Alexej Abyzov

Alexej Abyzov

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Alexej Abyzov

Alexej Abyzov

Publications by authors named "Alexej Abyzov"

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52Publications

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Chromatin organization modulates the origin of heritable structural variations in human genome.

Nucleic Acids Res 2019 Apr;47(6):2766-2777

Mayo Clinic, Department of Health Sciences Research, Center for Individualized Medicine, Rochester, MN 55905, USA.

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http://dx.doi.org/10.1093/nar/gkz103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451188PMC
April 2019

Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants.

Methods Mol Biol 2018 ;1768:173-190

Department of Psychiatry and Behavioral Sciences, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7778-9_11DOI Listing
February 2019

Molecular signatures of multiple myeloma progression through single cell RNA-Seq.

Blood Cancer J 2019 01 3;9(1). Epub 2019 Jan 3.

Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.

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http://dx.doi.org/10.1038/s41408-018-0160-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318319PMC
January 2019

Inferring modes of evolution from colorectal cancer with residual polyp of origin.

Oncotarget 2018 Jan 26;9(6):6780-6792. Epub 2017 Dec 26.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.

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http://www.oncotarget.com/fulltext/23687
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http://dx.doi.org/10.18632/oncotarget.23687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805514PMC
January 2018

Landscape and variation of novel retroduplications in 26 human populations.

PLoS Comput Biol 2017 Jun 29;13(6):e1005567. Epub 2017 Jun 29.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510864PMC
June 2017

Human induced pluripotent stem cells for modelling neurodevelopmental disorders.

Nat Rev Neurol 2017 May 18;13(5):265-278. Epub 2017 Apr 18.

Child Study Center, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/nrneurol.2017.45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5782822PMC
May 2017

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.

BMC Genomics 2017 04 24;18(1):321. Epub 2017 Apr 24.

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94304, USA.

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http://dx.doi.org/10.1186/s12864-017-3658-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402652PMC
April 2017

Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis.

Genome Res 2016 07 23;26(7):874-81. Epub 2016 May 23.

Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.

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http://dx.doi.org/10.1101/gr.205484.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937565PMC
July 2016

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Nat Commun 2016 Apr 18;7:11101. Epub 2016 Apr 18.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/ncomms11101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837449PMC
April 2016

Understanding genome structural variations.

Oncotarget 2016 Feb;7(7):7370-1

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.18632/oncotarget.6485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884923PMC
February 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

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

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.

Cell 2015 Jul;162(2):375-390

Program in Neurodevelopment and Regeneration, Yale University, New Haven, CT 06520, USA; Child Study Center, Yale University, New Haven, CT 06520, USA; Department of Neurobiology, Yale University, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519016PMC
July 2015

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Nat Commun 2015 Jun 1;6:7256. Epub 2015 Jun 1.

1] Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/ncomms8256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451611PMC
June 2015

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Bioinformatics 2015 May 17;31(9):1469-71. Epub 2014 Dec 17.

Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, Department of Statistics, Stanford University, Stanford, CA 94035, USA and Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410653PMC
May 2015

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

PLoS One 2011 30;6(11):e27859. Epub 2011 Nov 30.

Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027859PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227574PMC
April 2012

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Genome Res 2011 Jun 7;21(6):974-84. Epub 2011 Feb 7.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.114876.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106330PMC
June 2011

Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.

J Child Psychol Psychiatry 2011 Apr 4;52(4):504-16. Epub 2011 Jan 4.

Child Study Center, Department of Neurobiology, Yale University School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1111/j.1469-7610.2010.02348.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124336PMC
April 2011

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.

Bioinformatics 2011 Mar 13;27(5):595-603. Epub 2011 Jan 13.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042181PMC
March 2011

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.

PLoS Comput Biol 2010 May 27;6(5):e1000755. Epub 2010 May 27.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877725PMC
May 2010

RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes.

Proteins 2010 Feb;78(2):309-24

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1002/prot.22544DOI Listing
February 2010

MSB: a mean-shift-based approach for the analysis of structural variation in the genome.

Genome Res 2009 Jan 26;19(1):106-17. Epub 2008 Nov 26.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.080069.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612956PMC
January 2009

An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces.

PLoS Comput Biol 2008 Apr 25;4(4):e1000066. Epub 2008 Apr 25.

Department of Biology, Northeastern University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2289873PMC
April 2008

UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB.

Mol Cell 2007 Dec;28(6):1058-70

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.molcel.2007.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265384PMC
December 2007

A comprehensive analysis of non-sequential alignments between all protein structures.

BMC Struct Biol 2007 Nov 16;7:78. Epub 2007 Nov 16.

Department of Biology, Northeastern University 360 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/1472-6807-7-78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2213659PMC
November 2007

Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.

Nucleic Acids Res 2007 Jul 30;35(Web Server issue):W384-92. Epub 2007 May 30.

Department of Biology, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/nar/gkm232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933130PMC
July 2007

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method.

Nucleic Acids Res 2007 Jan 25;35(Database issue):D317-21. Epub 2006 Oct 25.

Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.

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http://nar.oxfordjournals.org/content/early/2006/10/25/nar.g
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkl809
Publisher Site
http://dx.doi.org/10.1093/nar/gkl809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635338PMC
January 2007

Friend, an integrated analytical front-end application for bioinformatics.

Bioinformatics 2005 Sep 2;21(18):3677-8. Epub 2005 Aug 2.

Department of Biology, Northeastern University, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti602DOI Listing
September 2005

Active site prediction for comparative model structures with thematics.

J Bioinform Comput Biol 2005 Feb;3(1):127-43

Department of Chemistry, United Arab Emirates University, Al-Ain, United Arab Emirates.

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February 2005

Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point.

Protein Sci 2004 Jul;13(7):1865-74

Biology Department, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1110/ps.04672604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279929PMC
July 2004