National Genomics Data Center

Publications

2021

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

CNCB-NGDC Members and Partners.

Nucleic Acids Res, Volume 49, Issue D1, 2021

2021

Genome Variation Map: a worldwide collection of genome variations across multiple species.

Li C, Tian D, Tang B, Liu X, Teng X, Zhao W, Zhang Z, Song S.

Nucleic Acids Res, Volume 49, Issue D1, 2021

2021

LncExpDB: an expression database of human long non-coding RNAs.

Li Z, Liu L, Jiang S, Li Q, Feng C, Du Q, Zou D, Xiao J, Zhang Z, Ma L.

Nucleic Acids Res, Volume 49, Issue D1, 2021

2021

Aging Atlas: a multi-omics database for aging biology.

Aging Atlas Consortium.

Nucleic Acids Res, Volume 49, Issue D1, 2021

2020

GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals.

Tian D, Wang P, Tang B, Teng X, Li C, Liu X, Zou D, Song S, Zhang Z.

Nucleic Acids Res, Volume 48, Issue D1, 2020

2020

EWAS Data Hub: a resource of DNA methylation array data and metadata.

Xiong Z, Li M, Yang F, Ma Y, Sang J, Li R, Li Z, Zhang Z, Bao Y.

Nucleic Acids Res, Volume 48, Issue D1, 2020

2020

LSD 3.0: a comprehensive resource for the leaf senescence research community.

Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z.

Nucleic Acids Res, Volume 48, Issue D1, 2020

2020

PADS Arsenal: a database of prokaryotic defense systems related genes.

Zhang Y, Zhang Z, Zhang H, Zhao Y, Zhang Z, Xiao J.

Nucleic Acids Res, Volume 48, Issue D1, 2020

2020

Database Resources of the National Genomics Data Center in 2020.

National Genomics Data Center Members and Partners.

Nucleic Acids Res, Volume 48, Issue D1, 2020

2020

An online coronavirus analysis platform from the National Genomics Data Center.

Gong Z, Zhu JW, Li CP, Jiang S, Ma LN, Tang BX, Zou D, Chen ML, Sun YB, Song SH, Zhang Z, Xiao JF, Xue YB, Bao YM, Du ZL, Zhao WM.

Zool Res, Volume 41, Issue 6, 2020

2020

Multi-omics annotation of human long non-coding RNAs.

Li Q, Li Z, Feng C, Jiang S, Zhang Z, Ma L.

Biochem Soc Trans, Volume 48, Issue 4, 2020

2020

SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice.

Yan J, Zou D, Li C, Zhang Z, Song S, Wang X.

Genomics Proteomics Bioinformatics, Volume 18, Issue 2, 2020

2020

IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.

Sang J, Zou D, Wang Z, Wang F, Zhang Y, Xia L, Li Z, Ma L, Li M, Xu B, Liu X, Wu S, Liu L, Niu G, Li M, Luo Y, Hu S, Hao L, Zhang Z.

Genomics Proteomics Bioinformatics, Volume 18, Issue 2, 2020

2020

Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling.

Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z.

Biol Direct, Volume 15, Issue 1, 2020

2020

The Elements of Data Sharing.

Zhang Z, Song S, Yu J, Zhao W, Xiao J, Bao Y.

Genomics Proteomics Bioinformatics, Volume 18, Issue 1, 2020

2020

The 2019 novel coronavirus resource.

Zhao WM, Song SH, Chen ML, Zou D, Ma LN, Ma YK, Li RJ, Hao LL, Li CP, Tian DM, Tang BX, Wang YQ, Zhu JW, Chen HX, Zhang Z, Xue YB, Bao YM.

Yi Chuan, Volume 42, Issue 2, 2020

2020

Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders.

Nawaz MS, Asghar R, Pervaiz N, Ali S, Hussain I, Xing P, Bao Y, Abbasi AA.

BMC Evol Biol, Volume 20, Issue 1, 2020

2020

Mapping regulatory variants controlling gene expression in drought response and tolerance in maize.

Liu S, Li C, Wang H, Wang S, Yang S, Liu X, Yan J, Li B, Beatty M, Zastrow-Hayes G, Song S, Qin F.

Genome Biol, Volume 21, Issue 1, 2020

2020

Metagenomic analysis of relative abundance and diversity of bacterial microbiota in Bemisia tabaci infesting cotton crop in Pakistan.

Shah SHJ, Malik AH, Zhang B, Bao Y, Qazi J.

Infect Genet Evol, Volume 84, Issue NULL, 2020

2019

Computational determination of gene age and characterization of evolutionary dynamics in human.

Yin H, Li M, Xia L, He C, Zhang Z.

Brief Bioinform, Volume 20, Issue 6, 2019

2019

LncBook: a curated knowledgebase of human long non-coding RNAs.

Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

NucMap: a database of genome-wide nucleosome positioning map across species.

Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human.

Niu G, Zou D, Li M, Zhang Y, Sang J, Xia L, Li M, Liu L, Cao J, Zhang Y, Wang P, Hu S, Hao L, Zhang Z.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

Database Resources of the BIG Data Center in 2019.

BIG Data Center Members.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies.

Li M, Zou D, Li Z, Gao R, Sang J, Zhang Y, Li R, Xia L, Zhang T, Niu G, Bao Y, Zhang Z.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

Plant editosome database: a curated database of RNA editosome in plants.

Li M, Xia L, Zhang Y, Niu G, Li M, Wang P, Zhang Y, Sang J, Zou D, Hu S, Hao L, Zhang Z.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

iDog: an integrated resource for domestic dogs and wild canids.

Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang YP, Wang GD, Zhao W.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium.

Nucleic Acids Res, Volume 47, Issue D1, 2019

2019

Characterization of Proteome Variation During Modern Maize Breeding.

Jiang LG, Li B, Liu SX, Wang HW, Li CP, Song SH, Beatty M, Zastrow-Hayes G, Yang XH, Qin F, He Y.

Mol Cell Proteomics, Volume 18, Issue 2, 2019

2019

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

Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z.

Bioinformatics, Volume 35, Issue 17, 2019

2019

Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science.

Song S, Zhang Z.

Mol Plant, Volume 12, Issue 3, 2019

2019

Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene.

Seemab S, Pervaiz N, Zehra R, Anwar S, Bao Y, Abbasi AA.

BMC Evol Biol, Volume 19, Issue 1, 2019

2019

Taxonomy of the order Mononegavirales: update 2019.

Amarasinghe GK, Ayllón MA, Bào Y, Basler CF, Bavari S, Blasdell KR, Briese T, Brown PA, Bukreyev A, Balkema-Buschmann A, Buchholz UJ, Chabi-Jesus C, Chandran K, Chiapponi C, Crozier I, de Swart RL, Dietzgen RG, Dolnik O, Drexler JF, Dürrwald R, Dundon WG, Duprex WP, Dye JM, Easton AJ, Fooks AR, Formenty PBH, Fouchier RAM, Freitas-Astúa J, Griffiths A, Hewson R, Horie M, Hyndman TH, Jiāng D, Kitajima EW, Kobinger GP, Kondō H, Kurath G, Kuzmin IV, Lamb RA, Lavazza A, Lee B, Lelli D, Leroy EM, Lǐ J, Maes P, Marzano SL, Moreno A, Mühlberger E, Netesov SV, Nowotny N, Nylund A, Økland AL, Palacios G, Pályi B, Pawęska JT, Payne SL, Prosperi A, Ramos-González PL, Rima BK, Rota P, Rubbenstroth D, Shī M, Simmonds P, Smither SJ, Sozzi E, Spann K, Stenglein MD, Stone DM, Takada A, Tesh RB, Tomonaga K, Tordo N, Towner JS, van den Hoogen B, Vasilakis N, Wahl V, Walker PJ, Wang LF, Whitfield AE, Williams JV, Zerbini FM, Zhāng T, Zhang YZ, Kuhn JH.

Arch Virol, Volume 164, Issue 7, 2019

2019

Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook.

Ma L, Cao J, Liu L, Li Z, Shireen H, Pervaiz N, Batool F, Raza RZ, Zou D, Bao Y, Abbasi AA, Zhang Z.

Curr Protoc Bioinformatics, Volume 67, Issue 1, 2019

2019

Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals.

Pervaiz N, Shakeel N, Qasim A, Zehra R, Anwar S, Rana N, Xue Y, Zhang Z, Bao Y, Abbasi AA.

BMC Evol Biol, Volume 19, Issue 1, 2019

2018

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

Sang J, Wang Z, Li M, Cao J, Niu G, Xia L, Zou D, Wang F, Xu X, Han X, Fan J, Yang Y, Zuo W, Zhang Y, Zhao W, Bao Y, Xiao J, Hu S, Hao L, Zhang Z.

Nucleic Acids Res, Volume 46, Issue D1, 2018

2018

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Song S, Tian D, Li C, Tang B, Dong L, Xiao J, Bao Y, Zhao W, He H, Zhang Z.

Nucleic Acids Res, Volume 46, Issue D1, 2018

2018

MarR-Family Transcription Factor HpaR Controls Expression of the vgrR-vgrS Operon of Xanthomonas campestris pv. campestris.

Pan Y, Liang F, Li RJ, Qian W.

Mol Plant Microbe Interact, Volume 31, Issue 3, 2018

2018

Database Resources of the BIG Data Center in 2018.

