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Zhang Zhang - Publications

Affiliations: 
National Genomics Data Center Beijing Institute of Genomics, Chinese Academy of Sciences & China National Center for Bioinformation 
Area:
Computational Biology, Bioinformatics
Website:
https://ngdc.cncb.ac.cn/people/zhang-zhang
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114 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. Plos Genetics. 19: e1011019. PMID 37934795 DOI: 10.1371/journal.pgen.1011019  0.552
2023 Gao X, Chen K, Xiong J, Zou D, Yang F, Ma Y, Jiang C, Gao X, Wang G, Gu S, Zhang P, Luo S, Huang K, Bao Y, Zhang Z, et al. The P10K database: a data portal for the protist 10 000 genomes project. Nucleic Acids Research. PMID 37930867 DOI: 10.1093/nar/gkad992  0.439
2023 Li L, Xu B, Tian D, Wang A, Zhu J, Li C, Li N, Zhao W, Shi L, Xue Y, Zhang Z, Bao Y, Zhao W, Song S. McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks. Briefings in Bioinformatics. PMID 37170752 DOI: 10.1093/bib/bbad174  0.335
2023 Ma L, Zhang Z. The contribution of databases towards understanding the universe of long non-coding RNAs. Nature Reviews. Molecular Cell Biology. PMID 37147495 DOI: 10.1038/s41580-023-00612-z  0.31
2022 Ma L, Zou D, Liu L, Shireen H, Abbasi AA, Bateman A, Xiao J, Zhao W, Bao Y, Zhang Z. Database Commons: A Catalog of Worldwide Biological Databases. Genomics, Proteomics & Bioinformatics. PMID 36572336 DOI: 10.1016/j.gpb.2022.12.004  0.351
2022 Li Z, Liu L, Feng C, Qin Y, Xiao J, Zhang Z, Ma L. LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. Nucleic Acids Research. PMID 36330950 DOI: 10.1093/nar/gkac999  0.403
2022 Duan G, Wu G, Chen X, Tian D, Li Z, Sun Y, Du Z, Hao L, Song S, Gao Y, Xiao J, Zhang Z, Bao Y, Tang B, Zhao W. HGD: an integrated homologous gene database across multiple species. Nucleic Acids Research. PMID 36318261 DOI: 10.1093/nar/gkac970  0.401
2022 Zhang M, Zong W, Zou D, Wang G, Zhao W, Yang F, Wu S, Zhang X, Guo X, Ma Y, Xiong Z, Zhang Z, Bao Y, Li R. MethBank 4.0: an updated database of DNA methylation across a variety of species. Nucleic Acids Research. PMID 36318250 DOI: 10.1093/nar/gkac969  0.382
2022 Liu X, Tian D, Li C, Tang B, Wang Z, Zhang R, Pan Y, Wang Y, Zou D, Zhang Z, Song S. GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. Nucleic Acids Research. PMID 36263826 DOI: 10.1093/nar/gkac924  0.362
2022 Hua Z, Tian D, Jiang C, Song S, Chen Z, Zhao Y, Jin Y, Huang L, Zhang Z, Yuan Y. Towards comprehensive integration and curation of chloroplast genomes. Plant Biotechnology Journal. PMID 36069606 DOI: 10.1111/pbi.13923  0.359
2022 Zhang Z. KaKs_calculator 3.0: Calculating selective pressure on coding and non-coding sequences. Genomics, Proteomics & Bioinformatics. PMID 34990803 DOI: 10.1016/j.gpb.2021.12.002  0.35
2021 Liu L, Li Z, Liu C, Zou D, Li Q, Feng C, Jing W, Luo S, Zhang Z, Ma L. LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Research. PMID 34751395 DOI: 10.1093/nar/gkab998  0.381
2021 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. EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Research. PMID 34718752 DOI: 10.1093/nar/gkab972  0.346
2021 Jiang S, Du Q, Feng C, Ma L, Zhang Z. CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. Nucleic Acids Research. PMID 34718745 DOI: 10.1093/nar/gkab979  0.441
2021 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, et al. GSA-Human: Genome Sequence Archive for Human. Yi Chuan = Hereditas. 43: 988-993. PMID 34702711 DOI: 10.16288/j.yczz.21-248  0.367
