Publications

2026 (4)

Direct Probabilistic Quantification of Mosaic Loss of Chromosome Y from Sequencing Data Lin J-R, Chang Y-C, Maslov AY, Song Y, Gao T, Shan J, Bennett D, Milman S, Barzilai N, Vijg J, Montagna C, Zhang ZD (2026) bioRxiv 2026.06.26.734767.  JOURNAL 

Bayesian Estimation of Mosaic Loss of Chromosome Y from Bulk RNA Sequencing Data Lin J-R, Zhang ZD (2026) bioRxiv 2026.05.20.726153.  JOURNAL 

Deletion Size and Background Genetic Variation Shape Congenital Heart Disease Phenotypes in 3,016 Individuals with 22q11.2 Deletion Syndrome Lin J-R, Miller D, Luong D, Nelson T, Crowley TB, Tran OT, Thiruvahindrapuram B, Hajianpour A, Campbell L, Busa T, Heine-Suner D, Garcia-Minaur S, Fernandez L, Murphy KC, Murphy D, Hawula W, Angkustsiri K, Shashi V, Schoch K, Bearden CE, Tomita Mitchell A, Mitchell ME, Carmel M, Weizman A, Michaelovsky E, Gothelf D, van den Bree MBM, Owen MJ, Vorstman JAS, Boot E, Vingerhoets C, van Amelsvoort T, Swillen A, Breckpot J, Vermeesch JR, Devriendt K, Schneider M, Eliez S, Digilio MC, Unolt M, Putotto C, Marino B, Pontillo M, Armando M, Vicari S, Repetto GM, Kates WR, Shprintzen RJ, Gur RE, Zackai EH, Goldmuntz E, Wang T, Raj S, Emanuel BS, McDonald-McGinn DM, Scherer SC, Bassett AS, Zhang ZD, Morrow BE (2026) medRxiv 2026.02.23.26346918.  JOURNAL 

Prevalence and Spectrum of Congenital Heart Disease in Individuals with Distal Chromosome 22q11.22-23 Deletions. Nelson TJ, McGinn DE, Crowley TB, Rockart L, Green A, Giunta V, Tran O, Miller D, Breckpot J, Swillen A, Digilio MC, Unolt M, Putotto C, Pulvirenti F, Marino B, Emanuel BS, Zackai EH, Zhang ZD, Goldmuntz E, Boot E, Bassett AS, Morrow BE, McDonald-McGinn DM (2026) Clin Genet 109(5):859-868.  JOURNAL   PUBMED   REPRINT 

2025 (4)

The Somatic Aneuploidy Landscape of Adult Glia Reveals 16p as a Hotspot and Differentiates Mosaicism in Normal Glia from Chromosomal Instability in Glioblastoma. Montagna C, Albert O, Sun S, Lin JR, Lee M, Chan C, Maslov A, Ellerby L, Huttner A, Zhang Z, Vijg J (2025) Res Sq :rs.3.rs-6497851.  JOURNAL   PUBMED 

Evidence for Improved DNA Repair in the Long-Lived Bowhead Whale. Firsanov D, Zacher M, Tian X, Sformo TL, Zhao Y, Tombline G, Lu JY, Zheng Z, Perelli L, Gurreri E, Zhang L, Guo J, Korotkov A, Volobaev V, Biashad SA, Zhang Z, Heid J, Maslov AY, Sun S, Wu Z, Gigas J, Hillpot EC, Martinez JC, Lee M, Williams A, Gilman A, Hamilton N, Strelkova E, Haseljic E, Patel A, Straight ME, Miller N, Ablaeva J, Tam LM, Couderc C, Hoopmann MR, Moritz RL, Fujii S, Pelletier A, Hayman DJ, Liu H, Cai Y, Leung AKL, Zhang Z, Nelson CB, Abegglen LM, Schiffman JD, Gladyshev VN, Maley CC, Modesti M, Genovese G, Simons MJP, Vijg J, Seluanov A, Gorbunova V (2025) Nature 648(8094):717-725.  JOURNAL   PUBMED   REPRINT 

Identification of Functional Rare Coding Variants in IGF-1 Gene in Humans with Exceptional Longevity. Ali A, Zhang ZD, Gao T, Aleksic S, Gavathiotis E, Barzilai N, Milman S (2025) Sci Rep 15(1):10199.  JOURNAL   PUBMED   REPRINT 

