Publications

2022 CeDR Atlas: a knowledgebase of cellular drug response.
CeDR Atlas: a knowledgebase of cellular drug response.

Wang YY, Kang H, Xu T, Hao L, Bao Y, Jia P.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34634794 DOI: 10.1093/nar/gkab897

2022 scMethBank: a database for single-cell whole genome DNA methylation maps.
scMethBank: a database for single-cell whole genome DNA methylation maps.

Zong W, Kang H, Xiong Z, Ma Y, Jin T, Gong Z, Yi L, Zhang M, Wu S, Wang G, Bao Y, Li R.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34570235 DOI: 10.1093/nar/gkab833

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

Xiong Z, Yang F, Li M, Ma Y, Zhao W, Wang G, Li Z, Zheng X, Zou D, Zong W, Kang H, Jia Y, Li R, Zhang Z, Bao Y.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34718752 DOI: 10.1093/nar/gkab972

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

CNCB-NGDC Members and Partners.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34718731 DOI: 10.1093/nar/gkab951

2022 CancerSCEM: a database of single-cell expression map across various human cancers.
CancerSCEM: a database of single-cell expression map across various human cancers.

Zeng J, Zhang Y, Shang Y, Mai J, Shi S, Lu M, Bu C, Zhang Z, Zhang Z, Li Y, Du Z, Xiao J.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34643725 DOI: 10.1093/nar/gkab905

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

Zhang Y, Zou D, Zhu T, Xu T, Chen M, Niu G, Zong W, Pan R, Jing W, Sang J, Liu C, Xiong Y, Sun Y, Zhai S, Chen H, Zhao W, Xiao J, Bao Y, Hao L, Zhang Z.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34591957 DOI: 10.1093/nar/gkab878

2022 BrainBase: a curated knowledgebase for brain diseases.
BrainBase: a curated knowledgebase for brain diseases.

Liu L, Zhang Y, Niu G, Li Q, Li Z, Zhu T, Feng C, Liu X, Zhang Y, Xu T, Chen R, Teng X, Zhang R, Zou D, Ma L, Zhang Z.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34718720 DOI: 10.1093/nar/gkab987

2022 CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.

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

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34718745 DOI: 10.1093/nar/gkab979

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

Liu L, Li Z, Liu C, Zou D, Li Q, Feng C, Jing W, Luo S, Zhang Z, Ma L.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34751395 DOI: 10.1093/nar/gkab998

2022 Regeneration Roadmap: database resources for regenerative biology.
Regeneration Roadmap: database resources for regenerative biology.

Kang W, Jin T, Zhang T, Ma S, Yan H, Liu Z, Ji Z, Cai Y, Wang S, Song M, Ren J, Hu B, Zhou Q, Zhang W, Qu J, Bao Y, Liu GH.

Nucleic acids research, Volume 50, Issue D1, 2022

PMID: 34591960 DOI: 10.1093/nar/gkab870

2021 Genome Warehouse: A Public Repository Housing Genome-scale Data.
Genome Warehouse: A Public Repository Housing Genome-scale Data.

Chen M, Ma Y, Wu S, Zheng X, Kang H, Sang J, Xu X, Hao L, Li Z, Gong Z, Xiao J, Zhang Z, Zhao W, Bao Y.

Genomics, proteomics & bioinformatics, Volume , Issue , 2021

PMID: 34175476 DOI: 10.1016/j.gpb.2021.04.001

2021 Aging Atlas: a multi-omics database for aging biology.
Aging Atlas: a multi-omics database for aging biology.

Aging Atlas Consortium.

Nucleic acids research, Volume 49, Issue D1, 2021

PMID: 33119753 DOI: 10.1093/nar/gkaa894

2021 LncExpDB: an expression database of human long non-coding RNAs.
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 research, Volume 49, Issue D1, 2021

PMID: 33045751 DOI: 10.1093/nar/gkaa850

2021 Genome Variation Map: a worldwide collection of genome variations across multiple species.
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 research, Volume 49, Issue D1, 2021

PMID: 33170268 DOI: 10.1093/nar/gkaa1005

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

CNCB-NGDC Members and Partners.

Nucleic acids research, Volume 49, Issue D1, 2021

PMID: 33175170 DOI: 10.1093/nar/gkaa1022

2021 SorGSD: updating and expanding the sorghum genome science database with new contents and tools.
SorGSD: updating and expanding the sorghum genome science database with new contents and tools.

Liu Y, Wang Z, Wu X, Zhu J, Luo H, Tian D, Li C, Luo J, Zhao W, Hao H, Jing HC.