2021 Jia L, Li Y, Huang F, Jiang Y, Li H, Wang Z, Chen T, Li J, Zhang Z, Yao W. LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes. Nucleic Acids Research. PMID 34643715 DOI: 10.1093/nar/gkab912  0.44
2021 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, ... ... Zhang Z, et al. Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. Nucleic Acids Research. PMID 34591957 DOI: 10.1093/nar/gkab878  0.419
2021 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 Z, et al. The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types. Genomics, Proteomics & Bioinformatics. PMID 34400360 DOI: 10.1016/j.gpb.2021.08.001  0.378
2021 Chen M, Ma Y, Wu S, Zheng X, Kang H, Sang J, Xu X, Hao L, Li Z, Gong Z, Xiao Writing J, Zhang Z, Zhao W, Bao Y. Genome Warehouse: A Public Repository Housing Genome-scale Data. Genomics, Proteomics & Bioinformatics. PMID 34175476 DOI: 10.1016/j.gpb.2021.04.001  0.408
2021 Teng X, Li Q, Li Z, Zhang Y, Niu G, Xiao J, Yu J, Zhang Z, Song S. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. Genomics, Proteomics & Bioinformatics. PMID 33581339 DOI: 10.1016/j.gpb.2020.10.003  0.416
2020 Miao W, Song L, Ba S, Zhang L, Guan G, Zhang Z, Ning K. Protist 10,000 Genomes Project. Innovation (New York, N.Y.). 1: 100058. PMID 34557722 DOI: 10.1016/j.xinn.2020.100058  0.314
2020 Song S, Ma L, Zou D, Tian D, Li C, Zhu J, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, ... ... Zhang Z, et al. The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. Genomics, Proteomics & Bioinformatics. PMID 33704069 DOI: 10.1016/j.gpb.2020.09.001  0.414
2020 Li C, Tian D, Tang B, Liu X, Teng X, Zhao W, Zhang Z, Song S. Genome Variation Map: a worldwide collection of genome variations across multiple species. Nucleic Acids Research. PMID 33170268 DOI: 10.1093/nar/gkaa1005  0.412
2020 Gong Z, Zhu J, Li C, Jiang S, Ma L, Tang B, Zou D, Chen M, Sun Y, Song S, Zhang Z, Xiao J, Xue Y, Bao Y, Du Z, et al. A coronavirus online analysis platform at the National Genomics Data Center. Zoological Research. 1-6. PMID 33045776 DOI: 10.24272/j.issn.2095-8137.2020.065  0.406
2020 Li Z, Liu L, Jiang S, Li Q, Feng C, Du Q, Zou D, Xiao J, Zhang Z, Ma L. LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Research. PMID 33045751 DOI: 10.1093/nar/gkaa850  0.386
2020 Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, ... ... Zhang Z, et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. PMID 32946576 DOI: 10.1093/Molbev/Msaa240  0.387
2020 Li Q, Li Z, Feng C, Jiang S, Zhang Z, Ma L. Multi-omics annotation of human long non-coding RNAs. Biochemical Society Transactions. PMID 32756901 DOI: 10.1042/BST20191063  0.41
2020 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, ... ... Zhang Z, et al. IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. Genomics, Proteomics & Bioinformatics. PMID 32683045 DOI: 10.1016/J.Gpb.2018.12.011  0.536
2020 Yan J, Zou D, Li C, Zhang Z, Song S, Wang X. SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. Genomics, Proteomics & Bioinformatics. PMID 32619768 DOI: 10.1016/J.Gpb.2020.03.002  0.437
2020 Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z. Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biology Direct. 15: 10. PMID 32539851 DOI: 10.1186/S13062-020-00264-5  0.394
2020 Zhang Z, Song S, Yu J, Zhao W, Xiao J, Bao Y. The Elements of Data Sharing. Genomics, Proteomics & Bioinformatics. PMID 32360769 DOI: 10.1016/J.Gpb.2020.04.001  0.428
