Publications by authors named "Jeffrey H Chuang"

49Publications

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis.

Elife 2020 11 13;9. Epub 2020 Nov 13.

Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, San Diego, United States.

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November 2020

Expression of the Neuronal tRNA n-Tr20 Regulates Synaptic Transmission and Seizure Susceptibility.

Neuron 2020 10 26;108(1):193-208.e9. Epub 2020 Aug 26.

Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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October 2020

pyBedGraph: a python package for fast operations on 1D genomic signal tracks.

Bioinformatics 2020 05;36(10):3234-3235

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.

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May 2020

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms.

Genome Biol 2019 11 25;20(1):251. Epub 2019 Nov 25.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

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November 2019

Longitudinal molecular trajectories of diffuse glioma in adults.

Nature 2019 12 20;576(7785):112-120. Epub 2019 Nov 20.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

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December 2019

Treating Cancer as an Invasive Species.

Mol Cancer Res 2020 01 16;18(1):20-26. Epub 2019 Sep 16.

The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.

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January 2020

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.

PLoS Comput Biol 2019 06 13;15(6):e1007026. Epub 2019 Jun 13.

The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America.

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June 2019

CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer.

BMC Cancer 2019 Jan 21;19(1):96. Epub 2019 Jan 21.

City of Hope Comprehensive Cancer Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA.

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January 2019

Whole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohorts.

PLoS One 2018 3;13(10):e0204912. Epub 2018 Oct 3.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America.

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March 2019

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.

PLoS Comput Biol 2018 03 29;14(3):e1006078. Epub 2018 Mar 29.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America.

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March 2018

Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures.

Nat Genet 2017 08;49(9):1288-1289

The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.

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August 2017

CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens.

Bioinformatics 2017 Oct;33(19):3110-3112

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA.

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October 2017

Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation.

Elife 2016 04 16;5. Epub 2016 Apr 16.

Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States.

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April 2016

Functional chromatin features are associated with structural mutations in cancer.

BMC Genomics 2014 Nov 23;15:1013. Epub 2014 Nov 23.

The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA.

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November 2014

Integrating chemical footprinting data into RNA secondary structure prediction.

PLoS One 2012 16;7(10):e45160. Epub 2012 Oct 16.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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March 2013

Transcriptional enhancers in protein-coding exons of vertebrate developmental genes.

PLoS One 2012 2;7(5):e35202. Epub 2012 May 2.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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September 2012

CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences.

BMC Bioinformatics 2012 Feb 14;13:32. Epub 2012 Feb 14.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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February 2012

Expression divergence measured by transcriptome sequencing of four yeast species.

BMC Genomics 2011 Dec 29;12:635. Epub 2011 Dec 29.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-3961, USA.

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December 2011

A mathematical model for the determination of steady-state cardiolipin remodeling mechanisms using lipidomic data.

PLoS One 2011 10;6(6):e21170. Epub 2011 Jun 10.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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October 2011

A molecular-imprint nanosensor for ultrasensitive detection of proteins.

Nat Nanotechnol 2010 Aug 27;5(8):597-601. Epub 2010 Jun 27.

Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA.

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August 2010

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

Mol Biol Evol 2010 Oct 21;27(10):2322-32. Epub 2010 May 21.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA.

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October 2010

Dynamic simulation of cardiolipin remodeling: greasing the wheels for an interpretative approach to lipidomics.

J Lipid Res 2010 Aug 21;51(8):2153-70. Epub 2010 Apr 21.

Division of Bioorganic Chemistry and Molecular Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA.

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August 2010

COMIT: identification of noncoding motifs under selection in coding sequences.

Genome Biol 2009 20;10(11):R133. Epub 2009 Nov 20.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.

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July 2010

A systematic approach to identify functional motifs within vertebrate developmental enhancers.

Dev Biol 2010 Jan 20;337(2):484-95. Epub 2009 Oct 20.

Department of Biopharmaceutical Sciences, Programs in Biological Sciences and Human Genetics, University of California, San Francisco, CA 94143-2811, USA.

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January 2010

Weak preservation of local neutral substitution rates across mammalian genomes.

BMC Evol Biol 2009 May 5;9:89. Epub 2009 May 5.

Boston College, Department of Biology, Chestnut Hill, MA 02467, USA.

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May 2009

cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation.

Bioinformatics 2008 Oct 20;24(20):2418-9. Epub 2008 Aug 20.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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October 2008

Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects.

BMC Evol Biol 2008 Jun 27;8:186. Epub 2008 Jun 27.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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June 2008

Brain mitochondrial lipid abnormalities in mice susceptible to spontaneous gliomas.

Lipids 2008 Oct 17;43(10):951-9. Epub 2008 Jun 17.

Biology Department, Boston College, Chestnut Hill, MA, USA,

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October 2008

Lipidomic analysis and electron transport chain activities in C57BL/6J mouse brain mitochondria.

J Neurochem 2008 Jul 1;106(1):299-312. Epub 2008 Jul 1.

Biology Department, Boston College, Chestnut Hill, Massachusetts 02467, USA.

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July 2008

Sequences conserved by selection across mouse and human malaria species.

BMC Genomics 2007 Oct 15;8:372. Epub 2007 Oct 15.

Boston College - Department of Biology, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.

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October 2007

Similarity of synonymous substitution rates across mammalian genomes.

J Mol Evol 2007 Sep 3;65(3):236-48. Epub 2007 Aug 3.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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September 2007

Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence.

Genome Res 2005 Feb 14;15(2):205-13. Epub 2005 Jan 14.

Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA.

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February 2005

Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome.

PLoS Biol 2004 Feb 17;2(2):E29. Epub 2004 Feb 17.

Department of Biochemistry and Biophysics, University of California, San Francisco, USA.

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February 2004