Biotechnology for biofuels, Volume 14, Issue 1, 2021

PMID: 34344425 DOI: 10.1186/s13068-021-02016-7

2021 Molecular evolutionary analysis of human primary microcephaly genes.
Molecular evolutionary analysis of human primary microcephaly genes.

Pervaiz N, Kang H, Bao Y, Abbasi AA.

BMC ecology and evolution, Volume 21, Issue 1, 2021

PMID: 33941077 DOI: 10.1186/s12862-021-01801-0

2021 RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks.
RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks.

Shi S, Qian Q, Yu S, Wang Q, Wang J, Zeng J, Du Z, Xiao J.

Briefings in bioinformatics, Volume 22, Issue 6, 2021

PMID: 34402866 DOI: 10.1093/bib/bbab326

2021 iSheep: an Integrated Resource for Sheep Genome, Variant and Phenotype.
iSheep: an Integrated Resource for Sheep Genome, Variant and Phenotype.

Wang ZH, Zhu QH, Li X, Zhu JW, Tian DM, Zhang SS, Kang HL, Li CP, Dong LL, Zhao WM, Li MH.

Frontiers in genetics, Volume 12, Issue , 2021

PMID: 34490043 DOI: 10.3389/fgene.2021.714852

2021 Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers.
Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers.

Liu X, Wang P, Teng X, Zhang Z, Song S.

Frontiers in oncology, Volume 11, Issue , 2021

PMID: 33718187 DOI: 10.3389/fonc.2021.624395

2021 The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types.
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types.

Chen T, Chen X, Zhang S, Zhu J, Tang B, Wang A, Dong L, Zhang Z, Yu C, Sun Y, Chi L, Chen H, Zhai S, Sun Y, Lan L, Zhang X, Xiao J, Bao Y, Wang Y, Zhang Z, Zhao W.

Genomics, proteomics & bioinformatics, Volume , Issue , 2021

PMID: 34400360 DOI: 10.1016/j.gpb.2021.08.001

2021 Genomic Epidemiology of SARS-CoV-2 in Pakistan.
Genomic Epidemiology of SARS-CoV-2 in Pakistan.

Song S, Li C, Kang L, Tian D, Badar N, Ma W, Zhao S, Jiang X, Wang C, Sun Y, Li W, Lei M, Li S, Qi Q, Ikram A, Salman M, Umair M, Shireen H, Batool F, Zhang B, Chen H, Yang Y, Ali Abbasi A, Li M, Xue Y, Bao Y.

Genomics, proteomics & bioinformatics, Volume , Issue , 2021

PMID: 34695600 DOI: 10.1016/j.gpb.2021.08.007

2021 GSA-Human: Genome Sequence Archive for Human.
GSA-Human: Genome Sequence Archive for Human.

Zhang SS, Chen X, Chen TT, Zhu JW, Tang BX, Wang AK, Dong LL, Zhang ZW, Sun YL, Yu CX, Zhai S, Sun YB, Chen HX, Du ZL, Xiao JF, Zhang Z, Bao YM, Wang YQ, Zhao WM.

Yi chuan = Hereditas, Volume 43, Issue 10, 2021

PMID: 34702711 DOI: 10.16288/j.yczz.21-248

2020 Metagenomic analysis of relative abundance and diversity of bacterial microbiota in Bemisia tabaci infesting cotton crop in Pakistan.
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.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, Volume 84, Issue , 2020

PMID: 32470630 DOI: 10.1016/j.meegid.2020.104381

2020 IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.
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

PMID: 32683045 DOI: 10.1016/j.gpb.2018.12.011

2020 Mapping regulatory variants controlling gene expression in drought response and tolerance in maize.
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 biology, Volume 21, Issue 1, 2020

PMID: 32631406 DOI: 10.1186/s13059-020-02069-1

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.
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 evolutionary biology, Volume 20, Issue 1, 2020

PMID: 33028204 DOI: 10.1186/s12862-020-01684-7

2020 The 2019 novel coronavirus resource.
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 = Hereditas, Volume 42, Issue 2, 2020

PMID: 32102777 DOI: 10.16288/j.yczz.20-030

2020 The Elements of Data Sharing.
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

PMID: 32360769 DOI: 10.1016/j.gpb.2020.04.001

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

PMID: 32619768 DOI: 10.1016/j.gpb.2020.03.002

2020 Multi-omics annotation of human long non-coding RNAs.
Multi-omics annotation of human long non-coding RNAs.

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

Biochemical Society transactions, Volume 48, Issue 4, 2020

PMID: 32756901 DOI: 10.1042/bst20191063

2020 An online coronavirus analysis platform from the National Genomics Data Center.
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.