2020 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, et al. The 2019 novel coronavirus resource. Yi Chuan = Hereditas. 42: 212-221. PMID 32102777 DOI: 10.16288/j.yczz.20-030  0.397
2019 Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z. LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Research. PMID 31599330 DOI: 10.1093/Nar/Gkz898  0.5
2019 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 Research. PMID 31584095 DOI: 10.1093/Nar/Gkz840  0.398
2019 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 Research. PMID 31566222 DOI: 10.1093/Nar/Gkz828  0.442
2019 Ma L, Cao J, Liu L, Li Z, Shireen H, Pervaiz N, Batool F, Raza RZ, Zou D, Bao Y, Abbasi AA, Zhang Z. Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook. Current Protocols in Bioinformatics. 67: e82. PMID 31524988 DOI: 10.1002/Cpbi.82  0.492
2019 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 Evolutionary Biology. 19: 128. PMID 31221090 DOI: 10.1186/S12862-019-1441-0  0.457
2019 Song S, Tian D, Zhang Z, Hu S, Yu J. Rice Genomics: Over the Past Two Decades and Into the Future. Genomics, Proteomics & Bioinformatics. PMID 30771506 DOI: 10.1016/J.Gpb.2019.01.001  0.52
2019 Song S, Zhang Z. Database Resources in BIG Data Center: Submission, Archive and Integration of Big Data in Plant Science. Molecular Plant. PMID 30716410 DOI: 10.1016/J.Molp.2019.01.020  0.39
2019 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 Research. PMID 30715521 DOI: 10.1093/Nar/Gkz073  0.622
2019 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. Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics (Oxford, England). PMID 30649200 DOI: 10.1093/Bioinformatics/Btz008  0.606
2019 Sweeney BA, Petrov AI, Burkov B, Finn RD, Bateman A, Szymanski M, Karlowski WM, Gorodkin J, Seemann SE, Cannone JJ, Gutell RR, Fey P, Basu S, Kay S, Cochrane G, ... ... Zhang Z, et al. RNAcentral: a hub of information for non-coding RNA sequences Nucleic Acids Research. 47. PMID 30395267 DOI: 10.1093/Nar/Gky1034  0.512
2018 Zhang YS, Xia L, Sang J, Li M, Liu L, Li MW, Niu GY, Cao JB, Teng XF, Zhou Q, Zhang Z. [The BIG Data Center's database resources]. Yi Chuan = Hereditas. 40: 1039-1043. PMID 30465537 DOI: 10.16288/j.yczz.18-190  0.393
2018 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. iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Research. PMID 30371881 DOI: 10.1093/Nar/Gky1041  0.535
2018 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 Research. PMID 30364969 DOI: 10.1093/Nar/Gky1027  0.434
2018 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 Research. PMID 30364952 DOI: 10.1093/Nar/Gky1026  0.421
2018 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 Research. PMID 30357418 DOI: 10.1093/Nar/Gky958  0.415
2018 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. NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Research. PMID 30335176 DOI: 10.1093/Nar/Gky980  0.447
2018 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 Research. PMID 30329098 DOI: 10.1093/nar/gky960  0.584
2018 Zhang Z, Xue Y, Zhao F. Bioinformatics Commons: The Cornerstone of Life and Health Sciences. Genomics, Proteomics & Bioinformatics. PMID 30268933 DOI: 10.1016/J.Gpb.2018.09.001  0.309
2018 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. PMID 30184145 DOI: 10.1093/Bib/Bby074  0.444
