dowell, B. Olwin, 2021, bioRxiv.

The Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom.

A. Gooding, R. Batey, S. Gilbert, 2008, RNA.

RNA processing events affecting C. elegans operons: A computational and mutational analysis

M. Allen, 2010 .

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

R. Dowell, J. Espinosa, H. Mellert, 2014, eLife.

HIF1A Employs CDK8-Mediator to Stimulate RNAPII Elongation in Response to Hypoxia

Henry W. Long, W. Hahn, R. Dowell, 2013, Cell.

A global analysis of C. elegans trans-splicing.

L. Hillier, R. Waterston, T. Blumenthal, 2011, Genome research.

Enhancer RNA profiling predicts transcription factor activity

T. Read, R. Dowell, Joseph Azofeifa, 2018, Genome research.

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq

Manuel E. Lladser, Robin D. Dowell, Joseph Azofeifa, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

A. Gerber, R. Dowell, M. Pufall, 2019, Genome Research.

FStitch: a fast and simple algorithm for detecting nascent RNA transcripts

Manuel E. Lladser, Robin D. Dowell, Joseph Azofeifa, 2014, BCB.

Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing.

T. Blumenthal, M. Allen, Erika L. Lasda, 2010, Genes & development.

Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA

C. Link, R. Dowell, Joseph M Cabral, 2018, bioRxiv.

Characterizing Primary transcriptional responses to short term heat shock in paired fraternal lymphoblastoid lines with and without Down syndrome

R. Dowell, M. Allen, Joseph F. Cardiello, 2023, bioRxiv.

transcriptome C . elegans of the descriptionCircLigase-based capture yields a refined and extended Multimodal RNA-seq using single-strand , double-strand , and Material Supplemental

Arun K. Ramani, Ayelet T. Lamm, John A. Calarco, 2011 .

RNA binding by the glucocorticoid receptor attenuates dexamethasone-induced gene activation

S. Spencer, R. Batey, D. Wuttke, 2023, Scientific reports.

Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome

D. Taatjes, R. Dowell, D. Bentley, 2023, bioRxiv.

Transcription dosage compensation does not occur in Down syndrome

R. Dowell, M. Allen, Justin A. Freeman, 2023, bioRxiv.

Aging disrupts gene expression timing during muscle regeneration

R. Dowell, B. Olwin, N. Betta, 2023, Stem Cell Reports.

Quantification of transcriptome changes to investigate the role of glucocorticoid receptor-RNA binding during dexamethasone treatment

R. Batey, M. Allen, D. S. Wuttke, 2023, BMC Research Notes.