Joanne Berghout

Joanne Berghout

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Joanne Berghout

Joanne Berghout

Publications by authors named "Joanne Berghout"

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Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms.

Pac Symp Biocomput 2019 ;24:308-319

Center for Biomedical Informatics and Biostatistics (CB2), The University of Arizona, Tucson, AZ 85721, USA2Department of Medicine COM-T, The University of Arizona, Tucson, AZ 85721, USA†Authors contributed equally to this work,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425966PMC
January 2020

Workshop during the Pacific Symposium of Biocomputing, Jan 3-7, 2019: Reading between the genes: interpreting non-coding DNA in high-throughput.

Pac Symp Biocomput 2019 ;24:444-448

Center for Biomedical Informatics and Biostatistics, Dept. of Medicine, University of Arizona, 1230 Cherry Ave, Tucson, AZ 85719, USA†all workshop co-chairs contributed equally, and are listed alphabetically,

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January 2020

Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine.

BMC Med Genomics 2019 07 11;12(Suppl 5):96. Epub 2019 Jul 11.

The Center for Biomedical Informatics & Biostatistics of the University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA.

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http://dx.doi.org/10.1186/s12920-019-0513-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624180PMC
July 2019

Single subject transcriptome analysis to identify functionally signed gene set or pathway activity.

Pac Symp Biocomput 2018 ;23:400-411

Center for Biomedical Informatics and Biostatistics (CB2) & The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85721, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5730358PMC
August 2018

Reading Between the Genes: Computational Models to Discover Function from Noncoding DNA.

Pac Symp Biocomput 2018 ;23:507-511

Center for Biomedical Informatics and Biostatistics, The Center for Applied Genetic and Genomic Medicine, BIO5 Institute, UA Cancer Center, and Dept of Medicine; University of Arizona 1657 E Helen St, Tucson, AZ 85719, USA,

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August 2018

N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.

BMC Med Genomics 2017 05 24;10(Suppl 1):27. Epub 2017 May 24.

Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, 85721, USA.

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http://dx.doi.org/10.1186/s12920-017-0263-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461551PMC
May 2017

kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects.

J Biomed Inform 2017 02 19;66:32-41. Epub 2016 Dec 19.

Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA; University of Arizona Cancer Center, The University of Arizona, Tucson, AZ 85721, USA; Institute for Genomics and Systems Biology, The University of Chicago, IL 60637, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316373PMC
February 2017

Analysis of protein-coding genetic variation in 60,706 humans.

Nature 2016 08;536(7616):285-91

Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://www.nature.com/articles/nature19057
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http://dx.doi.org/10.1038/nature19057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207PMC
August 2016

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions.

NPJ Genom Med 2016;1. Epub 2016 Apr 27.

BIO5 institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Illinois at Chicago, IL, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Center for Biomedical Informatics, Department of Medicine, University of Chicago, IL, USA; Computation Institute, Argonne National Laboratory and University of Chicago, IL, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory & University of Chicago, IL, USA; University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA; Section for Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, USA; Department of Biopharmaceutical Sciences, University of Illinois at Chicago, IL, USA.

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http://dx.doi.org/10.1038/npjgenmed.2016.6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966659PMC
April 2016

THEMIS is required for pathogenesis of cerebral malaria and protection against pulmonary tuberculosis.

Infect Immun 2015 Feb 1;83(2):759-68. Epub 2014 Dec 1.

Department of Human Genetics, McGill University, Montreal, QC, Canada Complex Traits Group, McGill University, Montreal, QC, Canada Department of Biochemistry, McGill University, Montreal, QC, Canada

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http://dx.doi.org/10.1128/IAI.02586-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4294254PMC
February 2015

CCDC88B is a novel regulator of maturation and effector functions of T cells during pathological inflammation.

J Exp Med 2014 Dec 17;211(13):2519-35. Epub 2014 Nov 17.

Department of Biochemistry, Department of Human Genetics, McGill and Genome Quebec Innovation Center, Complex Traits Group, McGill University, Montreal, Quebec H3A 0G4, Canada Department of Biochemistry, Department of Human Genetics, McGill and Genome Quebec Innovation Center, Complex Traits Group, McGill University, Montreal, Quebec H3A 0G4, Canada Department of Biochemistry, Department of Human Genetics, McGill and Genome Quebec Innovation Center, Complex Traits Group, McGill University, Montreal, Quebec H3A 0G4, Canada

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http://dx.doi.org/10.1084/jem.20140455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267237PMC
December 2014

Irf8-regulated genomic responses drive pathological inflammation during cerebral malaria.

PLoS Pathog 2013 11;9(7):e1003491. Epub 2013 Jul 11.

Department of Biochemistry and Complex Traits Group, McGill University, Montreal, Quebec, Canada.

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http://dx.doi.org/10.1371/journal.ppat.1003491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708918PMC
February 2014

Evidence for additive and interaction effects of host genotype and infection in malaria.

Proc Natl Acad Sci U S A 2012 Oct 4;109(42):16786-93. Epub 2012 Sep 4.

Mother and Child University Hospital Center (CHU) Sainte-Justine, Université de Montréal, Montréal, QC, Canada H3T 1C5.

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http://dx.doi.org/10.1073/pnas.1204945109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479498PMC
October 2012

Host resistance to malaria: using mouse models to explore the host response.

Mamm Genome 2011 Feb 30;22(1-2):32-42. Epub 2010 Nov 30.

Menzies Research Institute, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia.

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http://link.springer.com/10.1007/s00335-010-9302-6
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http://dx.doi.org/10.1007/s00335-010-9302-6DOI Listing
February 2011

Genetic and genomic analyses of host-pathogen interactions in malaria.

Trends Parasitol 2009 Sep 31;25(9):417-22. Epub 2009 Aug 31.

Department of Biochemistry, and Complex Traits Program, McGill University, Montreal, Canada.

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http://dx.doi.org/10.1016/j.pt.2009.05.012DOI Listing
September 2009

Spread and persistence of a rugulosin-producing endophyte in Picea glauca seedlings.

Mycol Res 2008 Jun 3;112(Pt 6):731-6. Epub 2008 Feb 3.

Ottawa-Carleton Institute of Chemistry, Carleton University, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1016/j.mycres.2008.01.007DOI Listing
June 2008

C5 deficiency and C5a or C5aR blockade protects against cerebral malaria.

J Exp Med 2008 May 21;205(5):1133-43. Epub 2008 Apr 21.

Tropical Disease Unit, Department of Medicine, McLaughlin-Rotman Centre for Global Health, Toronto General Hospital, Toronto, Ontario M5G 2C4, Canada.

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http://dx.doi.org/10.1084/jem.20072248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373845PMC
May 2008

Cardiac failure in C5-deficient A/J mice after Candida albicans infection.

Infect Immun 2006 Aug;74(8):4439-51

Biotechnology Research Institute, National Research Council, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2.

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http://dx.doi.org/10.1128/IAI.00159-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539620PMC
August 2006

Modification of the Limulus amebocyte lysate assay for the analysis of glucan in indoor environments.

Anal Bioanal Chem 2004 May 24;379(1):156-62. Epub 2004 Mar 24.

Ottawa Carleton Institute of Chemistry, Carleton University, K1S 5B6, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1007/s00216-004-2583-4DOI Listing
May 2004