2018 Xu X, Hao L, Zhu J, Tang B, Zhou Q, Song F, Chen T, Zhang S, Dong L, Lan L, Wang Y, Sang J, Liang F, Cao J, Liu F, ... ... Zhang Z, ... ... Zhang Z, et al. Database Resources of the BIG Data Center in 2018 Nucleic Acids Research. 46. PMID 29036542 DOI: 10.1093/Nar/Gkx897  0.511
2017 Li R, Liang F, Li M, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z. MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Research. PMID 29161430 DOI: 10.1093/Nar/Gkx1139  0.404
2017 Song S, Tian D, Li C, Tang B, Dong L, Xiao J, Bao Y, Zhao W, He H, Zhang Z. Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Research. PMID 29069473 DOI: 10.1093/Nar/Gkx986  0.505
2017 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, ... ... Zhang Z, et al. ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Research. PMID 29036693 DOI: 10.1093/Nar/Gkx875  0.446
2017 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. PMID 28962009 DOI: 10.1093/Molbev/Msx213  0.619
2017 Xia L, Zou D, Sang J, Xu X, Yin H, Li M, Wu S, Hu S, Hao L, Zhang Z. Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 28529082 DOI: 10.1016/J.Jgg.2017.05.003  0.482
2017 Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. Rna Biology. 0. PMID 28387604 DOI: 10.1080/15476286.2017.1312243  0.584
2017 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, ... ... Zhang Z, et al. GSA: Genome Sequence Archive(). Genomics, Proteomics & Bioinformatics. 15: 14-18. PMID 28387199 DOI: 10.1016/J.Gpb.2017.01.001  0.471
2017 Xu X, Ji Z, Zhang Z. CloudPhylo: a fast and scalable tool for phylogeny reconstruction. Bioinformatics (Oxford, England). 33: 438-440. PMID 28172557 DOI: 10.1093/Bioinformatics/Btw645  0.419
2017 Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, ... ... Zhang Z, et al. RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Research. 45: D128-D134. PMID 27794554 DOI: 10.1093/Nar/Gkw1008  0.497
2017 Hao L, Xia L, Sheng X, Li M, Niu G, Zhang Z. Gene Expression Nebulas: a data portal of RNA-Seq based gene expression profiles F1000research. 6. DOI: 10.7490/F1000Research.1113780.1  0.441
2016 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 Z, et al. Precision Medicine: What Challenges Are We Facing? Genomics, Proteomics & Bioinformatics. PMID 27744061 DOI: 10.1016/J.Gpb.2016.10.001  0.395
2016 Yin H, Wang G, Ma L, Yi SV, Zhang Z. What signatures dominantly associate with gene age? Genome Biology and Evolution. PMID 27609935 DOI: 10.1093/Gbe/Evw216  0.428
2016 Sun S, Xiao J, Zhang H, Zhang Z. Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli. Frontiers in Microbiology. 7: 1180. PMID 27536275 DOI: 10.3389/Fmicb.2016.01180  0.453
2016 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. 7: 998. PMID 27446038 DOI: 10.3389/Fmicb.2016.00998  0.455
2016 Yin H, Ma L, Wang G, Li M, Zhang Z. Old genes experience stronger translational selection than young genes. Gene. PMID 27259662 DOI: 10.1016/J.Gene.2016.05.041  0.422
2016 Wang G, Sun S, Zhang Z. Randomness in Sequence Evolution Increases over Time. Plos One. 11: e0155935. PMID 27224236 DOI: 10.1371/Journal.Pone.0155935  0.438
2016 Hao L, Zhang H, Zhang Z, Hu S, Xue Y. Information Commons for Rice (IC4R). Nucleic Acids Research. 44: D1172-80. PMID 26519466 DOI: 10.1093/Nar/Gkv1141  0.514
2015 Zou D, Ma L, Yu J, Zhang Z. Biological databases for human research. Genomics, Proteomics & Bioinformatics. 13: 55-63. PMID 25712261 DOI: 10.1016/J.Gpb.2015.01.006  0.519
