Publications by authors named "Kimberly Glass"

60Publications

PUMA: PANDA Using MicroRNA Associations.

Bioinformatics 2020 Jun 17. Epub 2020 Jun 17.

Channing Division of Network Medicine, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa571DOI Listing
June 2020

Involvement of fine particulate matter exposure with gene expression pathways in breast tumor and adjacent-normal breast tissue.

Environ Res 2020 07 15;186:109535. Epub 2020 Apr 15.

Channing Division of Network Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1016/j.envres.2020.109535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368092PMC
July 2020

Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues.

Cell Rep 2020 Jun;31(12):107795

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.107795DOI Listing
June 2020

Using network science tools to identify novel diet patterns in prodromal dementia.

Neurology 2020 05 22;94(19):e2014-e2025. Epub 2020 Apr 22.

From the University of Bordeaux (C.S., S.L.-A., C.H.), Inserm, Bordeaux Population Health Research Center, UMR 1219, France; Channing Division of Network Medicine (A.R.S., F.G., K.G.), Department of Medicine, Brigham and Women's Hospital, Harvard Medical School; and Department of Epidemiology (F.G.), Harvard T.H. Chan School of Public Health, Boston, MA.

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http://dx.doi.org/10.1212/WNL.0000000000009399DOI Listing
May 2020

Genome-Wide Association Study for Urinary and Fecal Incontinence in Women.

J Urol 2020 May 15;203(5):978-983. Epub 2019 Nov 15.

Division of Urogynecology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts.

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http://dx.doi.org/10.1097/JU.0000000000000655DOI Listing
May 2020

lionessR: single sample network inference in R.

BMC Cancer 2019 Oct 25;19(1):1003. Epub 2019 Oct 25.

Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, 02215, USA.

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http://dx.doi.org/10.1186/s12885-019-6235-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6815019PMC
October 2019

TFutils: Data structures for transcription factor bioinformatics.

F1000Res 2019 5;8:152. Epub 2019 Feb 5.

Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.12688/f1000research.17976.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600865PMC
June 2020

Network Medicine in the Age of Biomedical Big Data.

Front Genet 2019 11;10:294. Epub 2019 Apr 11.

Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States.

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http://dx.doi.org/10.3389/fgene.2019.00294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6470635PMC
April 2019

Estimating Sample-Specific Regulatory Networks.

iScience 2019 Apr 28;14:226-240. Epub 2019 Mar 28.

Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.03.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463816PMC
April 2019

Estimating drivers of cell state transitions using gene regulatory network models.

BMC Syst Biol 2017 Dec 13;11(1):139. Epub 2017 Dec 13.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, 02115, MA, USA.

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http://dx.doi.org/10.1186/s12918-017-0517-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729420PMC
December 2017

Understanding Tissue-Specific Gene Regulation.

Cell Rep 2017 Oct;21(4):1077-1088

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828531PMC
October 2017

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

BMC Bioinformatics 2017 Oct 3;18(1):437. Epub 2017 Oct 3.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s12859-017-1847-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627434PMC
October 2017

Regulatory network changes between cell lines and their tissues of origin.

BMC Genomics 2017 Sep 12;18(1):723. Epub 2017 Sep 12.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12864-017-4111-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596945PMC
September 2017

Exploring regulation in tissues with eQTL networks.

Proc Natl Acad Sci U S A 2017 09 29;114(37):E7841-E7850. Epub 2017 Aug 29.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1707375114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604022PMC
September 2017

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma.

J Allergy Clin Immunol 2018 04 20;141(4):1250-1258. Epub 2017 Jul 20.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2017.05.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775928PMC
April 2018

Multi-scale chromatin state annotation using a hierarchical hidden Markov model.

Nat Commun 2017 04 7;8:15011. Epub 2017 Apr 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/ncomms15011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385569PMC
April 2017

Estimating gene regulatory networks with pandaR.

Bioinformatics 2017 Jul;33(14):2232-2234

Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870629PMC
July 2017

PyPanda: a Python package for gene regulatory network reconstruction.

