Publications

  1. Mu JC, Mohiyuddin M, Li J, Asadi NB, Gerstein MB, Abyzov A, Wong WH, Lam HYK. Varsim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics. 2015 May 1; 31(9):1469-71.
  2. Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics. 2015 Apr 10. [Epub ahead of print]
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  3. Abyzov A, Li S, Kim DR, Mohiyuddin M, Stutz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun. 2015; 6:7256. Epub 2015 Jun 01.
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  4. Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics. 2014 Dec 17.
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  5. Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, 1000 Genomes Project Consortium, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res. 2013 Dec; 23(12):2042-52. Epub 2013 Sep 11
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  6. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 4; 342(6154):1235587.
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  7. Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child development and structural variation in the human genome. Child Dev. 2013 Jan-Feb; 84(1):34-48. Epub 2013 Jan 13.
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  8. Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature. 2012 Dec 20; 492(7429):438-42. Epub 2012 Nov 18
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  9. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1; 491(7422):56-65.
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  10. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6; 489(7414):91-100.
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  11. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414):57-74.
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  12. Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C. Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12656-61. Epub 2012 Jul 13.
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  13. Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Sci. 2011 Oct; 20(10):1745-54. Epub 2011 Sep 15.
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  14. Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011 Jun; 21(6):974-84. Epub 2011 Feb 07.
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  15. Vaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A, Grigorenko EL, Gerstein M, Weissman S. Annual Research Review: The promise of stem cell research for neuropsychiatric disorders. J Child Psychol Psychiatry. 2011 Apr; 52(4):504-16. Epub 2011 Jan 04.
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  16. Abyzov A, Gerstein M. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics. 2011 Mar 1; 27(5):595-603. Epub 2011 Jan 13.
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  17. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 3; 470(7332):59-65.
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  18. Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011; 7:522. Epub 2011 Aug 2
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  19. Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. Identification of genomic indels and structural variations using split reads. BMC Genomics. 2011; 12:375. Epub 2011 Jul 25.
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  20. Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. PLoS One. 2011; 6(11):e27859. Epub 2011 Nov 30.
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  21. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28; 467(7319):1061-73.
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  22. Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB. Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol. 2010 May; 6(5):e1000755. Epub 2010 May 27.
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  23. Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins. 2010 Feb 1; 78(2):309-24.
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  24. Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res. 2009 Jan; 19(1):106-17. Epub 2008 Nov 26.
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  25. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009; 10(2):R23. Epub 2009 Feb 23.
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  26. Abyzov A, Uzun A, Strauss PR, Ilyin VA. An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces. PLoS Comput Biol. 2008 Apr; 4(4):e1000066. Epub 2008 Apr 25.
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  27. Godoy VG, Jarosz DF, Simon SM, Abyzov A, Ilyin V, Walker GC. UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB. Mol Cell. 2007 Dec 28; 28(6):1058-70.
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  28. Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W384-92. Epub 2007 May 30.
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  29. Leslin CM, Abyzov A, Ilyin VA. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Res. 2007 Jan; 35(Database issue):D317-21. Epub 2006 Oct 25.
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  30. Abyzov A, Ilyin VA. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Struct Biol. 2007; 7:78. Epub 2007 Nov 16.
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  31. Abyzov A, Errami M, Leslin CM, Ilyin VA. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15; 21(18):3677-8. Epub 2005 Aug 02.
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  32. Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ. Active site prediction for comparative model structures with thematics. J Bioinform Comput Biol. 2005 Feb; 3(1):127-43.
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  33. Leslin CM, Abyzov A, Ilyin VA. Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. Bioinformatics. 2004 Jul 22; 20(11):1801-3. Epub 2004 Feb 26.
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  34. Ilyin VA, Abyzov A, Leslin CM. 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.
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  35. Abyzov A, Belkov A, Lanyov A, Spiridonov A, Walter M, Hulsbergen W. Efficiency Profile Method To Study The Hit Efficiency Of Drift Chambers. Part Nucl Lett. 2002; 5:40-52.