2015 Kang Y, Gu C, Yuan L, Wang Y, Zhu Y, Li X, Luo Q, Xiao J, Jiang D, Qian M, Khan AA, Chen F, Zhang Z, Yu J. Erratum for kang et Al., flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks. Mbio. 6. PMID 25587015 DOI: 10.1128/Mbio.02395-14  0.444
2015 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 Research. 43: D777-83. PMID 25404132 DOI: 10.1093/Nar/Gku1174  0.459
2015 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 Research. 43: D187-92. PMID 25399417 DOI: 10.1093/Nar/Gku1167  0.637
2015 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 Research. 43: D54-8. PMID 25294826 DOI: 10.1093/Nar/Gku920  0.439
2014 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. 5: e01867. PMID 25425232 DOI: 10.1128/Mbio.01867-14  0.556
2014 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, ... ... Zhang Z, et al. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics. 46: 1212-9. PMID 25240282 DOI: 10.1038/Ng.3098  0.535
2014 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. 29: 231-42. PMID 25238853 DOI: 10.1177/0748730414537788  0.485
2014 Zhang Z, Zhu W, Luo J. Bringing biocuration to China. Genomics, Proteomics & Bioinformatics. 12: 153-5. PMID 25042682 DOI: 10.1016/J.Gpb.2014.07.001  0.419
2014 Ma L, Cui P, Zhu J, Zhang Z, Zhang Z. Translational selection in human: more pronounced in housekeeping genes. Biology Direct. 9: 17. PMID 25011537 DOI: 10.1186/1745-6150-9-17  0.419
2014 Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J. Ribogenomics: the science and knowledge of RNA. Genomics, Proteomics & Bioinformatics. 12: 57-63. PMID 24769101 DOI: 10.1016/J.Gpb.2014.04.002  0.488
2014 Wu H, Fang Y, Yu J, Zhang Z. The quest for a unified view of bacterial land colonization. The Isme Journal. 8: 1358-69. PMID 24451209 DOI: 10.1038/Ismej.2013.247  0.528
2014 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 (Oxford, England). 30: 1297-9. PMID 24420766 DOI: 10.1093/Bioinformatics/Btu017  0.501
2014 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, et al. RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Research. 42: D1222-8. PMID 24136999 DOI: 10.1093/Nar/Gkt926  0.51
2013 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. Science China. Life Sciences. 56: 968-74. PMID 24022126 DOI: 10.1007/S11427-013-4540-Y  0.522
2013 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 (Oxford, England). 29: 1837-9. PMID 23732274 DOI: 10.1093/Bioinformatics/Btt284  0.551
2013 Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. Rna Biology. 10: 925-33. PMID 23696037 DOI: 10.4161/Rna.24604  0.607
2013 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. 523: 187-91. PMID 23612247 DOI: 10.1016/J.Gene.2013.03.011  0.499
2013 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. 8: e56961. PMID 23451119 DOI: 10.1371/Journal.Pone.0056961  0.439
2013 Zhang Z, Yu J. Does the genetic code have a eukaryotic origin? Genomics, Proteomics & Bioinformatics. 11: 41-55. PMID 23402863 DOI: 10.1016/J.Gpb.2013.01.001  0.511
2013 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. 8: e54082. PMID 23382867 DOI: 10.1371/Journal.Pone.0054082  0.509
2012 Dai L, Gao X, Guo Y, Xiao J, Zhang Z. Bioinformatics clouds for big data manipulation. Biology Direct. 7: 43; discussion 43. PMID 23190475 DOI: 10.1186/1745-6150-7-43  0.366
2012 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. 10: 186-96. PMID 23084774 DOI: 10.1016/J.Gpb.2012.08.001  0.534
2012 Zhang Z, Yu J. The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids. Genomics, Proteomics & Bioinformatics. 10: 175-80. PMID 23084772 DOI: 10.1016/J.Gpb.2012.08.002  0.533