Genetic Variants Associated with Age-Related Episodic Memory Decline Implicate Distinct Memory Pathologies. Ali A, Milman S, Weiss EF, Gao T, Napolioni V, Barzilai N, Zhang ZD, Lin JR (2025) Alzheimers Dement 21(1):e14379.  JOURNAL   PUBMED   REPRINT 

2024 (1)

Polygenic Prediction of Human Longevity on the Supposition of Pervasive Pleiotropy. Jabalameli MR, Lin JR, Zhang Q, Wang Z, Mitra J, Nguyen N, Gao T, Khusidman M, Sathyan S, Atzmon G, Milman S, Vijg J, Barzilai N, Zhang ZD (2024) Sci Rep 14(1):19981.  JOURNAL   PUBMED   REPRINT 

2023 (3)

Chromosome Instability and Aneuploidy in the Mammalian Brain. Albert O, Sun S, Huttner A, Zhang Z, Suh Y, Campisi J, Vijg J, Montagna C (2023) Chromosome Res 31(4):32.  JOURNAL   PUBMED   REPRINT 

Frailty Resilience Score: A Novel Measure of Frailty Resilience Associated with Protection from Frailty and Survival. Milman S, Lerman B, Ayers E, Zhang Z, Sathyan S, Levine M, Ye K, Gao T, Higgins-Chen A, Barzilai N, Verghese J (2023) J Gerontol A Biol Sci Med Sci 78(10):1771-1777.  JOURNAL   PUBMED   REPRINT 

Rare Coding Variants as Risk Modifiers of the 22q11.2 Deletion Implicate Postnatal Cortical Development in Syndromic Schizophrenia. Lin JR, Zhao Y, Jabalameli MR, Nguyen N, Mitra J, International 22q11.DS Brain and Behavior Consortium, Swillen A, Vorstman JAS, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, Owen MJ, Williams NM, Bassett AS, McDonald-McGinn DM, Gur RE, Bearden CE, Morrow BE, Lachman HM, Zhang ZD (2023) Mol Psychiatry 28(5):2071-2080.  JOURNAL   PUBMED   REPRINT   WEBSITE 

2022 (3)

Protocol for Gene Annotation, Prediction, and Validation of Genomic Gene Expansion. Zhang Q, Zhang ZD (2022) STAR Protoc 3(4):101692.  JOURNAL   PUBMED   REPRINT 

Unravelling Genetic Components of Longevity. Jabalameli MR, Zhang ZD (2022) Nat Aging 2(1):5-6.  JOURNAL   PUBMED   REPRINT 

Substance Abuse and the Risk of Severe COVID-19: Mendelian Randomization Confirms the Causal Role of Opioids but Hints a Negative Causal Effect for Cannabinoids. Jabalameli MR, Zhang ZD (2022) Front Genet 13:1070428.  JOURNAL   PUBMED   REPRINT 

2021 (5)

Genomic Expansion of Aldh1a1 Protects Beavers Against High Metabolic Aldehydes from Lipid Oxidation. Zhang Q, Tombline G, Ablaeva J, Zhang L, Zhou X, Smith Z, Zhao Y, Xiaoli AM, Wang Z, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Vijg J, Seluanov A, Gladyshev VN, Gorbunova V, Zhang ZD (2021) Cell Rep 37(6):109965.  JOURNAL   PUBMED   REPRINT 

Rare Genetic Coding Variants Associated with Human Longevity and Protection Against Age-Related Diseases. Lin JR, Sin-Chan P, Napolioni V, Torres GG, Mitra J, Zhang Q, Jabalameli MR, Wang Z, Nguyen N, Gao T, Regeneron Genetics Center, Laudes M, Görg S, Franke A, Nebel A, Greicius MD, Atzmon G, Ye K, Gorbunova V, Ladiges WC, Shuldiner AR, Niedernhofer LJ, Robbins PD, Milman S, Suh Y, Vijg J, Barzilai N, Zhang ZD (2021) Nat Aging 1(9):783-794.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Enhancer Release and Retargeting Activates Disease-Susceptibility Genes. Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG (2021) Nature 595(7869):735-740.  JOURNAL   PUBMED   REPRINT 

