Zhang Zhang

Affiliations:
  • Chinese Academy of Sciences, Beijing Institute of Genomics, Beijing, China
  • Yale University, Department of Ecology and Evolutionary Biology, New Haven, CT, USA (former)


According to our database1, Zhang Zhang authored at least 60 papers between 2006 and 2022.

Collaborative distances:

Timeline

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Bibliography

2022
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.
Nucleic Acids Res., 2022

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.
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Nucleic Acids Res., 2022

EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study.
Nucleic Acids Res., 2022

BrainBase: a curated knowledgebase for brain diseases.
Nucleic Acids Res., 2022

LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system.
Nucleic Acids Res., 2022

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.
Nucleic Acids Res., 2022

LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.
Nucleic Acids Res., 2022

KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences.
Genom. Proteom. Bioinform., 2022

2021
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.
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Nucleic Acids Res., 2021

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
Nucleic Acids Res., 2021

Genome Variation Map: a worldwide collection of genome variations across multiple species.
Nucleic Acids Res., 2021

LncExpDB: an expression database of human long non-coding RNAs.
Nucleic Acids Res., 2021

Genome Warehouse: A Public Repository Housing Genome-scale Data.
Genom. Proteom. Bioinform., 2021

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types.
Genom. Proteom. Bioinform., 2021

2020
EWAS Data Hub: a resource of DNA methylation array data and metadata.
Nucleic Acids Res., 2020

GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals.
Nucleic Acids Res., 2020

LSD 3.0: a comprehensive resource for the leaf senescence research community.
Nucleic Acids Res., 2020

SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice.
Genom. Proteom. Bioinform., 2020

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.
Genom. Proteom. Bioinform., 2020

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR.
Genom. Proteom. Bioinform., 2020

IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.
Genom. Proteom. Bioinform., 2020

The Elements of Data Sharing.
Genom. Proteom. Bioinform., 2020

2019
NucMap: a database of genome-wide nucleosome positioning map across species.
Nucleic Acids Res., 2019

iDog: an integrated resource for domestic dogs and wild canids.
Nucleic Acids Res., 2019

Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human.
Nucleic Acids Res., 2019

LncBook: a curated knowledgebase of human long non-coding RNAs.
Nucleic Acids Res., 2019

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies.
Nucleic Acids Res., 2019

Plant editosome database: a curated database of RNA editosome in plants.
Nucleic Acids Res., 2019

In Memory of Vladimir B. Bajic (1952-2019).
Genom. Proteom. Bioinform., 2019

Characterization and identification of long non-coding RNAs based on feature relationship.
Bioinform., 2019

Computational determination of gene age and characterization of evolutionary dynamics in human.
Briefings Bioinform., 2019

2018
Genome Variation Map: a data repository of genome variations in BIG Data Center.
Nucleic Acids Res., 2018

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.
Nucleic Acids Res., 2018

MethBank 3.0: a database of DNA methylomes across a variety of species.
Nucleic Acids Res., 2018

Bioinformatics Commons: The Cornerstone of Life and Health Sciences.
Genom. Proteom. Bioinform., 2018

Rice Genomics: over the Past Two Decades and into the Future.
Genom. Proteom. Bioinform., 2018

2017
CloudPhylo: a fast and scalable tool for phylogeny reconstruction.
Bioinform., 2017

2016
Precision Medicine: What Challenges Are We Facing?
Genom. Proteom. Bioinform., 2016

2015
MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.
Nucleic Acids Res., 2015

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.
Nucleic Acids Res., 2015

Biological Databases for Human Research.
Genom. Proteom. Bioinform., 2015

2014
RiceWiki: a wiki-based database for community curation of rice genes.
Nucleic Acids Res., 2014

Ribogenomics: the Science and Knowledge of RNA.
Genom. Proteom. Bioinform., 2014

PanGP: A tool for quickly analyzing bacterial pan-genome profile.
Bioinform., 2014

2013
Does the Genetic Code Have A Eukaryotic Origin?
Genom. Proteom. Bioinform., 2013

AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.
Bioinform., 2013

2012
The Pendulum Model for Genome Compositional Dynamics: from the Four Nucleotides to the Twenty Amino Acids.
Genom. Proteom. Bioinform., 2012

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition.
Genom. Proteom. Bioinform., 2012

Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis.
Genom. Proteom. Bioinform., 2012

Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes.
Genom. Proteom. Bioinform., 2012

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.
BMC Bioinform., 2012

2011
On the Organizational Dynamics of the Genetic Code.
Genom. Proteom. Bioinform., 2011

2010
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies.
Genom. Proteom. Bioinform., 2010

LOX: inferring Level Of eXpression from diverse methods of census sequencing.
Bioinform., 2010

2009
Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences.
PLoS Comput. Biol., 2009

Bringing Web 2.0 to bioinformatics.
Briefings Bioinform., 2009

2007
FGF: A web tool for Fishing Gene Family in a whole genome database.
Nucleic Acids Res., 2007

2006
TreeFam: a curated database of phylogenetic trees of animal gene families.
Nucleic Acids Res., 2006

Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates.
Genom. Proteom. Bioinform., 2006

KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging.
Genom. Proteom. Bioinform., 2006


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