Publications

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.  pubmed   reprint 

» HEDD: Human Enhancer Disease Database. Wang Z, Zhang Q, Lin JR, Cai Y, Mitra J, Zhang ZD (2018) Nucleic Acids Res 46:D113-D120.  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.  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.  pubmed   reprint 

2017 (7)

» Schizophrenia risk genes. Zhang ZD (2017) Access Science.  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.  pubmed   reprint   website 

» A neurogenetic model for the study of schizophrenia spectrum disorders: The International 22q11.2 Deletion Syndrome Brain Behavior Consortium. Gur R, Bassett A, McDonald-McGinn D, Bearden C, Chow E, Emanuel B, Owen M, Swillen A, van den Bree M, Vermeesch J, Vorstman J, Warren S, Lehner T, Morrow B, The International 22q11.2 Deletion Syndrome Brain Behavior Consortium (2017) Mol Psychiatry 22:1664-1672.  pubmed   reprint   website 

» Translation fidelity coevolves with longevity. Ke Z, Mallik P, Johnson AB, Luna F, Zhang ZD, Gladyshev V, Seluanov A, Gorbunova V (2017) Aging Cell 16(5):988-993.  pubmed   reprint 

» Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer binding protein alpha. Song Z, Xiaoli AM, Zhang Q, Zhang Y, Yang ES, Wang S, Chang R, Zhang ZD, Yang G, Strich R, Pessin JE, Yang F (2017) J Biol Chem 292(21):8918-8932.  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.  pubmed   reprint 

» Network analysis of mitonuclear GWAS reveals functional networks and tissue expression profiles of disease-associated genes. Johnson SC, Gonzales B, Milholland B, Zhang Q, Zhang Z, Suh S (2017) Hum Genet 136:55-65.  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 Y, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN (2016) eLife 5:e19130.  pubmed   reprint 

» Integrated post-GWAS analysis shed 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.  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.  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 Gen 25(14):2934-2947.  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.  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 7(12):1171-1184.  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, O Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM (2015) Epigenetics Chromatin 8:46.  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.  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.  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):288-291.  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, Zhang Z, Vijg J, Gladyshev V, Gorbunova V, Seluanov A (2015) Proc Natl Acad Sci U S A 112(4):1053-1058.  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):531-540.  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 R6, Auton A, Greally JM (2014) PLoS Genet 10(5):e1004402.  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):17350-17355.  pubmed   reprint 

» SubNet: a Java application for subnetwork extraction. Zhang Q, Zhang ZD (2013) Bioinformatics 29(19):2509-2511.  pubmed   reprint   website 

» A brief introduction to tiling microarrays: principles, concepts, and applications. Lemetre C, Zhang ZD (2013) Tiling Arrays: Methods and Protocols (Tin-Lap Lee and Alfred Chun Shui Luk eds.) Methods in Molecular Biology, vol. 1067:3-19.  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):749-761.  pubmed   reprint 

2012 (3)

» An integrated encyclopedia of DNA elements in the human genome. The ENCODE Project Consortium (2012) Nature 489:57-74.  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 335:806-807.  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. 175:182-191.  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(1):375.  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):1152-1154.  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, Stutz 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.  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(1):539.  pubmed   reprint 

» A map of human genome variation from population-scale sequencing. The 1000 Genomes Project Consortium (2010) Nature 467(7319):1061-1073.  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.  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):22421-22426.  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.  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.  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):181-187.  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.  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.  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):446-456.  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.  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):131-143.  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):815-819.  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):335-345.  pubmed   reprint 

» Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. The ENCODE Project Consortium (2007) Nature 447(7146):799-816.  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.  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):787-797.  pubmed   reprint   poster   website 

» Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Trinklein ND, Karaoz 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):720-731.  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):669-681.  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.  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):3016-3024.  pubmed   reprint   website 

» The DNA sequence, annotation and analysis of human chromosome 3. Muzny DM, et al (2006) Nature 440(7088):1194-1198.  pubmed   reprint 

» The finished DNA sequence of human chromosome 12. Scherer SE, et al (2006) Nature 440(7082):346-351.  pubmed   reprint 

» Microbial identification by mass cataloging. Zhang Z, Jackson GW, Fox GE, Willson RC (2006) BMC Bioinformatics 7:117.  pubmed   reprint 

2004 (2)

» Genome sequence of the Brown Norway rat yields insights into mammalian evolution. The Rat Genome Project Consortium (2004) Nature 428(6982):493-521.  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):580-590.  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 (2003) J Mol Evol 56(1):69-76.  pubmed   reprint 

2002 (2)

» Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset . Zhang Z, Willson RC, Fox GE (2002) Bioinformatics 18(2):244-250.  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):395-397.  pubmed   reprint   website 

2000 (1)

» Database of non-canonical base pairs found in known RNA structures. Nagaswamy U, Voss N, Zhang Z, Fox GE (2000) Nucleic Acids Res 28(1):375-376.  pubmed   reprint   website