Total papers: 49

(Last updated: Wed, 07/12/2017 12:14:03 PM EDT)

2017 (6)

  1. Landscape and variation of novel retroduplications in 26 human populations.
    Zhang Y, Li S, Abyzov A , Gerstein MB
    PLoS Comput Biol 13(6):e1005567 (2017).
  2. Patient-reported (EORTC QLQ-CIPN20) versus physician-reported (CTCAE) quantification of oxaliplatin- and paclitaxel/carboplatin-induced peripheral neuropathy in NCCTG/Alliance clinical trials.
    Le-Rademacher J, Kanwar R, Seisler D, Pachman DR, Qin R, Abyzov A , Ruddy KJ, Banck MS, Lavoie Smith EM, Dorsey SG, Aaronson NK, Sloan J, Loprinzi CL, Beutler AS
    Support Care Cancer [Epub ahead of print] (2017).
  3. Human induced pluripotent stem cells for modelling neurodevelopmental disorders.
    Ardhanareeswaran K, Mariani J, Coppola G, Abyzov A , Vaccarino FM
    Nat Rev Neurol 13(5):265-278 (2017).
  4. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.
    McConnell MJ, Moran JV, Abyzov A , Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM, Brain Somatic Mosaicism Network
    Science 356(6336) (2017).
  5. Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.
    Haraksingh RR, Abyzov A , Urban AE
    BMC Genomics 18(1):321 (2017).
  6. One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.
    Abyzov A , Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM
    Genome Res 27(4):512-523 (2017).

2016 (6)

  1. Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation.
    Druliner BR, Rashtak S, Ruan X, Bae T, Vasmatzis N, O'Brien D, Johnson R, Felmlee-Devine D, Washechek-Aletto J, Basu N, Liu H, Smyrk T, Abyzov A , Boardman LA
    Transl Oncol 9(4):280-6 (2016).
  2. Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis.
    Dhokarh D, Abyzov A
    Genome Res 26(7):874-81 (2016).
  3. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.
    Mitra AK, Mukherjee UK, Harding T, Jang JS, Stessman H, Li Y, Abyzov A , Jen J, Kumar S, Rajkumar V, Van Ness B
    Leukemia 30(5):1094-102 (2016).
  4. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.
    Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A , Kong Y, Regan L, Gerstein M
    Nat Commun 7:11101 (2016).
  5. Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance).
    Boora GK, Kanwar R, Kulkarni AA, Abyzov A , Sloan J, Ruddy KJ, Banck MS, Loprinzi CL, Beutler AS
    Cancer Med 5(4):631-9 (2016).
  6. Understanding genome structural variations.
    Abyzov A , Li S, Gerstein MB
    Oncotarget 7(7):7370-1 (2016).

2015 (7)

  1. The PsychENCODE project.
    PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A , Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N
    Nat Neurosci 18(12):1707-12 (2015).
  2. A global reference for human genetic variation.
    1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR
    Nature 526(7571):68-74 (2015).
  3. An integrated map of structural variation in 2,504 human genomes.
    Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A , Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO
    Nature 526(7571):75-81 (2015).
  4. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
    Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A , Wong WH, Lam HY
    Bioinformatics 31(16):2741-4 (2015).
  5. FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
    Mariani J, Coppola G, Zhang P, Abyzov A , Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM
    Cell 162(2):375-90 (2015).
  6. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.
    Abyzov A , Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB
    Nat Commun 6:7256 (2015).
  7. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
    Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A , Wong WH, Lam HY
    Bioinformatics 31(9):1469-71 (2015).

2013 (3)

  1. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.
    Abyzov A , Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, 1000 Genomes Project Consortium, Lee C, Gerstein M
    Genome Res 23(12):2042-52 (2013).
  2. Integrative annotation of variants from 1092 humans: application to cancer genomics.
    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, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M
    Science 342(6154):1235587 (2013).
  3. Child development and structural variation in the human genome.
    Zhang Y, Haraksingh R, Grubert F, Abyzov A , Gerstein M, Weissman S, Urban AE
    Child Dev 84(1):34-48 (2013).

