Publications

2018-2019

  • Zhou B, Ho SS, Leung LC, Ward TR, Ho M, Plastini MJ, Vermilyea SC, Emborg ME, Golos TG, Mourrain P, Perrin D, Parker KJ, Urban AE.  Haplotype-resolved Callithrix jacchus embryonic stem cell line for genome editing using CRISPR/Cas9. bioRxiv 373886; doi:  10.1101/373886
  • Zhou B*, Ho SS*, Greer SU, Spies N, Bell JM, Zhang X, Zhu X, Arthur, JG, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong WH, Ji HP, Abyzov A, Urban AE.  Haplotype-resolved and integrated genome analysis of cancer cell line HepG2. *co-authorship. Nucleic Acid Research. 2019 (in press)
  • Arthur JG, Chen X, Zhou B, Urban AE, Wong WH.  Detection of complex structural variation from paired-end sequencing data. bioRxiv 200170; doi:  10.1101/200170
  • Yang EW, Bahn JH, Hsiao EYH, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X.  Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.  Nature Communications. 2019 (accepted)
  • Zhou B, Ho SS, Greer SU, Zhu X, Bell JM, Arthur JG, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney MS, Haraksingh RR, Song G, Ji HP, Perrin D, Wong WH, Abyzov A, Urban AE.  Comprehensive, integrated, and phased whole-genome analysis of primary ENCODE cell line K562. Genome Research. Mar 2019 29:472-484.
  • Zhou B*, Arthur JG*, Ho SS, Pattni R, Huang Y, Wong WH, Urban AE. Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools. *Co-authorship. Scientific Data. 2018 Vol 5:180261.
  • Xavier J*, Zhou B*, Bilan F, Zhang X, Gilbert-Dussardier B, Viaux-Savelon S, Pattni R, Ho SS, Cohen D, Levinson DF, Urban AE, Laurent-Levinson C. 1q21.1 microduplication: large verbal-nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number. *Co-authorship. NPJ Genomic Medicine 2018 22;3:24.
  • Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science. Feb 2018 Vol. 359 (6375):550-555.
  • Zhou B, Ho SS, Zhang X, Pattni R, Haraksingh RR, Urban AE.  Whole-genome sequencing analysis of genomic copy number variation (CNV) using low-coverage and paired-end strategies is highly efficient and outperforms array-based CNV analysis. Journal of Medical Genetics. 2018 55:735-743.
  • Zhang X, Zhang Y, Zhu X, Purmann C, Haney MS, Ward T, Khechaduri A, Yao J, Weissman SM, Urban AE.  Local and global chromatin interactions are altered by large genomic deletions associated with human brain development. Nature Communications. 2018 12 17;9(1):5356.

2017

  • Abyzov AA, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amiri A, Wilson M, Gerstein MG, Weissman SM, Urban AE, Vaccarino FM. One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. Genome Research. 2017 Apr; 27(4):512-523.
  • Reierson G, Bernstein J, Froehlich-Santino W, Purmann C, Urban AE, Berquist S, O’Hara R, Hallmayer JF. Neuropsychiatric profile of Phelan-McDermid Syndrome (22q13 deletion): evidence for a late onset regression of motor and self help skills.
  • McConnell M*, 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 R, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub R, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh C, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM, Brain Somatic Mosaicism Network. Intersection of diverse neuronal genomes and neuropsychiatric disease: the Brain Somatic Mosaicism Network. Science. 2017 Apr 28; 356(6336): eaal1641.
  • Haraksingh RR, Abyzov AA, Urban AE. Comprehensive performance comparison of high-resolution array platforms for genome-wide CNV analysis in humans. BMC Genomics. 2017 Apr 24; 18:321.
  • Zhang Y*, Zhang X*, Zhou X*, Purmann C, Haney MS, Ward T, Yao X, Weissman SM‡, Urban AE‡. Local and global chromatin interactions are altered by large genomic deletions associated with human brain development. Submitted.
  • Zhou B*, Haney MS*, Zhu X, Pattni R, Abyzov AA, Urban AE. Detection and quantification of mosaic genomic DNA variation in primary somatic tissues using ddPCR. (Book chapter) In press.