2012 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. 10: 82-93. PMID 22768982 DOI: 10.1016/J.Gpb.2012.05.007  0.513
2012 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. 10: 4-10. PMID 22449396 DOI: 10.1016/S1672-0229(11)60028-4  0.527
2012 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. 13: 43. PMID 22435713 DOI: 10.1186/1471-2105-13-43  0.658
2012 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. Biochemical and Biophysical Research Communications. 419: 779-81. PMID 22390928 DOI: 10.1016/J.Bbrc.2012.02.101  0.419
2012 Wu H, Zhang Z, Hu S, Yu J. On the molecular mechanism of GC content variation among eubacterial genomes. Biology Direct. 7: 2. PMID 22230424 DOI: 10.1186/1745-6150-7-2  0.539
2011 Zhang Z, Yu J. On the organizational dynamics of the genetic code. Genomics, Proteomics & Bioinformatics. 9: 21-9. PMID 21641559 DOI: 10.1016/S1672-0229(11)60004-1  0.48
2010 Zhang Z, Yu J. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences. Biology Direct. 5: 63. PMID 21059261 DOI: 10.1186/1745-6150-5-63  0.545
2010 Qu H, Wu H, Zhang T, Zhang Z, Hu S, Yu J. Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Research in Microbiology. 161: 838-46. PMID 20868744 DOI: 10.1016/J.Resmic.2010.09.015  0.528
2010 Zhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics (Oxford, England). 26: 1918-9. PMID 20538728 DOI: 10.1093/Bioinformatics/Btq303  0.626
2010 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. 8: 77-80. PMID 20451164 DOI: 10.1016/S1672-0229(10)60008-3  0.48
2010 Zhang Z, Townsend JP. The filamentous fungal gene expression database (FFGED). Fungal Genetics and Biology : Fg & B. 47: 199-204. PMID 20025988 DOI: 10.1016/J.Fgb.2009.12.001  0.612
2009 Zhang Z, Townsend JP. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. Plos Computational Biology. 5: e1000421. PMID 19557160 DOI: 10.1371/Journal.Pcbi.1000421  0.559
2009 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. Journal of Molecular Evolution. 68: 414-23. PMID 19308632 DOI: 10.1007/S00239-009-9222-9  0.427
2009 Zhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Briefings in Bioinformatics. 10: 1-10. PMID 18842678 DOI: 10.1093/Bib/Bbn041  0.594
2007 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 Research. 35: W121-5. PMID 17584790 DOI: 10.1093/Nar/Gkm426  0.478
2007 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. 4: 259-63. PMID 17531802 DOI: 10.1016/S1672-0229(07)60007-2  0.468
2007 Hu J, Zhao X, Zhang Z, Yu J. Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Research in Microbiology. 158: 363-70. PMID 17449227 DOI: 10.1016/J.Resmic.2007.02.007  0.498
2007 Zhao X, Zhang Z, Yan J, Yu J. GC content variability of eubacteria is governed by the pol III alpha subunit. Biochemical and Biophysical Research Communications. 356: 20-5. PMID 17336933 DOI: 10.1016/J.Bbrc.2007.02.109  0.485
2007 Zhang Z, Yu J. Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics, Proteomics & Bioinformatics. 4: 173-81. PMID 17127215 DOI: 10.1016/S1672-0229(06)60030-2  0.483
2006 Zhang Z, Li J, Yu J. Computing Ka and Ks with a consideration of unequal transitional substitutions. Bmc Evolutionary Biology. 6: 44. PMID 16740169 DOI: 10.1186/1471-2148-6-44  0.474
2006 Li H, Coghlan A, Ruan J, Coin LJ, Hériché 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 Research. 34: D572-80. PMID 16381935 DOI: 10.1093/Nar/Gkj118  0.442
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