BIG Data Center Members.

Nucleic Acids Res, Volume 46, Issue D1, 2018

2018

MethBank 3.0: a database of DNA methylomes across a variety of species.

Li R, Liang F, Li M, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z.

Nucleic Acids Res, Volume 46, Issue D1, 2018

2018

PGAP-X: extension on pan-genome analysis pipeline.

Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X, Yang J, Wang L, Wang J, Fu H, Kang Y, Chen F, Yu J, Wu J, Xiao J.

BMC Genomics, Volume 19, Issue Suppl 1, 2018

2018

Biocuration: Distilling data into knowledge.

International Society for Biocuration.

PLoS Biol, Volume 16, Issue 4, 2018

2018

RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum.

Ma C, Chang M, Lv H, Zhang ZW, Zhang W, He X, Wu G, Zhao S, Zhang Y, Wang D, Teng X, Liu C, Li Q, Klungland A, Niu Y, Song S, Tong WM.

Genome Biol, Volume 19, Issue 1, 2018

2018

Bioinformatics Commons: The Cornerstone of Life and Health Sciences.

Zhang Z, Xue Y, Zhao F.

Genomics Proteomics Bioinformatics, Volume 16, Issue 4, 2018

2018

PGAweb: A Web Server for Bacterial Pan-Genome Analysis.

Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z, Xiao J.

Front Microbiol, Volume 9, Issue NULL, 2018

2018

[Database resources of the reference genome and genetic variation maps for the Chinese population].

Song S, Teng XF, Xiao JF.

Yi Chuan, Volume 40, Issue 11, 2018

2018

[GSA: Genome Sequence Archive].

Zhang SS, Chen TT, Zhu JW, Zhou Q, Chen X, Wang YQ, Zhao WM.

Yi Chuan, Volume 40, Issue 11, 2018

2018

[Prospects for national biological big data centers].

Ma YK, Bao YM.

Yi Chuan, Volume 40, Issue 11, 2018

2018

[The BIG Data Center's database resources].

Zhang YS, Xia L, Sang J, Li M, Liu L, Li MW, Niu GY, Cao JB, Teng XF, Zhou Q, Zhang Z.

Yi Chuan, Volume 40, Issue 11, 2018

2018

Rice Genomics: over the Past Two Decades and into the Future.

Song S, Tian D, Zhang Z, Hu S, Yu J.

Genomics Proteomics Bioinformatics, Volume 16, Issue 6, 2018

2017

MTD: a mammalian transcriptomic database to explore gene expression and regulation.

Sheng X, Wu J, Sun Q, Li X, Xian F, Sun M, Fang W, Chen M, Yu J, Xiao J.

Brief Bioinform, Volume 18, Issue 1, 2017

2017

The BIG Data Center: from deposition to integration to translation.

BIG Data Center Members.

Nucleic Acids Res, Volume 45, Issue D1, 2017

2017

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

Yuan L, Yu Y, Zhu Y, Li Y, Li C, Li R, Ma Q, Siu GK, Yu J, Jiang T, Xiao J, Kang Y.

BMC Genomics, Volume 18, Issue Suppl 1, 2017

2017

Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells.

Jin J, Li R, Jiang C, Zhang R, Ge X, Liang F, Sheng X, Dai W, Chen M, Wu J, Xiao J, Su W.

BMC Genomics, Volume 18, Issue Suppl 1, 2017

2017

CloudPhylo: a fast and scalable tool for phylogeny reconstruction.

Xu X, Ji Z, Zhang Z.

Bioinformatics, Volume 33, Issue 3, 2017

2017

GSA: Genome Sequence Archive.

Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, Tang B, Dong L, Ding N, Zhang Q, Bai Z, Dong X, Chen H, Sun M, Zhai S, Sun Y, Yu L, Lan L, Xiao J, Fang X, Lei H, Zhang Z, Zhao W.

Genomics Proteomics Bioinformatics, Volume 15, Issue 1, 2017

2017

Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice.

Xia L, Zou D, Sang J, Xu X, Yin H, Li M, Wu S, Hu S, Hao L, Zhang Z.

J Genet Genomics, Volume 44, Issue 5, 2017

2017

Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015.

Su W, Li X, Chen M, Dai W, Sun S, Wang S, Sheng X, Sun S, Gao C, Hou A, Zhou Y, Sun B, Gao F, Xiao J, Zhang Z, Jiang C.

Infect Genet Evol, Volume 53, Issue NULL, 2017

2017

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.

Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB.

RNA Biol, Volume 14, Issue 7, 2017

2017

An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ of Xanthomonas campestris.

Peng BY, Pan Y, Li RJ, Wei JW, Liang F, Wang L, Wang FF, Qian W.

