Farhad Hormozdiari

Farhad Hormozdiari

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Farhad Hormozdiari

Farhad Hormozdiari

Publications by authors named "Farhad Hormozdiari"

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Extreme Polygenicity of Complex Traits Is Explained by Negative Selection.

Am J Hum Genet 2019 Sep 8;105(3):456-476. Epub 2019 Aug 8.

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6732528PMC
September 2019

Genes with High Network Connectivity Are Enriched for Disease Heritability.

Am J Hum Genet 2019 May;104(5):896-913

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506868PMC
May 2019

Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species.

Am J Hum Genet 2019 Apr 21;104(4):611-624. Epub 2019 Mar 21.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451699PMC
April 2019

Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies.

J Comput Biol 2018 Oct 1. Epub 2018 Oct 1.

1 Department of Computer Science, University of California Los Angeles , Los Angeles, California.

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https://www.liebertpub.com/doi/10.1089/cmb.2018.0139
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http://dx.doi.org/10.1089/cmb.2018.0139DOI Listing
October 2018

Widespread Allelic Heterogeneity in Complex Traits.

Am J Hum Genet 2017 May;100(5):789-802

Department of Computer Science, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420356PMC
May 2017

Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure.

Genetics 2016 Dec 21;204(4):1379-1390. Epub 2016 Oct 21.

Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, California

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http://dx.doi.org/10.1534/genetics.116.189712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161272PMC
December 2016

Colocalization of GWAS and eQTL Signals Detects Target Genes.

Am J Hum Genet 2016 Dec 17;99(6):1245-1260. Epub 2016 Nov 17.

Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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http://www.cell.com/ajhg/pdf/S0002-9297(16)30439-6.pdf
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http://biorxiv.org/content/biorxiv/early/2016/08/29/065037.f
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http://dx.doi.org/10.1016/j.ajhg.2016.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142122PMC
December 2016

Chromosome conformation elucidates regulatory relationships in developing human brain.

Nature 2016 10 19;538(7626):523-527. Epub 2016 Oct 19.

Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1038/nature19847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358922PMC
October 2016

Imputing Phenotypes for Genome-wide Association Studies.

Am J Hum Genet 2016 Jul 9;99(1):89-103. Epub 2016 Jun 9.

Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297163013
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http://dx.doi.org/10.1016/j.ajhg.2016.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005435PMC
July 2016

Using genomic annotations increases statistical power to detect eGenes.

Bioinformatics 2016 06;32(12):i156-i163

Department of Computer Science Department of Human Genetics, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908356PMC
June 2016

Multiple testing correction in linear mixed models.

Genome Biol 2016 Apr 1;17:62. Epub 2016 Apr 1.

Computer Science Department, University of California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1186/s13059-016-0903-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818520PMC
April 2016

Fast and accurate mapping of Complete Genomics reads.

Methods 2015 Jun 22;79-80:3-10. Epub 2014 Oct 22.

Department of Computer Engineering, Bilkent University, Ankara, Turkey. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406782PMC
June 2015

Identification of causal genes for complex traits.

Bioinformatics 2015 Jun;31(12):i206-13

Department of Computer Science, Inter-Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA Department of Computer Science, Inter-Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, 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/btv240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542778PMC
June 2015

A spatial haplotype copying model with applications to genotype imputation.

J Comput Biol 2015 May 19;22(5):451-62. Epub 2014 Dec 19.

1 Department of Computer Science, University of California , Los Angeles, California.

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http://www.liebertpub.com/doi/10.1089/cmb.2014.0151
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http://dx.doi.org/10.1089/cmb.2014.0151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425418PMC
May 2015

Memory efficient assembly of human genome.

J Bioinform Comput Biol 2015 Apr 17;13(2):1550008. Epub 2014 Dec 17.

Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1142/S0219720015500080DOI Listing
April 2015

Identifying causal variants at loci with multiple signals of association.

Genetics 2014 Oct 7;198(2):497-508. Epub 2014 Aug 7.

Department of Computer Science, University of California, Los Angeles, California 90095 Department of Human Genetics, University of California, Los Angeles, California 90095

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http://dx.doi.org/10.1534/genetics.114.167908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196608PMC
October 2014

Integrating functional data to prioritize causal variants in statistical fine-mapping studies.

PLoS Genet 2014 Oct 30;10(10):e1004722. Epub 2014 Oct 30.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214605PMC
October 2014

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

Nucleic Acids Res 2014 Jul 8;42(Web Server issue):W494-500. Epub 2014 May 8.