Transposon-Triggered Innate Immune Response Confers Cancer Resistance to the Blind Mole Rat. Zhao Y, Oreskovic E, Zhang Q, Lu Q, Gilman A, Lin YS, He J, Zheng Z, Lu JY, Lee J, Ke Z, Ablaeva J, Sweet MJ, Horvath S, Zhang Z, Nevo E, Seluanov A, Gorbunova V (2021) Nat Immunol 22(10):1219-1230.  JOURNAL   PUBMED   REPRINT 

Deep Post-Gwas Analysis Identifies Potential Risk Genes and Risk Variants for Alzheimer's Disease, Providing New Insights into Its Disease Mechanisms. Wang Z, Zhang Q, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Zhang ZD (2021) Sci Rep 11(1):20511.  JOURNAL   PUBMED   REPRINT 

2020 (3)

Genetics of Extreme Human Longevity to Guide Drug Discovery for Healthy Ageing. Zhang ZD, Milman S, Lin JR, Wierbowski S, Yu H, Barzilai N, Gorbunova V, Ladiges WC, Niedernhofer LJ, Suh Y, Robbins PD, Vijg J (2020) Nat Metab 2(8):663-672.  JOURNAL   PUBMED   REPRINT 

Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity. Zhou X, Dou Q, Fan G, Zhang Q, Sanderford M, Kaya A, Johnson J, Karlsson EK, Tian X, Mikhalchenko A, Kumar S, Seluanov A, Zhang ZD, Gorbunova V, Liu X, Gladyshev VN (2020) Cell Rep 32(4):107949.  JOURNAL   PUBMED   REPRINT 

Inducible Aging in Hydra Oligactis Implicates Sexual Reproduction, Loss of Stem Cells, and Genome Maintenance as Major Pathways. Sun S, White RR, Fischer KE, Zhang Z, Austad SN, Vijg J (2020) Geroscience 42(4):1119-1132.  JOURNAL   PUBMED   REPRINT 

2019 (2)

The Nutritional Environment Determines Which and How Intestinal Stem Cells Contribute to Homeostasis and Tumorigenesis. Li W, Zimmerman SE, Peregrina K, Houston M, Mayoral J, Zhang J, Maqbool S, Zhang Z, Cai Y, Ye K, Augenlicht LH (2019) Carcinogenesis 40(8):937-946.  JOURNAL   PUBMED   REPRINT 

SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species. Tian X, Firsanov D, Zhang Z, Cheng Y, Luo L, Tombline G, Tan R, Simon M, Henderson S, Steffan J, Goldfarb A, Tam J, Zheng K, Cornwell A, Johnson A, Yang JN, Mao Z, Manta B, Dang W, Zhang Z, Vijg J, Wolfe A, Moody K, Kennedy BK, Bohmann D, Gladyshev VN, Seluanov A, Gorbunova V (2019) Cell 177(3):622-638.e22.  JOURNAL   PUBMED   REPRINT 

2018 (4)

Global, Integrated Analysis of Methylomes and Transcriptomes from Laser Capture Microdissected Bronchial and Alveolar Cells in Human Lung. Dong X, Shi M, Lee M, Toro R, Gravina S, Han W, Yasuda S, Wang T, Zhang Z, Vijg J, Suh Y, Spivack SD (2018) Epigenetics 13(3):264-274.  JOURNAL   PUBMED   REPRINT 

HEDD: Human Enhancer Disease Database. Wang Z, Zhang Q, Zhang W, Lin JR, Cai Y, Mitra J, Zhang ZD (2018) Nucleic Acids Res 46(D1):D113-D120.  JOURNAL   PUBMED   REPRINT   WEBSITE 

PGA: Post-Gwas Analysis for Disease Gene Identification. Lin JR, Jaroslawicz D, Cai Y, Zhang Q, Wang Z, Zhang ZD (2018) Bioinformatics 34(10):1786-1788.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Epigenetic Alterations to Polycomb Targets Precede Malignant Transition in a Mouse Model of Breast Cancer. Cai Y, Lin JR, Zhang Q, O'Brien K, Montagna C, Zhang ZD (2018) Sci Rep 8(1):5535.  JOURNAL   PUBMED   REPRINT 

2017 (7)

Schizophrenia Risk Genes. Zhang ZD (2017) Access Science.  JOURNAL   WEBSITE 

Integrated Rare Variant-Based Risk Gene Prioritization in Disease Case-Control Sequencing Studies. Lin JR, Zhang Q, Cai Y, Morrow BE, Zhang ZD (2017) PLoS Genet 13(12):e1007142.  JOURNAL   PUBMED   REPRINT   WEBSITE 

