Works matching AU Dowell, Robin A

Results: 50

Phase II trial of brain MRI surveillance in stage IV breast cancer.

Published in:

Neuro-Oncology, 2025, v. 27, n. 6, p. 1550, doi. 10.1093/neuonc/noaf018

By:

Ahmed, Kamran A;
Kim, Youngchul;
Armaghani, Avan J;
Arrington, John A;
Costa, Ricardo L;
Czerniecki, Brian J;
Diaz, Roberto;
Dowell, Robin A;
Extermann, Martine;
Forsyth, Peter A;
Lee, Kimberley T;
Loftus, Loretta;
Mills, Matthew N;
Phuoc, Vania H;
Rosa, Marilin;
Soliman, Hatem H;
Sam, Christine S;
Washington, Iman R;
Soyano, Aixa E;
Han, Hyo S

Publication type:

Article

The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation.

Published in:

PLoS Biology, 2021, v. 19, n. 8, p. 1, doi. 10.1371/journal.pbio.3001364

By:

Levandowski, Cecilia B.;
Jones, Taylor;
Gruca, Margaret;
Ramamoorthy, Sivapriya;
Dowell, Robin D.;
Taatjes, Dylan J.

Publication type:

Article

Detecting Differential Transcription Factor Activity from ATAC-Seq Data.

Published in:

Molecules, 2018, v. 23, n. 5, p. 1136, doi. 10.3390/molecules23051136

By:

Tripodi, Ignacio J.;
Allen, Mary A.;
Dowell, Robin D.;
Sanda, Takaomi

Publication type:

Article

A generative model for the behavior of RNA polymerase.

Published in:

Bioinformatics, 2017, v. 33, n. 2, p. 227, doi. 10.1093/bioinformatics/btw599

By:

Azofeifa, Joseph G.;
Dowell, Robin D.

Publication type:

Article

Extracellular matrix stiffness controls cardiac valve myofibroblast activation through epigenetic remodeling.

Published in:

Bioengineering & Translational Medicine, 2022, v. 7, n. 3, p. 1, doi. 10.1002/btm2.10394

By:

Walker, Cierra J.;
Batan, Dilara;
Bishop, Carrie T.;
Ramirez, Daniel;
Aguado, Brian A.;
Schroeder, Megan E.;
Crocini, Claudia;
Schwisow, Jessica;
Moulton, Karen;
Macdougall, Laura;
Weiss, Robert M.;
Allen, Mary A.;
Dowell, Robin;
Leinwand, Leslie A.;
Anseth, Kristi S.

Publication type:

Article

The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-50402-0

By:

Much, Christian;
Lasda, Erika L.;
Pereira, Isabela T.;
Vallery, Tenaya K.;
Ramirez, Daniel;
Lewandowski, Jordan P.;
Dowell, Robin D.;
Smallegan, Michael J.;
Rinn, John L.

Publication type:

Article

An intronic LINE-1 regulates IFNAR1 expression in human immune cells.

Published in:

Mobile DNA, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s13100-023-00308-3

By:

Buttler, Carmen A.;
Ramirez, Daniel;
Dowell, Robin D.;
Chuong, Edward B.

Publication type:

Article

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

Published in:

PLoS ONE, 2019, v. 14, n. 4, p. 1, doi. 10.1371/journal.pone.0206715

By:

Melnick, Marko;
Gonzales, Patrick;
Cabral, Joseph;
Allen, Mary A.;
Dowell, Robin D.;
Link, Christopher D.

Publication type:

Article

Genome characterization of the selected long- and short-sleep mouse lines.

Published in:

Mammalian Genome, 2016, v. 27, n. 11/12, p. 574, doi. 10.1007/s00335-016-9663-6

By:

Dowell, Robin;
Richmond, Phillip;
Odell, Aaron;
Malmer, Daniel;
Halper-Stromberg, Eitan;
Leach, Sonia;
Bennett, Beth;
Larson, Colin;
Radcliffe, Richard

Publication type:

Article

Metabolic and Transcriptomic Effects of Mediator Kinase Inhibition on the Interferon Response in Down Syndrome.

Published in:

FASEB Journal, 2022, v. 36, p. N.PAG, doi. 10.1096/fasebj.2022.36.S1.L7645

By:

Cozzolino, Kira A.;
Jones, Taylor;
Ajit, Deepa;
Dowell, Robin;
Taatjes, Dylan

Publication type:

Article

Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

Published in:

BMC Genomics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12864-025-11568-z

By:

Sigauke, Rutendo F.;
Sanford, Lynn;
Maas, Zachary L.;
Jones, Taylor;
Stanley, Jacob T.;
Townsend, Hope A.;
Allen, Mary A.;
Dowell, Robin D.

