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Yan J, Zou D, Li C, Zhang Z, Song SH, Wang XF: SR4R: an integrative SNP resource for genomic breeding and population research in rice. Genomics, Proteomics & Bioinformatics 2020, accepted.
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: The 2019 novel coronavirus resource. Yi Chuan 2020, 42(2):212-221. [PMID=32102777]
National Genomics Data Center Members and Partners: Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 2020, 48(D1):D24-D33. [PMID=31702008]
Tian D, Wang P, Tang B, Teng X, Li C, Liu X, Zou D, Song S, Zhang Z: GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res 2020, 48(D1):D927-D932. [PMID=31566222]
Xiong Z, Li M, Yang F, Ma Y, Sang J, Li R, Li Z, Zhang Z, Bao Y: EWAS Data Hub: a resource of DNA methylation array data and metadata. Nucleic Acids Res 2020, 48(D1):D890-D895. [PMID=31584095]
Li Z, Zhang Y, Zou D, Zhao Y, Wang H, Zhang Y, Xia X, Luo J, Guo H, Zhang Z: LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Res 2020, 48(D1):D1069-D1075. [PMID=31599330]
Sang J, Zou D, Wang ZN, Wang F, Zhang YS, Xia L, Li ZH, Ma LN, Li MW, Xu BX, Liu XN, Wu SY, Liu L, Niu GY, Li M, Luo YF, Hu SN, Hao LL, Zhang Z: Rice Genome Reannotation Using Massive RNA-Seq Data in IC4R. Genomics Proteomics & Bioinformatics 2019, in press.
Yin H, Li M, Xia L, He C, Zhang Z: Computational determination of gene age and characterization of evolutionary dynamics in human. Briefings in Bioinformatics, 2019, 20(6):2141-2149. [PMID=30184145]
Zhang Z, Yu J, Eisenhaber F, Gao X, Gojobori T: In Memory of Vladimir B. Bajic (1952-2019). Genomics Proteomics & Bioinformatics 2019, 17(5):473-474. [PMID=31837468]
Pervaiz N, Shakeel N, Qasim A, Zehra R, Anwar S, Rana N, Xue Y, Zhang Z, Bao Y, Abbasi AA: Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. BMC Evol Biol 2019, 19(1):128. [PMID=31221090]
Ma LN, Cao J, Liu L, Li Z, Shireen H, Pervaiz N, Batool F, Raza R, Zou D, Bao YM, Abbasi AA, Zhang Z: Community curation and expert curation of human long non-coding RNAs. Current Protocols in Bioinformatics 2019, 67(1):e82.
Song SH, Zhang Z: Database Resources in BIG Data Center: Submission, Archive and Integration of Big Data in Plant Science. Molecular Plant 2019, 12(3):279-281.[PMID=30716410]
Wang GY, Yin HY, Li BY, Yu CL, Wang F, Xu XJ, Cao JB, Bao YM, Wang LG, Abbasi AA, Bajic VB, Ma LN, Zhang Z: Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics 2019, 35(17):2949-2956. [PMID=30649200]
Zhang Z as corresponding author in BIG Data Center Members: Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019, 47(D1):D8-D14. [PMID=30365034]
Li M, Zou D, Li Z, Gao R, Sang J, Zhang Y, Li R, Xia L, Zhang T, Niu G, Bao Y, Zhang Z: EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res 2019, 47(D1):D983-D988. [PMID=30364969]
Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z: LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Res 2019, 47(D1):D128-D134. [PMID=30329098]
Li M, Xia L, Zhang Y, Niu G, Li M, Wang P, Zhang Y, Sang J, Zou D, Hu S, Hao L, Zhang Z: Plant Editosome Database: a curated database of RNA editosome in plants. Nucleic Acids Res 2019, 47(D1):D170-D174. [PMID=30364952]
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: Editome Disease Knowledgebase (EDK): A curated knowledgebase of editome-disease associations in human. Nucleic Acids Res 2019, 47(D1):D78-D83. [PMID=30357418]
Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang Y-P, Wang G-D, Zhao W: iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 2019, 47(D1):D793-D800. [PMID=30371881]
Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang ZW, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J: NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Res 2019, 47(D1):D163-D169. [PMID=30335176]
Zhang Z authored in The RNAcentral Consortium: RNAcentral: A hub of information for non-coding RNA sequences. Nucleic Acids Res 2019, 47(D1):D221-D229. [PMID=30395267]