School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 School of Informatics and Computing, Indiana University, Bloomington, IN, USA, 47405

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http://dx.doi.org/10.1093/nar/gku370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086126PMC
July 2014

Genome-wide association study for age-related hearing loss (AHL) in the mouse: a meta-analysis.

J Assoc Res Otolaryngol 2014 Jun 26;15(3):335-52. Epub 2014 Feb 26.

Department of Cell and Molecular Biology and Genetics, House Research Institute, Los Angeles, CA, USA.

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http://dx.doi.org/10.1007/s10162-014-0443-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010595PMC
June 2014

Allele-specific expression and eQTL analysis in mouse adipose tissue.

BMC Genomics 2014 Jun 13;15:471. Epub 2014 Jun 13.

Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1186/1471-2164-15-471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089026PMC
June 2014

Privacy preserving protocol for detecting genetic relatives using rare variants.

Bioinformatics 2014 Jun;30(12):i204-11

Department of Computer Science, Bioinformatics IDP, Department of Mathematics and Department of Human Genetics, University of California, LA 90095, USADepartment of Computer Science, Bioinformatics IDP, Department of Mathematics and Department of Human Genetics, University of California, LA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058916PMC
June 2014

Transcriptome-wide investigation of genomic imprinting in chicken.

Nucleic Acids Res 2014 Apr 21;42(6):3768-82. Epub 2014 Jan 21.

INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France, ENVT, UMR444 Laboratoire de Génétique Cellulaire, Toulouse F-31076, France, INRA, PEAT Pôle d'Expérimentation Avicole de Tours, Nouzilly F- 37380, France, INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan F-31326, France, INRA, GeT-PlaGe Genotoul, Castanet-Tolosan F-31326, France, INRA, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas F-78350, France, AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas F-78350, France, Department of Computer Sciences, University of California, Los Angeles, CA 90095, USA, INRA, UR83 Recherche Avicoles, Nouzilly F- 37380, France and Agrocampus Ouest, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, Animal Genetics Laboratory, Rennes F-35000, France.

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http://dx.doi.org/10.1093/nar/gkt1390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973300PMC
April 2014

Identifying genetic relatives without compromising privacy.

Genome Res 2014 Apr 10;24(4):664-72. Epub 2014 Mar 10.

Department of Computer Science, University of California, Los Angeles, Los Angeles, California 90095,USA;

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http://dx.doi.org/10.1101/gr.153346.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975065PMC
April 2014

eALPS: estimating abundance levels in pooled sequencing using available genotyping data.

J Comput Biol 2013 Nov 21;20(11):861-77. Epub 2013 Oct 21.

1 The Blavatnik School of Computer Science, Tel-Aviv University , Tel Aviv, Israel .

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http://dx.doi.org/10.1089/cmb.2013.0105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013753PMC
November 2013

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Bioinformatics 2013 Sep 3;29(18):2245-52. Epub 2013 Jul 3.

Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753566PMC
September 2013

Accelerating read mapping with FastHASH.

BMC Genomics 2013 21;14 Suppl 1:S13. Epub 2013 Jan 21.

Depts. of Computer Science and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S1-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549798PMC
August 2013

Limited RNA editing in exons of mouse liver and adipose.

Genetics 2013 Apr 14;193(4):1107-15. Epub 2013 Feb 14.

Agrocampus Ouest, Unité Mixte de Recherche (UMR) 1348 Physiology, Environment and Genetics for the Animal and Livestock Systems (PEGASE), Animal Genetics Laboratory, F-35000 Rennes, France.

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http://dx.doi.org/10.1534/genetics.112.149054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606090PMC
April 2013

CNVeM: copy number variation detection using uncertainty of read mapping.

J Comput Biol 2013 Mar 19;20(3):224-36. Epub 2013 Feb 19.

Computer Science Department, University of California Los Angeles, Los Angeles, CA 90095-1596, USA.

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http://dx.doi.org/10.1089/cmb.2012.0258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590897PMC
March 2013

Assembly of non-unique insertion content using next-generation sequencing.

BMC Bioinformatics 2011 28;12 Suppl 6:S3. Epub 2011 Jul 28.

Department of Computer Science, University of California Los Angeles, CA, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-S6-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194191PMC
December 2011

Sensitive and fast mapping of di-base encoded reads.

Bioinformatics 2011 Jul 17;27(14):1915-21. Epub 2011 May 17.

Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-5065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129524PMC
July 2011

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.

Bioinformatics 2011 Jun 19;27(11):1513-20. Epub 2011 Apr 19.

Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102223PMC
June 2011