Publication type:

Article

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

Published in:

BMC Bioinformatics, 2004, v. 5, p. 71, doi. 10.1186/1471-2105-5-71

By:

Dowell, Robin D.;
Eddy, Sean R.

Publication type:

Article

The Distributed Annotation System.

Published in:

BMC Bioinformatics, 2001, v. 2, p. 7, doi. 10.1186/1471-2105-2-7

By:

Dowell, Robin D.;
Jokerst, Rodney M;
Day, Allen;
Eddy, Sean R.;
Stein, Lincoln

Publication type:

Article

A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity.

Published in:

PLoS Genetics, 2016, v. 12, n. 1, p. 1, doi. 10.1371/journal.pgen.1005746

By:

Read, Timothy;
Richmond, Phillip A.;
Dowell, Robin D.

Publication type:

Article

A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response.

Published in:

Molecular & Cellular Biology, 2017, v. 37, n. 13, p. 1, doi. 10.1128/MCB.00626-16

By:

Audetat, K. Audrey;
Galbraith, Matthew D.;
Odell, Aaron T.;
Lee, Thomas;
Pandey, Ahwan;
Espinosa, Joaquin M.;
Dowell, Robin D.;
Taatjesa, Dylan J.

Publication type:

Article

Single cell analysis of transcriptome and open chromatin reveals the dynamics of hair follicle stem cell aging.

Published in:

Frontiers in Aging, 2023, p. 1, doi. 10.3389/fragi.2023.1192149

By:

Chi Zhang;
Dongmei Wang;
Dowell, Robin;
Rui Yi

Publication type:

Article

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

Published in:

Transcription (2154-1264), 2020, v. 11, n. 1, p. 3, doi. 10.1080/21541264.2019.1704128

By:

Cardiello, Joseph F.;
Sanchez, Gilson J.;
Allen, Mary A.;
Dowell, Robin D.

Publication type:

Article

miR-MaGiC improves quantification accuracy for small RNA-seq.

Published in:

BMC Research Notes, 2018, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13104-018-3418-2

By:

Russell, Pamela H.;
Vestal, Brian;
Shi, Wen;
Rudra, Pratyaydipta D.;
Dowell, Robin;
Radcliffe, Richard;
Saba, Laura;
Kechris, Katerina

Publication type:

Article

Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance.

Published in:

PLoS ONE, 2020, v. 15, n. 10, p. 1, doi. 10.1371/journal.pone.0240253

By:

Radcliffe, Richard A.;
Dowell, Robin;
Odell, Aaron T.;
Richmond, Phillip A.;
Bennett, Beth;
Larson, Colin;
Kechris, Katerina;
Saba, Laura M.;
Rudra, Pratyaydipta;
Wen, Shi

Publication type:

Article

Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data.

Published in:

PLoS ONE, 2020, v. 15, n. 4, p. 1, doi. 10.1371/journal.pone.0232332

By:

Tripodi, Ignacio J.;
Chowdhury, Murad;
Gruca, Margaret;
Dowell, Robin D.

Publication type:

Article

Determination of steady-state transcriptome modifications associated with repeated homotypic stress in the rat rostral posterior hypothalamic region.

Published in:

Frontiers in Neuroscience, 2023, p. 01, doi. 10.3389/fnins.2023.1173699

By:

Campeau, Serge;
McNulty, Connor;
Stanley, Jacob T.;
Gerber, Anthony N.;
Sasse, Sarah K.;
Dowell, Robin D.

Publication type:

Article

Tissue-specific transcriptional regulation has diverged significantly between human and mouse.

Published in:

Nature Genetics, 2007, v. 39, n. 6, p. 730, doi. 10.1038/ng2047

By:

Odom, Duncan T.;
Dowell, Robin D.;
Jacobsen, Elizabeth S.;
Gordon, William;
Danford, Timothy W.;
MacIsaac, Kenzie D.;
Rolfe, P. Alexander;
Conboy, Caitlin M.;
Gifford, David K.;
Fraenkel, Ernest

Publication type:

Article

Internal and external normalization of nascent RNA sequencing run-on experiments.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-023-05607-3

By:

Maas, Zachary L.;
Dowell, Robin D.