A Neurogenetic Model for the Study of Schizophrenia Spectrum Disorders: The International 22q11.2 Deletion Syndrome Brain Behavior Consortium. Gur RE, Bassett AS, McDonald-McGinn DM, Bearden CE, Chow E, Emanuel BS, Owen M, Swillen A, Van den Bree M, Vermeesch J, Vorstman JAS, Warren S, Lehner T, Morrow B (2017) Mol Psychiatry 22(12):1664-1672.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Translation Fidelity Coevolves with Longevity. Ke Z, Mallik P, Johnson AB, Luna F, Nevo E, Zhang ZD, Gladyshev VN, Seluanov A, Gorbunova V (2017) Aging Cell 16(5):988-993.  JOURNAL   PUBMED   REPRINT 

Cyclin C Regulates Adipogenesis by Stimulating Transcriptional Activity of CCAAT/enhancer-binding Protein Α. Song Z, Xiaoli AM, Zhang Q, Zhang Y, Yang EST, Wang S, Chang R, Zhang ZD, Yang G, Strich R, Pessin JE, Yang F (2017) J Biol Chem 292(21):8918-8932.  JOURNAL   PUBMED   REPRINT 

Transcriptomic Dynamics of Breast Cancer Progression in the MMTV-PyMT Mouse Model. Cai Y, Nogales-Cadenas R, Zhang Q, Lin JR, Zhang W, O'Brien K, Montagna C, Zhang ZD (2017) BMC Genomics 18(1):185.  JOURNAL   PUBMED   REPRINT 

Network Analysis of Mitonuclear GWAS Reveals Functional Networks and Tissue Expression Profiles of Disease-Associated Genes. Johnson SC, Gonzalez B, Zhang Q, Milholland B, Zhang Z, Suh Y (2017) Hum Genet 136(1):55-65.  JOURNAL   PUBMED   REPRINT 

2016 (5)

Cell Culture-Based Profiling Across Mammals Reveals DNA Repair and Metabolism as Determinants of Species Longevity. Ma S, Upneja A, Galecki A, Tsai YM, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN (2016) Elife 5:e19130.  JOURNAL   PUBMED   REPRINT 

Integrated Post-Gwas Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia. Lin JR, Cai Y, Zhang Q, Zhang W, Nogales-Cadenas R, Zhang ZD (2016) Genetics 204(4):1587-1600.  JOURNAL   PUBMED   REPRINT   WEBSITE 

MicroRNA Expression and Gene Regulation Drive Breast Cancer Progression and Metastasis in PyMT Mice. Nogales-Cadenas R, Cai Y, Lin JR, Zhang Q, Zhang W, Montagna C, Zhang ZD (2016) Breast Cancer Res 18(1):75.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Systems-Level Analysis of Human Aging Genes Shed New Light on Mechanisms of Aging. Zhang Q, Nogales-Cadenas R, Lin JR, Zhang W, Cai Y, Vijg J, Zhang ZD (2016) Hum Mol Genet 25(14):2934-2947.  JOURNAL   PUBMED   REPRINT 

Prioritization of Schizophrenia Risk Genes by a Network-Regularized Logistic Regression Method. Zhang W, Lin JR, Nogales-Cadenas R, Zhang Q, Cai Y, Zhang ZD (2016) Lecture Notes in Bioinformatics 9565:434-445.  JOURNAL   REPRINT 

2015 (6)

DNA Repair in Species with Extreme Lifespan Differences. MacRae SL, Croken MM, Calder RB, Aliper A, Milholland B, White RR, Zhavoronkov A, Gladyshev VN, Seluanov A, Gorbunova V, Zhang ZD, Vijg J (2015) Aging (Albany NY) 7(12):1171-84.  JOURNAL   PUBMED   REPRINT 

RNA:DNA Hybrids in the Human Genome Have Distinctive Nucleotide Characteristics, Chromatin Composition, and Transcriptional Relationships. Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM (2015) Epigenetics Chromatin 8:46.  JOURNAL   PUBMED   REPRINT 

From Gene Expression to Disease Phenotypes: Network-Based Approaches to Study Complex Human Diseases. Zhang Q, Zhang W, Nogales-Cadenas R, Lin JR, Cai Y, Zhang ZD (2015) Transcriptomics and Gene Regulation Translational Bioinformatics 9:115-140.  JOURNAL   REPRINT 

Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations. Chung JH, Cai J, Suskin BG, Zhang Z, Coleman K, Morrow BE (2015) Hum Mutat 36(8):797-807.  JOURNAL   PUBMED   REPRINT 

Comparative Analysis of Genome Maintenance Genes in Naked Mole Rat, Mouse, and Human. MacRae SL, Zhang Q, Lemetre C, Seim I, Calder RB, Hoeijmakers J, Suh Y, Gladyshev VN, Seluanov A, Gorbunova V, Vijg J, Zhang ZD (2015) Aging Cell 14(2):288-91.  JOURNAL   PUBMED   REPRINT 

INK4 Locus of the Tumor-Resistant Rodent, the Naked Mole Rat, Expresses a Functional p15/p16 Hybrid Isoform. Tian X, Azpurua J, Ke Z, Augereau A, Zhang ZD, Vijg J, Gladyshev VN, Gorbunova V, Seluanov A (2015) Proc Natl Acad Sci U S A 112(4):1053-8.  JOURNAL   PUBMED   REPRINT 

2014 (2)

Comparative Genetics of Longevity and Cancer: Insights from Long-Lived Rodents. Gorbunova V, Seluanov A, Zhang Z, Gladyshev VN, Vijg J (2014) Nat Rev Genet 15(8):531-40.  JOURNAL   PUBMED   REPRINT 

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder. Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, Stasiek E, Tozour J, Valicenti-McDermott M, Wang S, Abrahams BS, Hargitai J, Inbar D, Zhang Z, Buxbaum JD, Molholm S, Foxe JJ, Marion RW, Auton A, Greally JM (2014) PLoS Genet 10(5):e1004402.  JOURNAL   PUBMED   REPRINT 

2013 (4)

Naked Mole-Rat Has Increased Translational Fidelity Compared with the Mouse, as Well as a Unique 28S Ribosomal RNA Cleavage. Azpurua J, Ke Z, Chen IX, Zhang Q, Ermolenko DN, Zhang ZD, Gorbunova V, Seluanov A (2013) Proc Natl Acad Sci U S A 110(43):17350-5.  JOURNAL   PUBMED   REPRINT 

SubNet: A Java Application for Subnetwork Extraction. Lemetre C, Zhang Q, Zhang ZD (2013) Bioinformatics 29(19):2509-11.  JOURNAL   PUBMED   REPRINT   WEBSITE 

A Brief Introduction to Tiling Microarrays: Principles, Concepts, and Applications. Lemetre C, Zhang ZD (2013) Methods Mol Biol 1067:3-19.  JOURNAL   PUBMED   REPRINT 

The Origin, Evolution, and Functional Impact of Short Insertion-Deletion Variants Identified in 179 Human Genomes. Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G (2013) Genome Res 23(5):749-61.  JOURNAL   PUBMED   REPRINT 

2012 (3)

An Integrated Encyclopedia of DNA Elements in the Human Genome. ENCODE Project Consortium (2012) Nature 489(7414):57-74.  JOURNAL   PUBMED   REPRINT   WEBSITE 

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C (2012) Science 335(6070):823-8.  JOURNAL   PUBMED   REPRINT 

The Einstein Genome Gateway Using WASP - a High Throughput Multi-Layered Life Sciences Portal for XSEDE. Golden A, McLellan AS, Dubin RA, Jing Q, O Broin P, Moskowitz D, Zhang Z, Suzuki M, Hargitai J, Calder RB, Greally JM (2012) Stud Health Technol Inform 175:182-91.  PUBMED 

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 (2011) BMC Genomics 12:375.  JOURNAL   PUBMED   REPRINT 

ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M (2011) Bioinformatics 27(8):1152-4.  JOURNAL   PUBMED   REPRINT   WEBSITE 

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 (2011) Nature 470(7332):59-65.  JOURNAL   PUBMED   REPRINT 

2010 (3)

Detection of Copy Number Variation from Array Intensity and Sequencing Read Depth Using a Stepwise Bayesian Model. Zhang ZD, Gerstein MB (2010) BMC Bioinformatics 11:539.  JOURNAL   PUBMED   REPRINT 

