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List of works by Yong Zhang

A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos

scientific article published on 16 November 2020

A comprehensive view of nuclear receptor cancer cistromes

scientific article published on 22 September 2011

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases

scientific article

Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer

scientific article published on July 2009

BSeQC: quality control of bisulfite sequencing experiments

scientific article published on 23 September 2013

CAM: A quality control pipeline for MNase-seq data

scientific article published on 07 August 2017

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

scientific article (publication date: 2014)

CSTEA: a webserver for the Cell State Transition Expression Atlas

scientific article published on 9 May 2017

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data

scientific article

Canonical nucleosome organization at promoters forms during genome activation

scientific article

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

scientific article

Chromatin signature of embryonic pluripotency is established during genome activation

scientific article published on 24 March 2010

Cistrome: an integrative platform for transcriptional regulation studies

scientific article

CistromeFinder for ChIP-seq and DNase-seq data reuse

scientific article

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

scientific article

Classify hyperdiploidy status of multiple myeloma patients using gene expression profiles

scientific article

Comprehensive profiling reveals mechanisms of SOX2-mediated cell fate specification in human ESCs and NPCs

scientific article published on 26 January 2016

Computational inference of mRNA stability from histone modification and transcriptome profiles

scientific article

DiNuP: a systematic approach to identify regions of differential nucleosome positioning

scientific article

Direct induction of neural progenitor cells transiently passes through a partially reprogrammed state

scientific article published on 10 December 2016

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

scientific article published on 14 September 2016

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

scientific article

Dr.seq: a quality control and analysis pipeline for droplet sequencing.

scientific article published on 3 April 2016

Dynamic changes in subgraph preference profiles of crucial transcription factors

scientific article

Epigenome sequencing comes of age in development, differentiation and disease mechanism research

scientific article published on April 2011

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

scientific article

Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm

scientific article published on 28 February 2006

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

scientific article

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

scientific article

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization

scientific article published on 31 May 2021

Genome-wide analysis of mammalian DNA segment fusion/fission.

scientific article published on 14 November 2005

H3K4 Methyltransferase Set1a Is A Key Oct4 Coactivator Essential for Generation of Oct4 Positive Inner Cell Mass

scientific article published on 19 January 2016

HBO1 is a versatile histone acyltransferase critical for promoter histone acylations

scientific article published on 01 August 2021

Histone Demethylase LSD1 Promotes Adipocyte Differentiation through Repressing Wnt Signaling

scientific article published on 9 September 2016

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing

scientific article published on 07 June 2016

Identifying ChIP-seq enrichment using MACS.

scientific article published on 30 August 2012

Identifying Hfq-binding small RNA targets in Escherichia coli

scientific article published on 20 March 2006

Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq

scientific article

Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

Integrated analysis of multiple data sources reveals modular structure of biological networks

scientific article

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

scientific article published on 02 June 2013

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

scientific article

Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation

scientific article published in January 2012

Maternal Sall4 Is Indispensable for Epigenetic Maturation of Mouse Oocytes

scientific article published on 28 December 2016

Model-based analysis of ChIP-Seq (MACS)

scientific article

NONCODE: an integrated knowledge database of non-coding RNAs

scientific article

NPInter: the noncoding RNAs and protein related biomacromolecules interaction database

scientific article

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation

scientific article

Nucleosome dynamics define transcriptional enhancers

scientific article

PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale

scientific article published on November 2008

Phylophenetic properties of metabolic pathway topologies as revealed by global analysis

scientific article

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

scientific article published on 23 April 2018

SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells

scientific article

Systematic evaluation of factors influencing ChIP-seq fidelity

scientific article

Target analysis by integration of transcriptome and ChIP-seq data with BETA.

scientific article

The combination of Tet1 with Oct4 generates high-quality mouse-induced pluripotent stem cells

scientific article

The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast

scientific article published on 08 September 2004

Transcription factor-pathway coexpression analysis reveals cooperation between SP1 and ESR1 on dysregulating cell cycle arrest in non-hyperdiploid multiple myeloma.

scientific article

Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state.

scientific article

Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish

scientific article published on 11 August 2017

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

scientific article published on 24 February 2020

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