Genetics, Volume 206, Issue 4, 2017

2017

Region-specific RNA m6A methylation represents a new layer of control in the gene regulatory network in the mouse brain.

Chang M, Lv H, Zhang W, Ma C, He X, Zhao S, Zhang ZW, Zeng YX, Song S, Niu Y, Tong WM.

Open Biol, Volume 7, Issue 9, 2017

2017

Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia.

Yan H, Xie JB, Ji ZJ, Yuan N, Tian CF, Ji SK, Wu ZY, Zhong L, Chen WX, Du ZL, Wang ET, Chen WF.

Front Microbiol, Volume 8, Issue NULL, 2017

2016

Information Commons for Rice (IC4R).

IC4R Project Consortium, Hao L, Zhang H, Zhang Z, Hu S, Xue Y.

Nucleic Acids Res, Volume 44, Issue D1, 2016

2016

Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology.

Zhu L, Zhong J, Jia X, Liu G, Kang Y, Dong M, Zhang X, Li Q, Yue L, Li C, Fu J, Xiao J, Yan J, Zhang B, Lei M, Chen S, Lv L, Zhu B, Huang H, Chen F.

Nucleic Acids Res, Volume 44, Issue 2, 2016

2016

SorGSD: a sorghum genome SNP database.

Luo H, Zhao W, Wang Y, Xia Y, Wu X, Zhang L, Tang B, Zhu J, Fang L, Du Z, Bekele WA, Tai S, Jordan DR, Godwin ID, Snowdon RJ, Mace ES, Jing HC, Luo J.

Biotechnol Biofuels, Volume 9, Issue NULL, 2016

2016

Complete genome sequence and comparative genome analysis of a new special Yersinia enterocolitica.

Shi G, Su M, Liang J, Duan R, Gu W, Xiao Y, Zhang Z, Qiu H, Zhang Z, Li Y, Zhang X, Ling Y, Song L, Chen M, Zhao Y, Wu J, Jing H, Xiao J, Wang X.

Arch Microbiol, Volume 198, Issue 7, 2016

2016

Randomness in Sequence Evolution Increases over Time.

Wang G, Sun S, Zhang Z.

PLoS One, Volume 11, Issue 5, 2016

2016

Old genes experience stronger translational selection than young genes.

Yin H, Ma L, Wang G, Li M, Zhang Z.

Gene, Volume 590, Issue 1, 2016

2016

Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level.

Tian X, Zhang Z, Yang T, Chen M, Li J, Chen F, Yang J, Li W, Zhang B, Zhang Z, Wu J, Zhang C, Long L, Xiao J.

Front Microbiol, Volume 7, Issue NULL, 2016

2016

Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation.

Yu L, Wang GD, Ruan J, Chen YB, Yang CP, Cao X, Wu H, Liu YH, Du ZL, Wang XP, Yang J, Cheng SC, Zhong L, Wang L, Wang X, Hu JY, Fang L, Bai B, Wang KL, Yuan N, Wu SF, Li BG, Zhang JG, Yang YQ, Zhang CL, Long YC, Li HS, Yang JY, Irwin DM, Ryder OA, Li Y, Wu CI, Zhang YP.

Nat Genet, Volume 48, Issue 8, 2016

2016

Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli.

Sun S, Xiao J, Zhang H, Zhang Z.

Front Microbiol, Volume 7, Issue NULL, 2016

2016

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.

Li D, Huang Z, Song S, Xin Y, Mao D, Lv Q, Zhou M, Tian D, Tang M, Wu Q, Liu X, Chen T, Song X, Fu X, Zhao B, Liang C, Li A, Liu G, Li S, Hu S, Cao X, Yu J, Yuan L, Chen C, Zhu L.

Proc Natl Acad Sci U S A, Volume 113, Issue 41, 2016

2016

Characterization of Spectinomycin Resistance in Streptococcus suis Leads to Two Novel Insights into Drug Resistance Formation and Dissemination Mechanism.

Huang K, Zhang Q, Song Y, Zhang Z, Zhang A, Xiao J, Jin M.

Antimicrob Agents Chemother, Volume 60, Issue 10, 2016

2016

Precision Medicine: What Challenges Are We Facing?

Xue Y, Lameijer EW, Ye K, Zhang K, Chang S, Wang X, Wu J, Gao G, Zhao F, Li J, Han C, Xu S, Xiao J, Yang X, Ying X, Zhang X, Chen WH, Liu Y, Zhang Z, Huang K, Yu J.

Genomics Proteomics Bioinformatics, Volume 14, Issue 5, 2016

2016

What Signatures Dominantly Associate with Gene Age?

Yin H, Wang G, Ma L, Yi SV, Zhang Z.

Genome Biol Evol, Volume 8, Issue 10, 2016