Timothy E Reddy

Timothy E Reddy

UNVERIFIED PROFILE

Are you Timothy E Reddy?   Register this Author

Register author
Timothy E Reddy

Timothy E Reddy

Publications by authors named "Timothy E Reddy"

Are you Timothy E Reddy?   Register this Author

52Publications

1058Reads

33Profile Views

c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program.

J Exp Med 2019 Sep 30. Epub 2019 Sep 30.

Department of Immunology, Duke University Medical Center, Durham, NC

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1084/jem.20191030DOI Listing
September 2019

Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.

Methods Mol Biol 2018 ;1767:447-480

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-7774-1_25DOI Listing
February 2019

Predicting gene structure changes resulting from genetic variants via exon definition features.

Bioinformatics 2018 11;34(21):3616-3623

Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198862PMC
November 2018

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.

Cell Syst 2018 08 18;7(2):146-160.e7. Epub 2018 Jul 18.

University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2018.06.007DOI Listing
August 2018

Clustering gene expression time series data using an infinite Gaussian process mixture model.

PLoS Comput Biol 2018 01 16;14(1):e1005896. Epub 2018 Jan 16.

Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America.

View Article

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.pcbi.1005896
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1005896DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786324PMC
January 2018

A long-range flexible billboard model of gene activation.

Transcription 2017 08 9;8(4):261-267. Epub 2017 Jun 9.

a Department of Biostatistics & Bioinformatics , Duke University , Durham , NC , USA.

View Article

Download full-text PDF

Source
https://www.tandfonline.com/doi/full/10.1080/21541264.2017.1
Publisher Site
http://dx.doi.org/10.1080/21541264.2017.1317694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574526PMC
August 2017

Transversions have larger regulatory effects than transitions.

BMC Genomics 2017 05 19;18(1):394. Epub 2017 May 19.

Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, 27710, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-017-3785-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438547PMC
May 2017

Decoding the role of regulatory element polymorphisms in complex disease.

Curr Opin Genet Dev 2017 Apr 13;43:38-45. Epub 2016 Dec 13.

Department of Biostatistics & Bioinformatics, and Center for Genomic & Computational Biology, Duke University Medical Center, Durham, NC 27710, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gde.2016.10.007DOI Listing
April 2017

HKDC1 Is a Novel Hexokinase Involved in Whole-Body Glucose Use.

Endocrinology 2016 09 26;157(9):3452-61. Epub 2016 Jul 26.

Division of Endocrinology, Metabolism, and Molecular Medicine (A.E.L., C.M.P., M.P., A.R.A., K.S.H., W.L.L., B.T.L.), Department of Pathology (A.L., G.-Y.Y.), Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611; Department of Biostatistics and Bioinformatics (T.E.R.), and Center for Genomic and Computational Biology (C.G., T.E.R.), Duke University Medical School, and University Program in Genetics and Genomics (C.G.), Duke University, Durham, North Carolina 27710; Department of Pathology (X.D.), Loyola University Chicago, Maywood, Illinois 60153; and Jesse Brown Veterans Affairs Medical Center (B.T.L.), Chicago, Illinois 60612.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1210/en.2016-1288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007896PMC
September 2016

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells.

Cell Stem Cell 2016 09 11;19(3):406-14. Epub 2016 Aug 11.

Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2016.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010447PMC
September 2016

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

Cell 2016 Aug;166(5):1269-1281.e19

Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA. Electronic address:

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5046229PMC
http://dx.doi.org/10.1016/j.cell.2016.07.049DOI Listing
August 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Genomic approaches for understanding the genetics of complex disease.

Genome Res 2015 Oct;25(10):1432-41

Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27708, USA.

View Article

Download full-text PDF

Source
http://genome.cshlp.org/content/25/10/1432.full.pdf+html
Web Search
http://genome.cshlp.org/lookup/doi/10.1101/gr.190603.115
Publisher Site
http://dx.doi.org/10.1101/gr.190603.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579328PMC
October 2015

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.

Genome Res 2015 Aug 29;25(8):1158-69. Epub 2015 May 29.

Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA.

View Article

Download full-text PDF

Source
http://genome.cshlp.org/lookup/doi/10.1101/gr.179044.114
Publisher Site
http://dx.doi.org/10.1101/gr.179044.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510000PMC
August 2015

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.

Genome Res 2015 Aug 17;25(8):1206-14. Epub 2015 Jun 17.

Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27710, USA; Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27710, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.190090.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510004PMC
August 2015

From Prescription to Transcription: Genome Sequence as Drug Target.

Cell 2015 Jul;162(1):16-7

Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC 27708, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2015.06.033DOI Listing
July 2015

Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain.

ACS Synth Biol 2015 Jun 31;4(6):689-99. Epub 2014 Dec 31.

§Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/sb500322uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475448PMC
June 2015

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.

Nat Biotechnol 2015 May 6;33(5):510-7. Epub 2015 Apr 6.

1] Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA. [2] Center for Genomic &Computational Biology, Duke University, Durham, North Carolina, USA. [3] Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nbt.3199
Publisher Site
http://dx.doi.org/10.1038/nbt.3199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430400PMC
May 2015

Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.

Mol Ther 2015 Mar 10;23(3):523-32. Epub 2014 Dec 10.

1] Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA [2] Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA [3] Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S15250016163006
Publisher Site
http://dx.doi.org/10.1038/mt.2014.234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351462PMC
March 2015

New insights into gestational glucose metabolism: lessons learned from 21st century approaches.

Diabetes 2015 Feb;64(2):327-34

Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL Jesse Brown Veterans Affairs Medical Center, Chicago, IL

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2337/db14-0877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4876793PMC
February 2015

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1.

Nat Commun 2015 Feb 4;6:6069. Epub 2015 Feb 4.

1] Center for Genomic &Computational Biology, Duke University School of Medicine, Durham, North Carolina 27708, USA [2] Department of Biostatistics &Bioinformatics, Duke University Medical School, Durham, North Carolina 27710, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms7069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4318120PMC
February 2015

Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy.

Nat Commun 2015 Feb 18;6:6244. Epub 2015 Feb 18.

1] Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, North Carolina 27708, USA [2] Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA [3] Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/ncomms7244
Publisher Site
http://dx.doi.org/10.1038/ncomms7244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335351PMC
February 2015

Corrigendum to:Agent-based modeling of the context dependency in T cell recognition.

J Theor Biol 2012 Jun;303:152-3

Center for Blood Research, Harvard Medical School, Boston, MA 02115, USA .

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jtbi.2012.03.018DOI Listing
June 2012

Allele-specific distribution of RNA polymerase II on female X chromosomes.

Hum Mol Genet 2011 Oct 26;20(20):3964-73. Epub 2011 Jul 26.

Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, CIEMAS 2376, 101 Science Drive, Durham, 27708 NC, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/hmg/ddr315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177651PMC
October 2011

Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

PLoS Comput Biol 2007 May 10;3(5):e90. Epub 2007 Apr 10.

Program in Bioinformatics and Systems Biology, Boston University, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.0030090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866359PMC
May 2007

Assessing transcription factor motif drift from noisy decoy sequences.

Genome Inform 2005 ;16(1):59-67

Program in Bioinformatics and Systems Biology, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
January 2006

Agent-based modeling of the context dependency in T cell recognition.

J Theor Biol 2005 Oct;236(4):376-91

Department of Medicine, Stanford University, Palo Alto, CA 94305, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jtbi.2005.03.019DOI Listing
October 2005

Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow.

Genome Inform 2004 ;15(1):221-8

Boston University Bioinformatics Program, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
May 2005