Song SH, Tian DM, Zhang Z, Hu SN, Yu, J: Rice Genomics: Over the Past Two Decades and Into the Future. Genomics Proteomics Bioinformatics 2018, 16(6):397-404. [PMID=30771506]
Zhang Z, Xue Y, Zhao F: Bioinformatics Commons: The Cornerstone of Life and Health Sciences. Genomics Proteomics & Bioinformatics 2018, 16(4):223-225. [PMID=30268933]
Zhang Z listed in International Society for Biocuration: Biocuration: Distilling data into knowledge. PLoS Biology 2018, 16(4):e2002846. [PMID=29659566]
Li RJ, Liang F, Li W, Zou D, Sun SX, Zhao YB, Zhao WM, Bao YM, Xiao JF, Zhang Z: MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res 2018, 46(D1):D288-D295. [PMID=29161430]
Song SH, Tian DM, Li CP, Tang BX, Dong LL, Xiao JF, Bao YM, Zhao WM, He H, Zhang Z: Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Res 2018, 46(D1):D121-D126. [PMID=29069473]
Zhang Z as corresponding author in BIG Data Center Members: Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018, 46(D1):D14-D20. [PMID=29036542]
Sang J, Wang ZN,..., Hao LL, Zhang Z: ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res 2018, 46(D1):D121-D126. [PMID=29036693]
Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP: Detection of regional variation in selection intensity within protein-coding genes using DNA sequence polymorphism and divergence. Molecular Biology and Evolution 2017, 34(11):3006-3022. [PMID=28962009]
Xia L, Zou D, Sang J, Xu XJ, Yin HY, Li MW, Wu SY, Hu SN, Hao LL, Zhang Z: Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics, 2017, 44(5):235-241. [PMID=28529082]
Salhi A, Essack M, Alam T,..., Zhang Z, Bajic V: DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology 2017, 14(7):963-971.[PMID=28387604]
Wang YQ, ..., Zhang Z, Zhao WM: GSA: Genome Sequence Archive. Genomics, Proteomics & Bioinformatics 2017, 15(1):14-18. [PMID=28387199] [Cover Story; Preview]
Xu XJ, Ji ZH, Zhang Z: CloudPhylo: a fast and scalable tool for phylogeny reconstruction. Bioinformatics 2017, 33 (3):438-440. [PMID=28172557]
Zhang Z authored in The RNAcentral Consortium: RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017, 45(D1):D128-D134. [PMID=27794554]
Zhang Z as corresponding author in BIG Data Center Members: The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24. [PMID=27899658]
Zhao W, Zhang S, Tang B, Chen T, Hao L, Sang J, Li R, Xiao J, Zhang Z: Constructing the international database management system for omics big data. Big Data Research 2016, 2(6):43-52. (In Chinese)
Xue Y, ..., Zhang Z., Huang K, Yu J: Precision Medicine: What Challenges Are We Facing? Genomics Proteomics Bioinformatics 2016, 14(5):253-261. [PMID=27744061]
Yin HY, Wang GY, Ma LN, Yi SV, Zhang Z: What signatures dominantly associate with gene age? Genome Biology and Evolution 2016, 8(10):3083-9. [PMID=27609935]
Sun SX, Xiao JF, Zhang HY*, Zhang Z: Pangenome evidence for higher codon usage bias and stronger translational selection in core genes of Escherichia coli. Frontiers in Microbiology 2016, 7:1180. [PMID=27536275]
Yin HY, Ma LN, Wang GY, Li MW, Zhang Z: Old genes experience stronger translational selection than young genes. Gene 2016, 590(1):29-34. [PMID=27259662]
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: Comparative genomics analysis of Streptomyces species reveals their adaptation to the marine environment and their diversity at the genomic level. Frontiers in Microbiology 2016, 7:998. [PMID=27446038]
Wang GY, Sun SX, Zhang Z: Randomness in sequence evolution increases over time. PLoS One 2016, 11(5): e0155935. [PMID=27224236]
Zhang Z as corresponding author in IC4R Project Consortium: Information Commons for Rice (IC4R). Nucleic Acids Res 2016, 44(D1):D1172-1180. [PMID=26519466]
Zhang Y, Chen LL, Zhang Z: The Curation and Analysis of Rice Stress-Resistance Genes Based on RiceWiki. Hans Journal of Computational Biology 2015, 5(3):29-40. (in Chinese)