2015

  • Urban AE, Purmann C. Using iPSCs and genomics to catch CNVs in the act.
    Nat Genet. 2015 Jan 28;47(2):100-1.
  • Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M. Identification of human neuronal protein complexes reveals biochemical activities and convergent mechanisms of action in Autism Spectrum Disorders. Cell Syst. 2015 Nov 25;1(5):361-374.
  • Esplin ED, Chaib H, Haney M, Martin B, Homeyer M, Urban AE, Bernstein JA. 46,XY disorders of sex development and congenital diaphragmatic hernia: A case with dysmorphic facies, truncus arteriosus, bifid thymus, gut malrotation, rhizomelia, and adactyly. Am J Med Genet A. 2015 Apr 21

2014

  • Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Furman D, Montgomery SB, Urban AE, Koller D, Levinson DF. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Molecular Psychiatry. 2014 Dec;19(12):1267-74.
  • Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, and Koller D. Characterizing the Genetic Basis of Transcriptome Diversity through RNA-Sequencing of 922 Individuals. Genome Res. 2014 Jan;24(1):14-24.
  • Li J*, Shi M*, Ma Z*, Zhao S, Euskirchen G, Ziskin J, Urban AE, Hallmayer JF, Snyder MP. Integrated Systems Analysis Reveals A Molecular Network Underlying Autism Spectrum Disorders. Molecular Systems Biology. 2014 Dec 30;10(12):774.

2013

  • Battle, A., S. Mostafavi, X. Zhu, J. B. Potash, M. M. Weissman, C. McCormick, C. D. Haudenschild, K. B. Beckman, J. Shi, R. Mei, A. E. Urban, S. B. Montgomery, D. F. Levinson, and D. Koller. Characterizing the Genetic Basis of Transcriptome Diversity through Rna-Sequencing of 922 Individuals. Genome Res  (2013).
  • Mostafavi, S., A. Battle, X. Zhu, A. E. Urban, D. Levinson, S. B. Montgomery, and D. Koller. Normalizing Rna-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge. PLoS One 8, no. 7 (2013): e68141.
  • Zhang, Y., R. Haraksingh, F. Grubert, A. Abyzov, M. Gerstein, S. Weissman, and A. E. Urban. Child Development and Structural Variation in the Human Genome. Child Dev 84, no. 1 (2013): 34-48

2012

  • Winkelmann J, Lin L, Schormair B, Kornum BR, Faraco J, Plazzi G, Melberg A, Cornellio F, Urban AE, Pizza F, Grubert F, Graf E, Strom T, Mignot EM. Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy. Hum Mol Genet. 2012 Feb 23.
  • Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P‡, 1000 Genomes Project Consortium2. The 1000 Genomes Project: data management and community access. Nat Methods. 2012 Apr 27;9(5):459-62.
  • Urban AE. A role of genomic copy number variation in the complex behavioral phenotype of alcohol dependence: a commentary. Alcohol Clin Exp Res. 2012 Sep;36(9):1483-6.
  • O'Huallachain M, Karczewski KJ, Weissman SM, Urban AE, Snyder MP. Extensive genetic variation in somatic human tissues. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18018-23.
    Epub 2012 Oct 5.

  • Wu J, Stewart D, Grubert F, Urban AE, Snyder M, Marth G. Copy Number Variation detection from 1000 Genomes project exon capture sequencing data. BMC Bioinformatics. 2012 Nov 17;13:305. doi: 10.1186/1471-2105-13-305.
  • Abyzov A, Mariani J*, Palejev D*, Zhang Y*, Haney MS*, Tomasini L*, Rosenberg-Belmaker L, Ferrandino A, Wilson M, Grigorenko EL, Huttner A, Weissman SM, 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.

2011

  • Vaccarino FM, Urban AE, Stevens H, Szekely A, Abyzov A, Grigorenko E, Gerstein M, Weissman S. The promise of stem cell research for neuropsychiatric disorders. J Child Psychology Psychiatry. 2011 Jan 4. 
  • Mills RE*, Walter K*, Stewart C*, Handsaker RE*, Chen K*, Alkan C*, Abyzov A*, Yoon SC*, Ye S*, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, …, Stütz AM, Urban AE, Walker JA, ..., Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO & the 1000 Genomes Project. Mapping structural variation at fine scale by population-scale genome sequencing. Nature. 2011 Feb 3;470:59-65.
  • Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to characterize and genotype atypical CNVs using high-throughput sequencing coupled with population and family structure. Genome Res. 2011 Apr 14. [Epub ahead of print]
  • Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME‡, Awadalla P‡; 1000 Genomes Project2. Variation in genome-wide mutation rates within and between human families.    Nat Genet. 2011 Jun 12;43(7):712-4.
  • Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA; 1000 Genomes Project2, Bustamante CD. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8.
  • Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. Identification of genomic indels and structural variation using split reads. BMC Genomics. 2011 Jul 25;12(1):375