Zoological research, Volume 41, Issue 6, 2020

PMID: 33045776 DOI: 10.24272/j.issn.2095-8137.2020.065

2020 Database Resources of the National Genomics Data Center in 2020.
Database Resources of the National Genomics Data Center in 2020.

National Genomics Data Center Members and Partners.

Nucleic acids research, Volume 48, Issue D1, 2020

PMID: 31702008 DOI: 10.1093/nar/gkz913

2020 PADS Arsenal: a database of prokaryotic defense systems related genes.
PADS Arsenal: a database of prokaryotic defense systems related genes.

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

Nucleic acids research, Volume 48, Issue D1, 2020

PMID: 31620779 DOI: 10.1093/nar/gkz916

2020 LSD 3.0: a comprehensive resource for the leaf senescence research community.
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 research, Volume 48, Issue D1, 2020

PMID: 31599330 DOI: 10.1093/nar/gkz898

2020 EWAS Data Hub: a resource of DNA methylation array data and metadata.
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 research, Volume 48, Issue D1, 2020

PMID: 31584095 DOI: 10.1093/nar/gkz840

2020 GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals.
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 research, Volume 48, Issue D1, 2020

PMID: 31566222 DOI: 10.1093/nar/gkz828

2020 Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling.
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.

Biology direct, Volume 15, Issue 1, 2020

PMID: 32539851 DOI: 10.1186/s13062-020-00264-5

2019 iDog: an integrated resource for domestic dogs and wild canids.
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 research, Volume 47, Issue D1, 2019

PMID: 30371881 DOI: 10.1093/nar/gky1041

2019 Taxonomy of the order Mononegavirales: update 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.

Archives of virology, Volume 164, Issue 7, 2019

PMID: 31089958 DOI: 10.1007/s00705-019-04247-4

2019 Plant editosome database: a curated database of RNA editosome in plants.
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 research, Volume 47, Issue D1, 2019

PMID: 30364952 DOI: 10.1093/nar/gky1026

2019 EWAS Atlas: a curated knowledgebase of epigenome-wide association studies.
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 research, Volume 47, Issue D1, 2019

PMID: 30364969 DOI: 10.1093/nar/gky1027

2019 Database Resources of the BIG Data Center in 2019.
Database Resources of the BIG Data Center in 2019.

BIG Data Center Members.

Nucleic acids research, Volume 47, Issue D1, 2019

PMID: 30365034 DOI: 10.1093/nar/gky993

2019 Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human.
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 research, Volume 47, Issue D1, 2019

PMID: 30357418 DOI: 10.1093/nar/gky958

2019 NucMap: a database of genome-wide nucleosome positioning map across species.
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 research, Volume 47, Issue D1, 2019

PMID: 30335176 DOI: 10.1093/nar/gky980

2019 LncBook: a curated knowledgebase of human long non-coding RNAs.
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 research, Volume 47, Issue D1, 2019

PMID: 30329098 DOI: 10.1093/nar/gky960

2019 RNAcentral: a hub of information for non-coding RNA sequences.
RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium.

Nucleic acids research, Volume 47, Issue D1, 2019

PMID: 30395267 DOI: 10.1093/nar/gky1034

2019 Characterization of Proteome Variation During Modern Maize Breeding.
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.

Molecular & cellular proteomics : MCP, Volume 18, Issue 2, 2019

PMID: 30409858 DOI: 10.1074/mcp.ra118.001021

2019 Characterization and identification of long non-coding RNAs based on feature relationship.
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 (Oxford, England), Volume 35, Issue 17, 2019

PMID: 30649200 DOI: 10.1093/bioinformatics/btz008

2019 Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science.
Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science.

Song S, Zhang Z.

Molecular plant, Volume 12, Issue 3, 2019

PMID: 30716410 DOI: 10.1016/j.molp.2019.01.020

2019 Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene.
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 evolutionary biology, Volume 19, Issue 1, 2019

PMID: 30849938 DOI: 10.1186/s12862-019-1400-9

2019 Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook.
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.

Current protocols in bioinformatics, Volume 67, Issue 1, 2019

PMID: 31524988 DOI: 10.1002/cpbi.82

2019 Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals.
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 evolutionary biology, Volume 19, Issue 1, 2019

PMID: 31221090 DOI: 10.1186/s12862-019-1441-0

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

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

Briefings in bioinformatics, Volume 20, Issue 6, 2019

PMID: 30184145 DOI: 10.1093/bib/bby074