Publication type:

Article

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

Published in:

Journal of Mathematical Biology, 2017, v. 74, n. 1/2, p. 77, doi. 10.1007/s00285-016-1014-4

By:

Lladser, Manuel;
Azofeifa, Joseph;
Allen, Mary;
Dowell, Robin

Publication type:

Article

LIET model: capturing the kinetics of RNA polymerase from loading to termination Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf246

By:

Stanley, Jacob T;
Barone, Georgia E F;
Townsend, Hope A;
Sigauke, Rutendo F;
Allen, Mary A;
Dowell, Robin D

Publication type:

Article

Enhancer RNA transcription pinpoints functional genetic variants linked to asthma.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-57693-x

By:

Sasse, Sarah K.;
Dahlin, Amber;
Sanford, Lynn;
Gruca, Margaret A.;
Gupta, Arnav;
Gally, Fabienne;
Wu, Ann Chen;
Iribarren, Carlos;
Dowell, Robin D.;
Weiss, Scott T.;
Gerber, Anthony N.

Publication type:

Article

Survey of cryptic unstable transcripts in yeast.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2622-5

By:

Vera, Jessica M.;
Dowell, Robin D.

Publication type:

Article

Model based heritability scores for high-throughput sequencing data.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1539-6

By:

Rudra, Pratyaydipta;
Shi, W. Jenny;
Vestal, Brian;
Russell, Pamela H.;
Odell, Aaron;
Dowell, Robin D.;
Radcliffe, Richard A.;
Saba, Laura M.;
Kechris, Katerina

Publication type:

Article

Retrospective Reflections of a Whistleblower: Opinions on Misconduct Responses.

Published in:

Accountability in Research: Policies & Quality Assurance, 2013, v. 20, n. 5/6, p. 339, doi. 10.1080/08989621.2013.822249

By:

Allen, Mary;
Dowell, Robin

Publication type:

Article

Correction: Discriminating between HuR and TTP binding sites using the k-spectrum kernel method.

Published in:

2017

By:

Bhandare, Shweta;
Goldberg, Debra S.;
Dowell, Robin

Publication type:

Correction Notice

Discriminating between HuR and TTP binding sites using the k-spectrum kernel method.

Published in:

PLoS ONE, 2017, v. 12, n. 3, p. 1, doi. 10.1371/journal.pone.0174052

By:

Bhandare, Shweta;
Goldberg, Debra S.;
Dowell, Robin

Publication type:

Article

Automated Discovery of Functional Generality of Human Gene Expression Programs.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 8, p. 1426, doi. 10.1371/journal.pcbi.0030148

By:

Gerber, Georg K.;
Dowell, Robin D.;
Jaakkola, Tommi S.;
Gifford, David K.

Publication type:

Article

TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.

Published in:

Genome Biology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s13059-025-03545-2

By:

Jones, Taylor;
Sigauke, Rutendo F.;
Sanford, Lynn;
Taatjes, Dylan J.;
Allen, Mary A.;
Dowell, Robin D.

Publication type:

Article

Transcription dosage compensation does not occur in Down syndrome.

Published in:

BMC Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1186/s12915-023-01700-4

By:

Hunter, Samuel;
Hendrix, Jo;
Freeman, Justin;
Dowell, Robin D.;
Allen, Mary A.

Publication type:

Article

Core transcriptional regulatory circuitry in human hepatocytes.

Published in:

Molecular Systems Biology, 2006, v. 2, n. 1, p. E1, doi. 10.1038/msb4100059

By:

Odom, Duncan T;
Dowell, Robin D;
Jacobsen, Elizabeth S;
Nekludova, Lena;
Rolfe, P Alexander;
Danford, Timothy W;
Gifford, David K;
Fraenkel, Ernest;
Bell, Graeme I;
Young, Richard A

Publication type:

Article

The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 10, p. 2690, doi. 10.1093/molbev/msx205

By:

Scott, Amber L.;
Richmond, Phillip A.;
Dowell, Robin D.;
Selmecki, Anna M.

Publication type:

Article

Characterizing primary transcriptional responses to short term heat shock in Down syndrome.

Published in:

PLoS ONE, 2024, v. 19, n. 8, p. 1, doi. 10.1371/journal.pone.0307375

By:

Cardiello, Joseph F.;
Westfall, Jessica;
Dowell, Robin;
Allen, Mary Ann

Publication type:

Article

Polyploidy can drive rapid adaptation in yeast.

Published in:

Nature, 2015, v. 519, n. 7543, p. 349, doi. 10.1038/nature14187

By:

Selmecki, Anna M.;
Maruvka, Yosef E.;
Richmond, Phillip A.;
Guillet, Marie;
Shoresh, Noam;
Sorenson, Amber L.;
De, Subhajyoti;
Kishony, Roy;
Michor, Franziska;
Dowell, Robin;
Pellman, David

Publication type:

Article

DYRK1A in blood and immune function: implications in leukemia, inflammatory disorders, infection and Down syndrome.

