Fereydoun Hormozdiari

Fereydoun Hormozdiari

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Fereydoun Hormozdiari

Fereydoun Hormozdiari

Publications by authors named "Fereydoun Hormozdiari"

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46Publications

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Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants.

Bioinformatics 2019 Oct 4. Epub 2019 Oct 4.

Institute for Computational Biomedicine, Englander Institute for Precision Medicine, The Meyer Cancer Center, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz737DOI Listing
October 2019

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants.

iScience 2019 Aug 23;18:28-36. Epub 2019 Jul 23.

Genome Center, University of California, Davis, USA; MIND Institute, University of California, Davis, USA; Biochemistry and Molecular Medicine, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.07.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6682328PMC
August 2019

Discovery of tandem and interspersed segmental duplications using high throughput sequencing.

Bioinformatics 2019 Apr 1. Epub 2019 Apr 1.

UC-Davis Genome Center, University of California, Davis, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz237DOI Listing
April 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

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

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

TAD fusion score: discovery and ranking the contribution of deletions to genome structure.

Genome Biol 2019 03 21;20(1):60. Epub 2019 Mar 21.

Genome Center, UC Davis, Davis, USA.

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http://dx.doi.org/10.1186/s13059-019-1666-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427865PMC
March 2019

Combinatorial Approach for Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders.

Genetics 2018 12 8;210(4):1483-1495. Epub 2018 Oct 8.

Genome Center, University of California, Davis, California 95616

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http://www.genetics.org/lookup/doi/10.1534/genetics.118.3012
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http://dx.doi.org/10.1534/genetics.118.301280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283174PMC
December 2018

Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii.

Parasit Vectors 2018 04 4;11(1):225. Epub 2018 Apr 4.

Department of Pathology, Microbiology, and Immunology, UC Davis, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1186/s13071-018-2817-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885317PMC
April 2018

Toolkit for automated and rapid discovery of structural variants.

Methods 2017 10 2;129:3-7. Epub 2017 Jun 2.

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

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http://dx.doi.org/10.1016/j.ymeth.2017.05.030DOI Listing
October 2017

Genomic Patterns of De Novo Mutation in Simplex Autism.

Cell 2017 Oct 28;171(3):710-722.e12. Epub 2017 Sep 28.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.08.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679715PMC
October 2017

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

The discovery of integrated gene networks for autism and related disorders.

Genome Res 2015 Jan 5;25(1):142-54. Epub 2014 Nov 5.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.178855.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317170PMC
January 2015

Resolving the complexity of the human genome using single-molecule sequencing.

Nature 2015 Jan 10;517(7536):608-11. Epub 2014 Nov 10.

1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.

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https://www.nature.com/articles/nature13907.pdf
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254/
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http://www.nature.com/articles/nature13907
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http://dx.doi.org/10.1038/nature13907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254PMC
January 2015

Great ape genetic diversity and population history.

Nature 2013 Jul 3;499(7459):471-5. Epub 2013 Jul 3.

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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http://dx.doi.org/10.1038/nature12228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165PMC
July 2013

Simultaneous structural variation discovery among multiple paired-end sequenced genomes.

Genome Res 2011 Dec 2;21(12):2203-12. Epub 2011 Nov 2.

School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

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http://dx.doi.org/10.1101/gr.120501.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227108PMC
December 2011

Alu repeat discovery and characterization within human genomes.

Genome Res 2011 Jun 3;21(6):840-9. Epub 2010 Dec 3.

School of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.

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http://dx.doi.org/10.1101/gr.115956.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106317PMC
June 2011

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

Bioinformatics 2011 Jun 9;27(11):1481-8. Epub 2011 Apr 9.

School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btr184DOI Listing
June 2011

Protein-protein interaction network evaluation for identifying potential drug targets.

J Comput Biol 2010 May;17(5):669-84

School of Computing Science, Simon Fraser University, Burnaby, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0032DOI Listing
May 2010

Towards improved assessment of functional similarity in large-scale screens: a study on indel length.

J Comput Biol 2010 Jan;17(1):1-20

School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.

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http://dx.doi.org/10.1089/cmb.2009.0031DOI Listing
January 2010

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

Genome Res 2009 Jul 15;19(7):1270-8. Epub 2009 May 15.

School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.

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http://dx.doi.org/10.1101/gr.088633.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704429PMC
July 2009

Biomolecular network motif counting and discovery by color coding.

Bioinformatics 2008 Jul;24(13):i241-9

School of Mathematical Sciences, Tel Aviv University, Ramat Aviv, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btn163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718641PMC
July 2008

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.

Bioinformatics 2008 Jul;24(13):i32-40

Lab for Computational Biology, Simon Fraser University, Burnaby, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btn173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718651PMC
July 2008

Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.

PLoS Comput Biol 2007 Jul;3(7):e118

School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.0030118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913096PMC
July 2007

Relationship between insertion/deletion (indel) frequency of proteins and essentiality.

BMC Bioinformatics 2007 Jun 28;8:227. Epub 2007 Jun 28.

CIHR/MSFHR Strategic Training Program in Bioinformatics, Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/1471-2105-8-227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1925122PMC
June 2007