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 (2010) Nature 467(7319):1061-73.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Identification and Analysis of Unitary Pseudogenes: Historic and Contemporary Gene Losses in Humans and Other Primates. Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M (2010) Genome Biol 11(3):R26.  JOURNAL   PUBMED   REPRINT 

2009 (5)

EBNA1 Regulates Cellular Gene Expression by Binding Cellular Promoters. Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB, Lacy J, Snyder M, Gerstein M, Weissman SM (2009) Proc Natl Acad Sci U S A 106(52):22421-6.  JOURNAL   PUBMED   REPRINT 

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB (2009) PLoS Comput Biol 5(7):e1000432.  JOURNAL   PUBMED   REPRINT   WEBSITE 

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 (2009) Genome Biol 10(2):R23.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Rapid in Vivo Exploration of a 5S rRNA Neutral Network. Zhang ZD, Nayar M, Ammons D, Rampersad J, Fox GE (2009) J Microbiol Methods 76(2):181-7.  JOURNAL   PUBMED   REPRINT 

PeakSeq Enables Systematic Scoring of ChIP-seq Experiments Relative to Controls. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB (2009) Nat Biotechnol 27(1):66-75.  JOURNAL   PUBMED   REPRINT   WEBSITE 

2008 (4)

Modeling ChIP Sequencing in Silico with Applications. Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M (2008) PLoS Comput Biol 4(8):e1000158.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates. Zhang ZD, Weinstock G, Gerstein M (2008) J Mol Evol 66(5):446-56.  JOURNAL   PUBMED   REPRINT 

Systematic Analysis of Transcribed Loci in ENCODE Regions Using RACE Sequencing Reveals Extensive Transcription in the Human Genome. Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M (2008) Genome Biol 9(1):R3.  JOURNAL   PUBMED   REPRINT 

Analysis of Nuclear Receptor Pseudogenes in Vertebrates: How the Silent Tell Their Stories. Zhang ZD, Cayting P, Weinstock G, Gerstein M (2008) Mol Biol Evol 25(1):131-43.  JOURNAL   PUBMED   REPRINT   WEBSITE 

2007 (8)

Divergence of Transcription Factor Binding Sites Across Related Yeast Species. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M (2007) Science 317(5839):815-9.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Transcription Factor Binding Site Identification in Yeast: A Comparison of High-Density Oligonucleotide and PCR-based Microarray Platforms. Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M (2007) Funct Integr Genomics 7(4):335-45.  JOURNAL   PUBMED   REPRINT 

Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ (2007) Nature 447(7146):799-816.  JOURNAL   PUBMED   REPRINT   WEBSITE 

Mapping of Transcription Factor Binding Regions in Mammalian Cells by ChIP: Comparison of Array- and Sequencing-Based Technologies. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M (2007) Genome Res 17(6):898-909.  JOURNAL   PUBMED   REPRINT 

Statistical Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions. Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB (2007) Genome Res 17(6):787-97.  JOURNAL   PUBMED   REPRINT   POSTER   WEBSITE 

Integrated Analysis of Experimental Data Sets Reveals Many Novel Promoters in 1% of the Human Genome. Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z (2007) Genome Res 17(6):720-31.  JOURNAL   PUBMED   REPRINT 

What Is a Gene, Post-Encode? History and Updated Definition. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007) Genome Res 17(6):669-81.  JOURNAL   PUBMED   REPRINT   POSTER 

Tilescope: Online Analysis Pipeline for High-Density Tiling Microarray Data. Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M (2007) Genome Biol 8(5):R81.  JOURNAL   PUBMED   REPRINT   POSTER   WEBSITE 

2006 (4)

A Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and chIP-chip Experiments: Systematically Incorporating Validated Biological Knowledge. Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M (2006) Bioinformatics 22(24):3016-24.  JOURNAL   PUBMED   REPRINT   WEBSITE 

The DNA Sequence, Annotation and Analysis of Human Chromosome 3. Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA (2006) Nature 440(7088):1194-8.  JOURNAL   PUBMED   REPRINT 