2012 (5)

  1. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.
    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
    Nature 492(7429):438-42 (2012).
  2. An integrated map of genetic variation from 1,092 human genomes.
    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA
    Nature 491(7422):56-65 (2012).
  3. An integrated encyclopedia of DNA elements in the human genome.
    ENCODE Project Consortium
    Nature 489(7414):57-74 (2012).
  4. Architecture of the human regulatory network derived from ENCODE data.
    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 Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M
    Nature 489(7414):91-100 (2012).
  5. Regulatory element copy number differences shape primate expression profiles.
    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
    Proc Natl Acad Sci U S A 109(31):12656-61 (2012).

2011 (8)

  1. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.
    Bhardwaj N, Abyzov A , Clarke D, Shou C, Gerstein MB
    Protein Sci 20(10):1745-54 (2011).
  2. AlleleSeq: analysis of allele-specific expression and binding in a network framework.
    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
    Mol Syst Biol 7:522 (2011).
  3. Identification of genomic indels and structural variations using split reads.
    Zhang ZD, Du J, Lam H, Abyzov A , Urban AE, Snyder M, Gerstein M
    BMC Genomics 12:375 (2011).
  4. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
    Abyzov A , Urban AE, Snyder M, Gerstein M
    Genome Res 21(6):974-84 (2011).
  5. Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.
    Vaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A , Grigorenko EL, Gerstein M, Weissman S
    J Child Psychol Psychiatry 52(4):504-16 (2011).
  6. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
    Abyzov A , Gerstein M
    Bioinformatics 27(5):595-603 (2011).
  7. Mapping copy number variation by population-scale genome sequencing.
    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, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project
    Nature 470(7332):59-65 (2011).
  8. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.
    Haraksingh RR, Abyzov A , Gerstein M, Urban AE, Snyder M
    PLoS One 6(11):e27859 (2011).

2010 (3)

  1. A map of human genome variation from population-scale sequencing.
    1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA
    Nature 467(7319):1061-73 (2010).
  2. Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.
    Bhardwaj N, Carson MB, Abyzov A , Yan KK, Lu H, Gerstein MB
    PLoS Comput Biol 6(5):e1000755 (2010).
  3. RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes.
    Abyzov A , Bjornson R, Felipe M, Gerstein M
    Proteins 78(2):309-24 (2010).

2009 (2)

  1. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
    Korbel JO, Abyzov A , Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB
    Genome Biol 10(2):R23 (2009).
  2. MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
    Wang LY, Abyzov A , Korbel JO, Snyder M, Gerstein M
    Genome Res 19(1):106-17 (2009).

2008 (1)

  1. An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces.
    Abyzov A , Uzun A, Strauss PR, Ilyin VA
    PLoS Comput Biol 4(4):e1000066 (2008).

2007 (4)

  1. UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB.
    Godoy VG, Jarosz DF, Simon SM, Abyzov A , Ilyin V, Walker GC
    Mol Cell 28(6):1058-70 (2007).
  2. A comprehensive analysis of non-sequential alignments between all protein structures.
    Abyzov A , Ilyin VA
    BMC Struct Biol 7:78 (2007).
  3. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
    Uzun A, Leslin CM, Abyzov A , Ilyin V
    Nucleic Acids Res 35(Web Server issue):W384-92 (2007).
  4. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method.
    Leslin CM, Abyzov A , Ilyin VA
    Nucleic Acids Res 35(Database issue):D317-21 (2007).

2005 (2)

  1. Friend, an integrated analytical front-end application for bioinformatics.
    Abyzov A , Errami M, Leslin CM, Ilyin VA
    Bioinformatics 21(18):3677-8 (2005).
  2. Active site prediction for comparative model structures with thematics.
    Shehadi IA, Abyzov A , Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ
    J Bioinform Comput Biol 3(1):127-43 (2005).

2004 (2)

  1. Structural exon database, SEDB, mapping exon boundaries on multiple protein structures.
    Leslin CM, Abyzov A , Ilyin VA
    Bioinformatics 20(11):1801-3 (2004).
  2. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point.
    Ilyin VA, Abyzov A , Leslin CM
    Protein Sci 13(7):1865-74 (2004).