Zhengdong D. Zhang

发表

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

M. Gerstein, J. Korbel, A. Abyzov, 2009, Genome Biology.

Mapping copy number variation by population scale genome sequencing

Kenny Q. Ye, G. T. Marth, Hugo Y. K. Lam, 2010, Nature.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

Raymond K. Auerbach, M. Gerstein, N. Carriero, 2009, Nature Biotechnology.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Lisa M. D'Souza, Colin N. Dewey, Martin S. Taylor, 2004, Nature.

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

Joseph K. Pickrell, M. DePristo, E. Banks, 2012, Science.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Yijun Ruan, Chia-Lin Wei, Mark B Gerstein, 2007, Genome research.

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

M. Gerstein, J. Harrow, A. Frankish, 2010, Genome Biology.

From Gene Expression to Disease Phenotypes: Network-Based Approaches to Study Complex Human Diseases

Zhengdong D. Zhang, R. Nogales-Cadenas, Quanwei Zhang, 2016 .

Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model

Zhengdong D. Zhang, R. Nogales-Cadenas, C. Montagna, 2017, BMC Genomics.

Divergence of transcription factor binding sites across related yeast species.

Mark Gerstein, Haiyuan Yu, Michael R. Seringhaus, 2007, Science.

Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies

Zhengdong D. Zhang, B. Morrow, Quanwei Zhang, 2017, PLoS genetics.

What is a gene, post-ENCODE? History and updated definition.

M. Gerstein, J. Korbel, Zhengdong D. Zhang, 2007, Genome research.

Identification of genomic indels and structural variations using split reads

Hugo Y. K. Lam, M. Gerstein, A. Abyzov, 2011, BMC Genomics.

Comparative genetics of longevity and cancer: insights from long-lived rodents

Zhengdong D. Zhang, V. Gladyshev, J. Vijg, 2014, Nature Reviews Genetics.

INK4 locus of the tumor-resistant rodent, the naked mole rat, expresses a functional p15/p16 hybrid isoform

Zhengdong D. Zhang, V. Gladyshev, J. Vijg, 2014, Proceedings of the National Academy of Sciences.

Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates

M. Gerstein, G. Weinstock, Zhengdong D. Zhang, 2008, Journal of Molecular Evolution.

MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice

Jhih-Rong Lin, Quanwei Zhang, Cristina Montagna, 2016, Breast Cancer Research.

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

Mark Gerstein, Gil McVean, Laurent Duret, 2013, Genome research.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

Mark Gerstein, Joel Rozowsky, Alexander E Urban, 2008, Genome Biology.

Tilescope: online analysis pipeline for high-density tiling microarray data

Mark Gerstein, Hugo Y. K. Lam, Joel Rozowsky, 2007, Genome Biology.

Erratum: SubNet: A Java application for subnetwork extraction (Bioinformatics (2013) 29:19 (2509-2511) doi: 10.1093/bioinformatics/btt430)

Christophe Lemetre, Zhengdong D. Zhang, Quanwei Zhang, 2013 .

Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage

Quanwei Zhang, Dmitri N. Ermolenko, Andrei Seluanov, 2013, Proceedings of the National Academy of Sciences.

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

MacArthur Protein-Coding Genes A Systematic Survey of Loss-of-Function Variants in Human

Klaudia Walter, Joseph K. Pickrell, Jennifer Harrow, 2012 .

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.

Zhiping Weng, Richard M Myers, Anason S. Halees, 2007, Genome research.

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

Mark Gerstein, Michael R. Seringhaus, Anthony R. Borneman, 2007, Functional & Integrative Genomics.

Genetics of extreme human longevity to guide drug discovery for healthy ageing

Shayne D. Wierbowski, Haiyuan Yu, Zhengdong D. Zhang, 2020, Nature Metabolism.

Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity.

Maxwell D. Sanderford, Zhengdong D. Zhang, Sudhir Kumar, 2020, Cell reports.

The genome of North American beaver provides insights into the mechanisms of its longevity and cancer resistance

Zhengdong D. Zhang, V. Gladyshev, J. Vijg, 2020, bioRxiv.

DNA repair in species with extreme lifespan differences

Zhengdong D. Zhang, A. Aliper, A. Zhavoronkov, 2015, Aging.

Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways

Zhengdong D. Zhang, S. Austad, J. Vijg, 2020, GeroScience.

Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung

Zhengdong D. Zhang, J. Vijg, Y. Suh, 2018, Epigenetics.

SIRT 6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species Graphical

Zhengdong D. Zhang, B. Kennedy, V. Gladyshev, 2019 .

Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer’s disease, providing new insights into its disease mechanisms

Zhengdong D. Zhang, Quanwei Zhang, Jhih-rong Lin, 2020, Scientific Reports.

Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity

Zhengdong D. Zhang, A. Galecki, V. Gladyshev, 2016, eLife.