Zou D, Sun S, Li R, Liu J, Zhang J, Zhang Z: MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data. Nucleic Acids Res 2015, 43(Database issue):D54-58. [PMID=25294826]
Zou D, Ma L, Yu J, Zhang Z: Biological databases for human research. Genomics Proteomics Bioinformatics 2015, 13(1):55-63. [PMID=25712261]
Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z: LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res 2015, 43(Database issue):D187-192. [PMID=25399417]
Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, Yang HC, Liu YH, Zhu JW, Irwin DM, Wang GD, Zhang YP: DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res 2015, 43(Database issue):D777-783. [PMID=25404132]
Zhao Y, Jia X, Yang J, Ling Y, Zhang Z, Yu J, Wu J, Xiao J: PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinformatics 2014, 30(9):1297-1299.[PMID=24420766]
Zhang Z, Zhu W, Luo J: Bringing biocuration to China. Genomics Proteomics Bioinformatics 2014, 12(4):153-155. [PMID=25042682]
Zhang Z, Sang J, Ma L, Wu G, Wu H, Huang D, Zou D, Liu S, Li A, Hao L, Tian M, Xu C, Wang X, Wu J, Xiao J, Dai L, Chen LL, Hu S, Yu J: RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Res 2014, 42(Database issue):D1222-1228. [PMID=24136999]
Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, Xu J, Zheng X, Ren L, Wang G, Zhang Y, Huo L, Zhao Z, Cao D, Lu C, Li C, Zhou Y, Liu Z, Fan Z, Shan G, Li X, Wu S, Song L, Hou G, Jiang Y, Jeney Z, Yu D, Wang L, Shao C, Song L, Sun J, Ji P, Wang J, Li Q, Xu L, Sun F, Feng J, Wang C, Wang S, Wang B, Li Y, Zhu Y, Xue W, Zhao L, Wang J, Gu Y, Lv W, Wu K, Xiao J, Wu J, Zhang Z, Yu J, Sun X: Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet 2014, 46(11):1212-1219. [PMID=25240282]
Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J: Ribogenomics: the science and knowledge of RNA. Genomics Proteomics Bioinformatics 2014, 12(2):57-63. [PMID=24769101]
Wu H, Fang Y, Yu J, Zhang Z: The quest for a unified view of bacterial land colonization. The ISME journal 2014, 8(7):1358-1369. [PMID=24451209]
Wu G, Zhu J, Yu J, Zhou L, Huang JZ, Zhang Z: Evaluation of five methods for genome-wide circadian gene identification. Journal of biological rhythms 2014, 29(4):231-242.[PMID=25238853]
Ma L, Cui P, Zhu J, Zhang Z, Zhang Z: Translational selection in human: more pronounced in housekeeping genes. Biol Direct 2014, 9:17. [PMID=25011537]
Kang Y, Gu C, Yuan L, Wang Y, Zhu Y, Li X, Luo Q, Xiao J, Jiang D, Qian M, Ahmed Khan A, Chen F, Zhang Z, Yu J: Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks. mBio 2014, 5(6):e01867. [PMID=25425232]
Zhang Z, Yu J: Does the genetic code have a eukaryotic origin?. Genomics Proteomics Bioinformatics 2013, 11(1):41-55. [PMID=23402863]
Zhang Z, Wong GK, Yu J: Protein coding. Encyclopedia of Life Sciences (eLS) 2013. [Link]
Wu J, Xiao J, Wang L, Zhong J, Yin H, Wu S, Zhang Z, Yu J: Systematic analysis of intron size and abundance parameters in diverse lineages. Sci China Life Sci 2013, 56(10):968-974. [PMID=24022126]
Tong X, Yang Y, Wang W, Bai Z, Ma L, Zheng X, Sun H, Zhang Z, Zhao M, Yu J, Ge RL: Expression profiling of abundant genes in pulmonary and cardiac muscle tissues of Tibetan Antelope (Pantholops hodgsonii). Gene 2013, 523(2):187-191. [PMID=23612247]
Ma L, Bajic VB, Zhang Z: On the classification of long non-coding RNAs. RNA Biol 2013, 10(6):925-933. [PMID=23696037]
Dai L, Xu C, Tian M, Sang J, Zou D, Li A, Liu G, Chen F, Wu J, Xiao J, Wang X, Yu J, Zhang Z: Community intelligence in knowledge curation: an application to managing scientific nomenclature. PLoS One 2013, 8(2):e56961. [PMID=23451119]
Dai L, Tian M, Wu J, Xiao J, Wang X, Townsend JP, Zhang Z: AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics 2013, 29(14):1837-1839. [PMID=23732274]
Chen M, Xiao J, Zhang Z, Liu J, Wu J, Yu J: Identification of human HK genes and gene expression regulation study in cancer from transcriptomics data analysis. PLoS One 2013, 8(1):e54082. [PMID=23382867]