  • Stewart D, Kural D, Strömberg MP, Lee W-P, Walker J, Konkel M, Stütz AM, Urban AE, Grubert G, Lam HYK, Batzer M, Korbel JO, Huff C, Xing J, Marth G, and the 1000 Genomes Project. Comprehensive discovery and characterization of mobile element insertions from the 1000 Genomes Pilot Project data. PLoS Genet. 2011 Aug;7(8):e1002236.
  • Marth GT, Yu F*, Indap AR*, Garimella K*, Gravel S*, Leong WF*, Tyler-Smith C*, Bainbridge M, …, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R; 1000 Genomes Project2. The functional spectrum of low-frequency coding variation. Genome Biol. 2011 Sep 14;12(9):R84.
  • Haraksingh R, Abyzov A, Gerstein M, Urban AE, Snyder M. Genome-wide mapping of Copy Number Variation in humans: comparative analysis of high resolution of array platforms. PLoS One. 2011 Nov; 6(11):e27859. Epub 2011 Nov 30.

2010

  • Kasowski M*, Grubert F*, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO‡, Snyder M‡. Variation in transcription factor binding among humans. Science. 2010 Apr 9;328(5975):232-5
  • Grigorenko EL, Urban AE, Mencl E. Behavior, brain and genome in genomic disorders: finding the correspondences. J Dev Behav Pediatr. 2010 Sep;31(7):602-9.
  • 1000 Genomes Project Consortium2, Durbin RM, Abecasis GR, Altshuler DL, 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):1050-1.
  • Sudmant PH*, Kitzman JO*, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project2, Eichler EE. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6.

2009

  • Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, Lee C, Gerstein MB, Kuefer R, Rubin MA. Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer. 2009 Apr;48(4):366-380.

  • Korbel JO*, Tirosh-Wagner T*, Urban AE*, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, …, Shaffer LG, Shohat M, Van Riper AJ, Warburton D, Weissman S, Gerstein MB, Snyder M‡, Korenberg JR‡. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12031-6.
  • Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB, Lacy J, Snyder M, Gerstein M, Weissman SM. EBNA1 regulates cellular gene expression by binding cellular promoters. Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22421-6.

2008

  • Wu JQ*, Du J*, Rozowsky J, Zhang ZD, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Systematic analysis of transcribed loci in the ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 2008 Jan 3;9(1): R3 [Epub ahead of print]
  • Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol. 2008 Jun;18(3):366-74. Epub 2008 May 27.
  • Pelizzola M*, Koga Y*, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM. MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res. 2008 Sep 2.
  • Pan X, Urban AE, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M, Weissman SM. A procedure for highly specific, sensitive and unbiased whole-genome amplification. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15499-504. Epub 2008 Oct 1.

  • Kim PM*, Lam HYK*, Urban AE, Korbel JO, Chen X, Snyder M, Gerstein MB. Analysis of copy-number-variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 2008 Dec;18(12):1865-74. Epub 2008 Oct 8.
  • Hasin Y*, Olender T*, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO. High-resolution copy-number-variation map reflects human olfactory receptor diversity and evolution. PLoS Genetics. 2008 Nov;4(11):e1000249.

2007

  • Korbel JO*, Urban AE*, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS,
    Weissman SM, Snyder M‡, Gerstein MB‡. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10110-5.
  • ENCODE Project Consortium1. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
  • Korbel JO*, Urban AE*, Affourtit JP*, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M‡, Snyder M‡. Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007 Oct19;318(5849):420-6. Epub 2007 Sep 27.

2006

  • Urban AE*, Korbel JO*, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM‡, Snyder M‡. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4534-9.

  • Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 2007 Jun;17(6):886-97. Epub 2006 Nov 21.

2004

  • ENCODE Project Consortium1. The ENCODE (ENCyclopedia OF DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.
  • Bertone P*, Stolc V*, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science. 2004 Dec 24;306(5705):2242-6.

2003

  • Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, Snyder M. Identification of novel functional elements in the human genome.Cold Spring Harb Symp Quant Biol. 2003;68:317-22.
  • ( or )

    *these authors contributed equally

    ‡are co-corresponding authors

    1 The ENCODE Consortium, during its pilot phase, had initially more than 200 members who were contributing various types of experimental and/or analytical work to the project, including Dr. Urban as a member of the microarray group at Yale, and who are listed as co-authors in the full publications.
    2 The 1000 Genomes studies had more than 540 co-authors, with only the writing team of a given paper listed in the short format references and all the consortium members whose contribution made them co-authors being listed in the full publications; Dr. Urban is one of the co-authors as a member of both the analytical and structural variation groups of the 1000 Genomes Consortium.
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