Sensitivity of primary fibroblasts in culture to atmospheric oxygen does not correlate with species lifespan

Zhengdong D. Zhang, E. Nevo, V. Gladyshev, 2016 .

Unravelling genetic components of longevity

Zhengdong D. Zhang, M. Jabalameli, 2022, Nature Aging.

JWA, a novel microtubule-associated protein, regulates homeostasis of intracellular amino acids in PC12 cells

Zhengdong D. Zhang, Hai-rong Chen, C. Zou, 2003 .

Introduction to Tiling Microarrays : Principles , Concepts , and Applications

Zhengdong D. Zhang, C. Lemetre, 2013 .

A brief introduction to tiling microarrays: principles, concepts, and applications.

Zhengdong D. Zhang, C. Lemetre, 2013, Methods in molecular biology.

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Pilib Ó Broin, Zhengdong D. Zhang, C. Seoighe, 2015, bioRxiv.

Network analysis of mitonuclear GWAS reveals functional networks and tissue expression profiles of disease-associated genes

Zhengdong D. Zhang, Y. Suh, Quanwei Zhang, 2016, Human Genetics.

Ectopic cervical thymi and no thymic involution until midlife in naked mole rats

Zhengdong D. Zhang, V. Gladyshev, S. Emmrich, 2021, Aging cell.

Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome.

Richard A Gibbs, David A Wheeler, George Weinstock, 2004, Genome research.

Ectopic cervical thymi and no thymic involution until midlife in naked mole-rats

Zhengdong D. Zhang, V. Gladyshev, S. Emmrich, 2021, bioRxiv.

The DNA sequence, annotation and analysis of human chromosome 3

Wei Huang, Hans Lehrach, Paul Havlak, 2006, Nature.

HEDD: Human Enhancer Disease Database

Zhen Wang, Ying Cai, Wen Zhang, 2017, Nucleic Acids Res..

The nutritional environment determines which and how intestinal stem cells contribute to homeostasis and tumorigenesis.

Kenny Q. Ye, Samuel E. Zimmerman, Zhengdong D. Zhang, 2019, Carcinogenesis.

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder

John J. Foxe, A. Auton, B. Abrahams, 2014, bioRxiv.

Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation

Zhengdong D. Zhang, J. Vijg, Xiao Dong, 2019, bioRxiv.

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.

Zhiping Weng, Yutao Fu, Mark B Gerstein, 2007, Genome research.

SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species

Zhengdong D. Zhang, B. Kennedy, V. Gladyshev, 2019, Cell.

Genetic signature of human longevity in PKC and NF‐κB signaling

Trina M. Norden-Krichmar, N. Schork, Zhengdong D. Zhang, 2021, Aging cell.

Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer-binding protein α

Zhengdong D. Zhang, Fajun Yang, Gongshe Yang, 2017, The Journal of Biological Chemistry.

Transposon-triggered innate immune response confers cancer resistance to the blind mole rat

S. Horvath, Zhengdong D. Zhang, M. Sweet, 2021, Nature Immunology.

ACT: aggregation and correlation toolbox for analyses of genome tracks

Lucas Lochovsky, Mark Gerstein, Jie Wang, 2011, Bioinform..

The finished DNA sequence of human chromosome 12

Paul Havlak, Christian J. Buhay, Donna M. Muzny, 2006, Nature.

Whole‐Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations

Jonathan H. Chung, K. Coleman, Zhengdong D. Zhang, 2015, Human mutation.

Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human

Zhengdong D. Zhang, V. Gladyshev, C. Lemetre, 2015, Aging cell.

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

M. Gerstein, G. Weinstock, Philip Cayting, 2007, Molecular biology and evolution.

Systems-level analysis of human aging genes shed new light on mechanisms of aging.

Jhih-Rong Lin, Jan Vijg, Quanwei Zhang, 2016, Human molecular genetics.

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

Alex V. Kotlar, Sunny X. Tang, E. Zackai, 2020, Molecular Psychiatry.

Bioinformatics Original Paper a Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and Chip-chip Experiments: Systematically Incorporating Validated Biological Knowledge

Mark Gerstein, Jan O. Korbel, Michael Snyder, 2022 .

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants

Mark Gerstein, Michael Snyder, Yong Kong, 2009, PLoS Comput. Biol..

Modeling ChIP Sequencing In Silico with Applications

Mark Gerstein, Michael Snyder, Joel S. Rozowsky, 2008, PLoS Comput. Biol..

Rare genetic coding variants associated with human longevity and protection against age-related diseases

Kenny Q. Ye, Zhengdong D. Zhang, M. Greicius, 2021, Nature Aging.

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model

Mark Gerstein, Zhengdong D. Zhang, M. Gerstein, 2010, BMC Bioinformatics.

EBNA1 regulates cellular gene expression by binding cellular promoters

M. Gerstein, Michael P. Snyder, Zhengdong D. Zhang, 2009, Proceedings of the National Academy of Sciences.

Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation

Zhengdong D. Zhang, V. Gladyshev, Zachary Smith, 2021, Cell reports.

