Alexander E. Urban, Ph.D. - Publications

Yale University, New Haven, CT 
 Stanford University, Palo Alto, CA 
Psychiatry and Behavioral Sciences and Genetics

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, ... ... Urban AE, et al. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science (New York, N.Y.). 364. PMID 30975860 DOI: 10.1126/science.aau8650  0.44
2019 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, ... ... Urban AE, et al. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Research. PMID 30864654 DOI: 10.1093/nar/gkz169  0.36
2019 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, ... ... Urban AE, et al. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. Genome Research. PMID 30737237 DOI: 10.1101/gr.234948.118  0.36
2018 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. 9: 5356. PMID 30559385 DOI: 10.1038/s41467-018-07766-x  0.44
2018 Zhou B, Haney MS, Zhu X, Pattni R, Abyzov A, Urban AE. 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 in Molecular Biology (Clifton, N.J.). 1768: 173-190. PMID 29717444 DOI: 10.1007/978-1-4939-7778-9_11  0.36
2017 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 (New York, N.Y.). PMID 29217587 DOI: 10.1126/science.aan8690  0.36
2017 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, ... ... Urban AE, et al. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science (New York, N.Y.). 356. PMID 28450582 DOI: 10.1126/science.aal1641  0.36
2017 Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, 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. PMID 28235832 DOI: 10.1101/gr.215517.116  0.36
2014 Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, ... ... Urban AE, et al. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Molecular Psychiatry. 19: 1267-74. PMID 24296977 DOI: 10.1038/mp.2013.161  0.44
2014 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, Koller D. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Research. 24: 14-24. PMID 24092820 DOI: 10.1101/gr.155192.113  0.44
2013 Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D. Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge. Plos One. 8: e68141. PMID 23874524 DOI: 10.1371/journal.pone.0068141  0.44
2013 Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child development and structural variation in the human genome. Child Development. 84: 34-48. PMID 23311762 DOI: 10.1111/cdev.12051  0.44
2012 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, ... ... Urban AE, et al. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature. 492: 438-42. PMID 23160490 DOI: 10.1038/nature11629  0.44
2012 Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT. Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. Bmc Bioinformatics. 13: 305. PMID 23157288 DOI: 10.1186/1471-2105-13-305  0.44
2012 O'Huallachain M, Karczewski KJ, Weissman SM, Urban AE, Snyder MP. Extensive genetic variation in somatic human tissues. Proceedings of the National Academy of Sciences of the United States of America. 109: 18018-23. PMID 23043118 DOI: 10.1073/pnas.1213736109  0.44
2012 Urban AE. A role of genomic copy number variation in the complex behavioral phenotype of alcohol dependence: a commentary. Alcoholism, Clinical and Experimental Research. 36: 1483-6. PMID 22909245 DOI: 10.1111/j.1530-0277.2012.01915.x  0.44
2012 Winkelmann J, Lin L, Schormair B, Kornum BR, Faraco J, Plazzi G, Melberg A, Cornelio F, Urban AE, Pizza F, Poli F, Grubert F, Wieland T, Graf E, Hallmayer J, et al. Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy. Human Molecular Genetics. 21: 2205-10. PMID 22328086 DOI: 10.1093/hmg/dds035  0.44
2011 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. 6: e27859. PMID 22140474 DOI: 10.1371/journal.pone.0027859  0.44
2011 Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, et al. A comprehensive map of mobile element insertion polymorphisms in humans. Plos Genetics. 7: e1002236. PMID 21876680 DOI: 10.1371/journal.pgen.1002236  0.44
2011 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. 12: 375. PMID 21787423 DOI: 10.1186/1471-2164-12-375  0.44
2011 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 Research. 21: 974-84. PMID 21324876 DOI: 10.1101/gr.114876.110  0.44
2011 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, ... ... Urban AE, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/nature09708  0.44
2011 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. Journal of Child Psychology and Psychiatry, and Allied Disciplines. 52: 504-16. PMID 21204834 DOI: 10.1111/j.1469-7610.2010.02348.x  0.44
2010 Grigorenko EL, Urban AE, Mencl E. Behavior, brain, and genome in genomic disorders: finding the correspondences. Journal of Developmental and Behavioral Pediatrics : Jdbp. 31: 602-9. PMID 20814258 DOI: 10.1097/DBP.0b013e3181f5a0a1  0.44
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, et al. Variation in transcription factor binding among humans. Science (New York, N.Y.). 328: 232-5. PMID 20299548 DOI: 10.1126/science.1183621  0.44
2009 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. Proceedings of the National Academy of Sciences of the United States of America. 106: 22421-6. PMID 20080792 DOI: 10.1073/pnas.0911676106  0.44
2009 Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, et al. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proceedings of the National Academy of Sciences of the United States of America. 106: 12031-6. PMID 19597142 DOI: 10.1073/pnas.0813248106  0.44
2008 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. 4: e1000249. PMID 18989455 DOI: 10.1371/journal.pgen.1000249  0.44
2008 Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, 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 Research. 18: 1865-74. PMID 18842824 DOI: 10.1101/gr.081422.108  0.44
2008 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. Proceedings of the National Academy of Sciences of the United States of America. 105: 15499-504. PMID 18832167 DOI: 10.1073/pnas.0808028105  0.44
2008 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 Research. 18: 1652-9. PMID 18765822 DOI: 10.1101/gr.080721.108  0.44
2008 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. Current Opinion in Structural Biology. 18: 366-74. PMID 18511261 DOI: 10.1016/  0.44
2008 Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biology. 9: R3. PMID 18173853 DOI: 10.1186/gb-2008-9-1-r3  0.36
2007 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, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science (New York, N.Y.). 318: 420-6. PMID 17901297 DOI: 10.1126/science.1149504  0.44
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. Proceedings of the National Academy of Sciences of the United States of America. 104: 10110-5. PMID 17551006 DOI: 10.1073/pnas.0703834104  0.44
2007 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 Research. 17: 886-97. PMID 17119069 DOI: 10.1101/gr.5014606  0.44
2007 Sayward FG, Yang J, Nelson FK, Euskirchen G, Urban AE, Bertone P, Rinn J, Weissman S, Gerstein M, Snyder M, Miller PL. Design issues in implementing a portable Sample Tracking and Analysis Research Support (STARS) system for PCR based microarray research 2006 Ieee Conference On Information Sciences and Systems, Ciss 2006 - Proceedings. 1578-1598. DOI: 10.1109/CISS.2006.286390  0.44
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. Proceedings of the National Academy of Sciences of the United States of America. 103: 4534-9. PMID 16537408 DOI: 10.1073/pnas.0511340103  0.44
2004 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 (New York, N.Y.). 306: 2242-6. PMID 15539566 DOI: 10.1126/science.1103388  0.44
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Urban AE, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/science.1105136  0.44
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, et al. Identification of novel functional elements in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 68: 317-22. PMID 15338632  0.44
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