Published in:

Frontiers in Cell & Developmental Biology, 2025, p. 1, doi. 10.3389/fcell.2025.1587089

By:

Rozen, Esteban J.;
Dowell, Robin D.;
Allen, Mary A.

Publication type:

Article

Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast.

Published in:

Genetics, 2010, v. 185, n. 2, p. 513, doi. 10.1534/genetics.110.113944

By:

Wolf, Joshua J.;
Dowell, Robin D.;
Mahony, Shaun;
Rabani, Michal;
Gifford, David K.;
Fink, Gerald R.

Publication type:

Article

Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.100197

By:

Cozzolino, Kira A.;
Sanford, Lynn;
Hunter, Samuel;
Molison, Kayla;
Erickson, Benjamin;
Courvan, Meaghan C. S.;
Jones, Taylor;
Ajit, Deepa;
Galbraith, Matthew D.;
Espinosa, Joaquín M.;
Bentley, David;
Allen, Mary Ann;
Dowell, Robin D.;
Taatjes, Dylan J.

Publication type:

Article

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

Published in:

Psychopharmacology, 2019, v. 236, n. 5, p. 1653, doi. 10.1007/s00213-019-05253-9

By:

Smith, David G.;
Martinelli, Roberta;
Besra, Gurdyal S.;
Illarionov, Petr A.;
Szatmari, Istvan;
Brazda, Peter;
Allen, Mary A.;
Xu, Wenqing;
Wang, Xiang;
Nagy, László;
Dowell, Robin D.;
Rook, Graham A. W.;
Rosa Brunet, Laura;
Lowry, Christopher A.

Publication type:

Article

CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-65

By:

Rokicki, Joe;
Knox, David;
Dowell, Robin D.;
Copley, Shelley D.

Publication type:

Article

Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment.

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02153-7

By:

Rubin, Jonathan D.;
Stanley, Jacob T.;
Sigauke, Rutendo F.;
Levandowski, Cecilia B.;
Maas, Zachary L.;
Westfall, Jessica;
Taatjes, Dylan J.;
Dowell, Robin D.

Publication type:

Article

Remodeling of Zn<sup>2+</sup> homeostasis upon differentiation of mammary epithelial cells.

Published in:

Metallomics, 2020, v. 12, n. 3, p. 346, doi. 10.1039/c9mt00301k

By:

Han, Yu;
Sanford, Lynn;
Simpson, David M.;
Dowell, Robin D.;
Palmer, Amy E.

Publication type:

Article

Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines.

Published in:

BMC Research Notes, 2023, v. 16, n. 1, p. 1, doi. 10.1186/s13104-023-06465-1

By:

Ramirez, Daniel;
B. Chuong, Edward;
D. Dowell, Robin

Publication type:

Article

Erratum: High-resolution computational models of genome binding events.

Published in:

2006

By:

Qi, Yuan;
Rolfe, Alex;
MacIsaac, Kenzie D;
Gerber, Georg K;
Pokholok, Dmitry;
Zeitlinger, Julia;
Danford, Timothy;
Dowell, Robin D;
Fraenkel, Ernest;
Jaakkola, Tommi S;
Young, Richard A;
Gifford, David K

Publication type:

Correction Notice

High-resolution computational models of genome binding events.

Published in:

Nature Biotechnology, 2006, v. 24, n. 8, p. 963, doi. 10.1038/nbt1233

By:

Yuan Qi;
Rolfe, Alex;
MacIsaac, Kenzie D.;
Gerber, Georg K.;
Pokholok, Dmitry;
Zeitlinger, Julia;
Danford, Timothy;
Dowell, Robin D.;
Fraenkel, Ernest;
Jaakkola, Tommi S.;
Young, Richard A.;
Gifford, David K.

Publication type:

Article

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

Published in:

BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-022-08352-8

By:

Hunter, Samuel;
Sigauke, Rutendo F.;
Stanley, Jacob T.;
Allen, Mary A.;
Dowell, Robin D.

Publication type:

Article

Evidence for Association Between Low Frequency Variants in CHRNA6/CHRNB3 and Antisocial Drug Dependence.

Published in:

Behavior Genetics, 2016, v. 46, n. 5, p. 693, doi. 10.1007/s10519-016-9792-4

By:

Kamens, Helen;
Corley, Robin;
Richmond, Phillip;
Darlington, Todd;
Dowell, Robin;
Hopfer, Christian;
Stallings, Michael;
Hewitt, John;
Brown, Sandra;
Ehringer, Marissa

Publication type:

Article