Bioinformatics 2016 11 10;32(21):3363-3365. Epub 2016 Jul 10.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079480PMC
November 2016

Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa.

Genomics 2016 10 11;108(3-4):126-133. Epub 2016 Aug 11.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2016.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121035PMC
October 2016

COPD subtypes identified by network-based clustering of blood gene expression.

Genomics 2016 Mar 8;107(2-3):51-58. Epub 2016 Jan 8.

Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA; Division of General Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2016.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761317PMC
March 2016

Finding New Order in Biological Functions from the Network Structure of Gene Annotations.

PLoS Comput Biol 2015 Nov 20;11(11):e1004565. Epub 2015 Nov 20.

Physics Department, University of Maryland, College Park, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654495PMC
November 2015

A network model for angiogenesis in ovarian cancer.

BMC Bioinformatics 2015 Apr 11;16:115. Epub 2015 Apr 11.

Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12859-015-0551-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408593PMC
April 2015

Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring.

Genome Med 2015 14;7(1):12. Epub 2015 Feb 14.

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA USA ; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA USA.

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http://dx.doi.org/10.1186/s13073-015-0137-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355149PMC
March 2015

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

Mol Cell 2015 Jan 8;57(2):304-316. Epub 2015 Jan 8.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10972765140095
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http://dx.doi.org/10.1016/j.molcel.2014.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305004PMC
January 2015

Sexually-dimorphic targeting of functionally-related genes in COPD.

BMC Syst Biol 2014 Nov 28;8:118. Epub 2014 Nov 28.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12918-014-0118-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269917PMC
November 2014

Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets.

Sci Rep 2014 Feb 26;4:4191. Epub 2014 Feb 26.

1] Department of Physics, University of Maryland, College Park, MD, USA [2] Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA [3] Santa Fe Institute, Santa Fe, NM.

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http://dx.doi.org/10.1038/srep04191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935204PMC
February 2014

Combinatorial recruitment of CREB, C/EBPβ and c-Jun determines activation of promoters upon keratinocyte differentiation.

PLoS One 2013 7;8(11):e78179. Epub 2013 Nov 7.

Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078179PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820678PMC
July 2014

Passing messages between biological networks to refine predicted interactions.

PLoS One 2013 31;8(5):e64832. Epub 2013 May 31.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064832PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669401PMC
January 2014

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis.

Dev Cell 2012 Oct 4;23(4):796-811. Epub 2012 Oct 4.

Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.devcel.2012.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477283PMC
October 2012

Implications of functional similarity for gene regulatory interactions.

J R Soc Interface 2012 Jul 1;9(72):1625-36. Epub 2012 Feb 1.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1098/rsif.2011.0585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367803PMC
July 2012

Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine.

Lab Chip 2012 Jan 5;12(2):376-80. Epub 2011 Dec 5.

McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.

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http://dx.doi.org/10.1039/c1lc20698bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205155PMC
January 2012

Suppression of the C/EBP family of transcription factors in adipose tissue causes lipodystrophy.

J Mol Endocrinol 2011 Jun 15;46(3):175-92. Epub 2011 Apr 15.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Building 37, Room 3128, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1530/JME-10-0172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159190PMC
June 2011

CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes.

Proc Natl Acad Sci U S A 2010 Nov 8;107(47):20311-6. Epub 2010 Nov 8.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Building 37, Room 3128, Bethesda, MD 20892, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1008688107
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http://dx.doi.org/10.1073/pnas.1008688107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996703PMC
November 2010

The relation of humor and child development: social, adaptive, and emotional aspects.

J Child Neurol 2010 Oct 17;25(10):1248-60. Epub 2010 Jun 17.

Michigan State University, East Lansing, MI 48824, USA.

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http://dx.doi.org/10.1177/0883073810373144DOI Listing
October 2010

Comprehension of humor in children with nonverbal learning disabilities, reading disabilities, and without learning disabilities.

Ann Dyslexia 2008 Dec 26;58(2):163-80. Epub 2008 Aug 26.

Michigan State University, East Lansing, MI, USA.

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http://dx.doi.org/10.1007/s11881-008-0016-3DOI Listing
December 2008