Prioritization of Schizophrenia Risk Genes by a Network-Regularized Logistic Regression Method

Ying Cai, Wen Zhang, Zhengdong D. Zhang, 2016, IWBBIO.

Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia

Jhih-Rong Lin, Quanwei Zhang, Rubén Nogales-Cadenas, 2016, Genetics.

Enhancer release and retargeting activates disease-susceptibility genes

K. Frazer, Zhengdong D. Zhang, Sreejith J. Nair, 2021, Nature.

NCIR: a database of non-canonical interactions in known RNA structures

Qin Zhao, George E. Fox, Zhengdong Zhang, 2002, Nucleic Acids Res..

Rapid in vivo exploration of a 5S rRNA neutral network.

Zhengdong D. Zhang, G. Fox, D. Ammons, 2009, Journal of microbiological methods.

Epigenetic alterations to Polycomb targets precede malignant transition in a mouse model of breast cancer

Zhengdong D. Zhang, C. Montagna, Quanwei Zhang, 2018, Scientific Reports.

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

Zhengdong D. Zhang, M. Jabalameli, Z. D. Zhang, 2022, Frontiers in Genetics.

Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset

Richard C. Willson, George E. Fox, Zhengdong Zhang, 2002, Bioinform..

Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia

M. Owen, Zhengdong D. Zhang, R. Gur, 2023, Molecular Psychiatry.

Protocol for gene annotation, prediction, and validation of genomic gene expansion

Zhengdong D. Zhang, Quanwei Zhang, 2022, STAR protocols.

Translation fidelity coevolves with longevity

Zhengdong D. Zhang, E. Nevo, V. Gladyshev, 2017, Aging cell.

Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model

Zhengdong D. Zhang, C. Montagna, Quanwei Zhang, 2017, BMC Genomics.

Database of non-canonical base pairs found in known RNA structures

George E. Fox, Zhengdong Zhang, Neil Voss, 2000, Nucleic Acids Res..

DNA repair and anti-cancer mechanisms in the longest-living mammal: the bowhead whale

J. George, Zhengdong D. Zhang, V. Gladyshev, 2023, bioRxiv.

Microbial identification by mass cataloging

Richard C. Willson, George E. Fox, Zhengdong Zhang, 2006, BMC Bioinformatics.

MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice

Zhengdong D. Zhang, C. Montagna, Quanwei Zhang, 2016, Breast Cancer Research.

Chromatin regulators in the TBX1 network confer risk for conotruncal heart defects in 1 22q11.2DS and sporadic congenital heart disease 2

M. Owen, C. Marshall, Zhengdong D. Zhang, 2022 .

Mapping copy number variation by population scale genome sequencing

Joshua M. Korn, Kenny Q. Ye, G. T. Marth, 2010, Nature.

Divergence of transcription factor binding sites across related yeast species.

Michael R. Seringhaus, M. Gerstein, Haiyuan Yu, 2007, Science.

DNA repair and anti-cancer mechanisms in the longest-living mammal: the bowhead whale

J. George, Zhengdong D. Zhang, V. Gladyshev, 2023, bioRxiv.

The Einstein Genome Gateway using WASP - A High Throughput Multi-Layered Life Sciences Portal for XSEDE

Aaron Golden, John M. Greally, Zhengdong Zhang, 2012, HealthGrid.

Common 5S rRNA Variants Are Likely To Be Accepted in Many Sequence Contexts

Lisa M. D'Souza, Zhengdong D. Zhang, G. Fox, 2002, Journal of Molecular Evolution.

Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer-binding protein α

Zhengdong D. Zhang, Fajun Yang, Gongshe Yang, 2017, Journal of Biological Chemistry.

Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer’s disease, providing new insights into its disease mechanisms

Zhengdong D. Zhang, Quanwei Zhang, Jhih-rong Lin, 2021, Scientific Reports.

Sensitivity of primary fibroblasts in culture to atmospheric oxygen does not correlate with species lifespan

Zhengdong D. Zhang, E. Nevo, V. Gladyshev, 2016, Aging.

Tilescope: online analysis pipeline for high-density tiling microarray data

Hugo Y. K. Lam, M. Gerstein, Zhengdong D. Zhang, 2007, Genome Biology.

PGA: post-GWAS analysis for disease gene identification

Zhen Wang, Ying Cai, Zhengdong D. Zhang, 2018, Bioinform..

SubNet: a Java application for subnetwork extraction

Zhengdong D. Zhang, Quanwei Zhang, Zhengdong D. Zhang, 2013, Bioinform..

Chromatin regulators in the TBX1 network confer risk for conotruncal heart defects in 22q11.2DS

M. Owen, C. Marshall, Zhengdong D. Zhang, 2023, NPJ genomic medicine.