Zhang Z, Yu J: The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids. Genomics Proteomics Bioinformatics 2012, 10(4):175-180. [PMID=23084772]
Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L: ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem Biophys Res Commun 2012, 419(4):779-781. [PMID=22390928]
Wu H, Zhang Z, Hu S, Yu J: On the molecular mechanism of GC content variation among eubacterial genomes. Biol Direct 2012, 7(1):2. [PMID=22230424]
Wu H, Qu H, Wan N, Zhang Z, Hu S, Yu J: Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition.Genomics Proteomics Bioinformatics 2012, 10(4):186-196. [PMID=23084774]
Dai L, Gao X, Guo Y, Xiao J, Zhang Z: Bioinformatics clouds for big data manipulation. Biol Direct 2012, 7:43; discussion 43. [PMID=23190475]
Cui P, Ding F, Lin Q, Zhang L, Li A, Zhang Z, Hu S, Yu J: Distinct contributions of replication and transcription to mutation rate variation of human genomes. Genomics Proteomics Bioinformatics 2012, 10(1):4-10.[PMID=22449396]
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J: Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13(1):43. [PMID=22435713]
Cui P, Liu W, Zhao Y, Lin Q, Zhang D, Ding F, Xin C, Zhang Z, Song S, Sun F, Yu J, Hu S: Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis. Genomics Proteomics Bioinformatics 2012, 10(2):82-93. [PMID=22768982]
Zhang Z, Bajic VB, Yu J, Cheung K-H, Townsend JP: Data Integration in Bioinformatics: Current Efforts and Challenges. In: Bioinformatics - Trends and Methodologies. Edited by Mahdavi MA, vol. 1. Rijeka, Croatia: InTech; 2011: 41-56. [Link]
Zhang Z, Yu J: On the organizational dynamics of the genetic code. Genomics Proteomics Bioinformatics 2011, 9(1-2):21-29. [PMID=21641559]
Zhang Z, Yu J: Modeling compositional dynamics based on GC and purine contents of protein-coding sequences. Biol Direct 2010, 5(1):63. [PMID=21059261]
Zhang Z, Townsend JP: The filamentous fungal gene expression database (FFGED). Fungal Genet Biol 2010, 47(3):199-204. [PMID=20025988]
Zhang Z, Lopez-Giraldez F, Townsend JP: LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 2010, 26(15):1918-1919.[PMID=20538728]
Wang D, Zhang Y, Zhang Z, Zhu J, Yu J: KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics 2010, 8(1):77-80. [PMID=20451164]
Qu H, Wu H, Zhang T, Zhang Z, Hu S, Yu J: Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Res Microbiol 2010, 161(10):838-846. [PMID=20868744]
Zhang Z, Townsend JP: Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Comput Biol 2009, 5(6):e1000421.[PMID=19557160]
Zhang Z, Cheung KH, Townsend JP: Bringing Web 2.0 to bioinformatics. Briefings in Bioinformatics 2009, 10(1):1-10. [PMID=18842678]
Li J, Zhang Z, Vang S, Yu J, Wong GK, Wang J: Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol 2009, 68(4):414-423.[PMID=19308632]
Zheng H, Shi J, Fang X, Li Y, Vang S, Fan W, Wang J, Zhang Z, Wang W, Kristiansen K, Wang J: FGF: a web tool for Fishing Gene Family in a whole genome database. Nucleic Acids Res 2007, 35(Web Server issue):W121-125. [PMID=17584790]
Zhao X, Zhang Z, Yan J, Yu J: GC content variability of eubacteria is governed by the pol III alpha subunit. Biochem Biophys Res Commun 2007, 356(1):20-25.[PMID=17336933]
Hu J, Zhao X, Zhang Z, Yu J: Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Res Microbiol 2007, 158(4):363-370. [PMID=17449227]
Zhang Z, Yu J: Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics Proteomics Bioinformatics 2006, 4(3):173-181.[PMID=17127215]
Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 2006, 4(4):259-263. [PMID=17531802]
Zhang Z, Li J, Yu J: Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol Biol 2006, 6:44. [PMID=16740169]
Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R: TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res 2006, 34(Database issue):D572-580. [PMID=16381935]
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