The Finished DNA Sequence of Human Chromosome 12. Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Lovering RC, Wheeler DA, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Draper H, Gonzalez-Garay ML, Havlak P, Jackson LR, Jacob LS, Kelly SH, Li L, Li Z, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Pasternak S, Perez LM, Plopper FJ, Santibanez J, Shen H, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Zhang J, Zhou J, Allen CC, Amin AG, Anyalebechi V, Bailey M, Barbaria JA, Bimage KE, Bryant NP, Burch PE, Burkett CE, Burrell KL, Calderon E, Cardenas V, Carter K, Casias K, Cavazos I, Cavazos SR, Ceasar H, Chacko J, Chan SN, Chavez D, Christopoulos C, Chu J, Cockrell R, Cox CD, Dang M, Dathorne SR, David R, Davis CM, Davy-Carroll L, Deshazo DR, Donlin JE, D'Souza L, Eaves KA, Simons R, Emery-Cohen AJ, Escotto M, Flagg N, Forbes LD, Gabisi AM, Garza M, Hamilton C, Henderson N, Hernandez O, Hines S, Hogues ME, Huang M, Idlebird DG, Johnson R, Jolivet A, Jones S, Kagan R, King LM, Leal B, Lebow H, Lee S, LeVan JM, Lewis LC, London P, Lorensuhewa LM, Loulseged H, Lovett DA, Lucier A, Lucier RL, Ma J, Madu RC, Mapua P, Martindale AD, Martinez E, Massey E, Mawhiney S, Meador MG, Mendez S, Mercado C, Mercado IC, Merritt CE, Miner ZL, Minja E, Mitchell T, Mohabbat F, Mohabbat K, Montgomery B, Moore N, Morris S, Munidasa M, Ngo RN, Nguyen NB, Nickerson E, Nwaokelemeh OO, Nwokenkwo S, Obregon M, Oguh M, Oragunye N, Oviedo RJ, Parish BJ, Parker DN, Parrish J, Parks KL, Paul HA, Payton BA, Perez A, Perrin W, Pickens A, Primus EL, Pu LL, Puazo M, Quiles MM, Quiroz JB, Rabata D, Reeves K, Ruiz SJ, Shao H, Sisson I, Sonaike T, Sorelle RP, Sutton AE, Svatek AF, Svetz LA, Tamerisa KS, Taylor TR, Teague B, Thomas N, Thorn RD, Trejos ZY, Trevino BK, Ukegbu ON, Urban JB, Vasquez LI, Vera VA, Villasana DM, Wang L, Ward-Moore S, Warren JT, Wei X, White F, Williamson AL, Wleczyk R, Wooden HS, Wooden SH, Yen J, Yoon L, Yoon V, Zorrilla SE, Nelson D, Kucherlapati R, Weinstock G, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team (2006) Nature 440(7082):346-51.  JOURNAL   PUBMED   REPRINT 

Microbial Identification by Mass Cataloging. Zhang Z, Jackson GW, Fox GE, Willson RC (2006) BMC Bioinformatics 7:117.  JOURNAL   PUBMED   REPRINT 

2004 (2)

Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium (2004) Nature 428(6982):493-521.  JOURNAL   PUBMED   REPRINT 

Genomic Analysis of the Nuclear Receptor Family: New Insights into Structure, Regulation, and Evolution from the Rat Genome. Zhang Z, Burch PE, Cooney AJ, Lanz RB, Pereira FA, Wu J, Gibbs RA, Weinstock G, Wheeler DA (2004) Genome Res 14(4):580-90.  JOURNAL   PUBMED   REPRINT   POSTER 

2003 (1)

Common 5S rRNA Variants Are Likely to Be Accepted in Many Sequence Contexts. Zhang Z, D'Souza LM, Lee YH, Fox GE, New Collective Author (2003) J Mol Evol 56(1):69-76.  JOURNAL   PUBMED   REPRINT 

2002 (2)

Identification of Characteristic Oligonucleotides in the Bacterial 16S Ribosomal RNA Sequence Dataset. Zhang Z, Willson RC, Fox GE, New Collective Author (2002) Bioinformatics 18(2):244-50.  JOURNAL   PUBMED   REPRINT 

NCIR: A Database of Non-Canonical Interactions in Known RNA Structures. Nagaswamy U, Larios-Sanz M, Hury J, Collins S, Zhang Z, Zhao Q, Fox GE (2002) Nucleic Acids Res 30(1):395-7.  JOURNAL   PUBMED   REPRINT   WEBSITE 

2000 (1)

Database of Non-Canonical Base Pairs Found in Known RNA Structures. Nagaswamy U, Voss N, Zhang Z, Fox GE, New Collective Author (2000) Nucleic Acids Res 28(1):375-6.  JOURNAL   PUBMED   REPRINT   WEBSITE