Zhang Zhang

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Zhang Zhang, Ph.D.

Professor in the CAS 100-Talent Program

Executive Director of BIG Data Center

Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS)

No.1 Beichen West Road, Chaoyang District

Beijing 100101, China

Email: zhangzhang(AT)big.ac.cn

Tel.: +86-10-84097261

Fax: +86-10-84097298

Lab site: http://cbb.big.ac.cn

Personal profiles: Google Scholar, BIG Data Center

Publons: https://publons.com/author/388485


Contents

PROFESSIONAL EXPERIENCE

  • Executive Director of BIG Data Center, BIG, CAS, China, 2016−Present
  • Professor in the CAS 100-Talent Program, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), China, 2011−Present
  • Research Scientist, King Abdullah University of Science and Technology, Kingdom of Saudi Arabia, 2009−2011
  • Postdoctoral Associate, Yale University, United States of America, 2007−2009

EDUCATION

  • Ph.D. in Computer Science, Institute of Computing Technology, Chinese Academy of Sciences, China, 2007
  • M.S. in Computer Science, Nanjing University of Science and Technology, China, 2004
  • B.S. in Computer Science, Ningxia University, China, 2002

RESEARCH INTERESTS

  • Big Data Integration and Analytics
  • Computational Evolutionary and Health Genomics

PROFESSIONAL ACTIVITIES

  • Academic Degree Committee Member: Beijing Institute of Genomics, CAS (2015—)
  • Asian Associate Editor: Briefings in Bioinformatics (2017—)
  • Editorial Board Member: Biology Direct (2013—)
  • Associate Editor-in-Chief: Genomics, Proteomics & Bioinformatics (2012—)
  • Journal Reviewer: Bioinformatics, Biology Direct, BioSystems, BMC Bioinformatics, BMC Evolutionary Biology, BMC Genomics, BMC Plant Biology, BMC Systems Biology, Briefings in Bioinformatics, Chinese Bulletin of Life Sciences, Current Bioinformatics, Database, Evolutionary Bioinformatics, Gene, Genome Biology, Genomics Proteomics & Bioinformatics, Hereditas, In Silico Biology, Integrative Zoology, Journal of Bioinformatics and Computational Biology, Journal of Genetics and Genomics, Journal of Molecular Evolution, Molecular Biology and Evolution, PLoS ONE, PLoS Pathogens, RNA, Scientific Data, Scientific Reports
  • Grant Referee: UK BBSRC
  • Executive Committee Member: International Society for Biocuration (2016—)
  • Member: Genetics Society of China, International Society for Biocuration (ISB)

PUBLICATIONS (*Corresponding author; #First-author equivalent)

  1. Li RJ, Liang F, Li W, Zou D, Sun SX, Zhao YB, Zhao WM, Bao YM, Xiao JF, Zhang Z* (2018) MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res, accepted and in press.
  2. Song SH, Tian DM, Li CP, Tang BX, Dong LL, Xiao JF, Bao YM, Zhao WM, He H, Zhang Z* (2018) Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Res, accepted and in press.
  3. Zhang Z* as corresponding author in BIG Data Center Members (2018) Database Resources of the BIG Data Center in 2018. Nucleic Acids Res, accepted and in press. Pubmed.png
  4. Sang J, Wang ZN,..., Hao LL, Zhang Z* (2018) ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res, accepted and in press. Pubmed.png
  5. Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP (2017) Detection of regional variation in selection intensity within protein-coding genes using DNA sequence polymorphism and divergence. Molecular Biology and Evolution, accepted and in press, Pubmed.png
  6. Xia L, Zou D, Sang J, Xu XJ, Yin HY, Li MW, Wu SY, Hu SN, Hao LL, Zhang Z* (2017) Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics, 44(5):235-241. Pubmed.png
  7. Salhi A, Essack M, Alam T,..., Zhang Z*, Bajic V (2017) DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology , 14(7):963-971. Pubmed.png
  8. Wang YQ, ..., Zhang Z*, Zhao WM: GSA: Genome Sequence Archive. Genomics, Proteomics & Bioinformatics 2017, 15(1):14-18. Pubmed.png [Cover Story; Preview]
  9. Xu XJ, Ji ZH, Zhang Z*: CloudPhylo: a fast and scalable tool for phylogeny reconstruction. Bioinformatics 2017, 33 (3):438-440. Pubmed.png
  10. Zhang Z authored in The RNAcentral Consortium: RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017, 45(D1):D128-D134. Pubmed.png
  11. Zhang, Z.* as Corresponding author in BIG Data Center Members (2017) The BIG Data Center: from deposition to integration to translation, Nucleic Acids Res, 45(D1):D18-D24. Pubmed.png
  12. Zhang, Z. authored in The RNAcentral Consortium. (2017) RNAcentral: a comprehensive database of non-coding RNA sequences., Nucleic Acids Res, 45(D1):D128-D134. Pubmed.png
  13. 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)
  14. Xue, Y.,...,Zhang, Z., Huang, K., Yu, J. (2016) Precision Medicine: What Challenges Are We Facing?, Genomics Proteomics Bioinformatics, 14(5):253-261. Pubmed.png
  15. Yin, H.Y, Wang, G.Y., Ma, L.N., Yi, S.V., Zhang, Z.* (2016) What signatures dominantly associate with gene age? Genome Biology and Evolution, 8(10):3083-9.Pubmed.png
  16. Sun, S.X., Xiao, J.F., Zhang, H.Y.*, Zhang, Z.* (2016) Pangenome evidence for higher codon usage bias and stronger translational selection in core genes of Escherichia coli, Frontiers in Microbiology, 7:1180. Pubmed.png
  17. Yin, H.Y., Ma, L.N., Wang, G.Y., Li, M.W., Zhang, Z.*. (2016) Old genes experience stronger translational selection than young genes, Gene, 590(1):29–34.Pubmed.png
  18. Wang, G.Y., Sun, S.X., Zhang, Z.* (2016) Randomness in sequence evolution increases over time, PLoS One, 11(5): e0155935.Pubmed.png
  19. Zhang, Z.* as corresponding author in The IC4R Project Consortium (2016) Information Commons for Rice (IC4R), Nucleic Acids Research, 44(D1):D1172-80. Pubmed.png
  20. Zou, D., Ma, L.N., Yu, J.*, Zhang, Z.* (2015) Biological databases for human research, Genomics Proteomics Bioinformatics, 13(1):55-63. Pubmed.png
  21. Zhang, Y., Chen, L.L., Zhang, Z. (2015) The Curation and Analysis of Rice Stress-Resistance Genes Based on RiceWiki, Hans Journal of Computational Biology, 5(3):29-40. Pdf.gif
  22. Bai, B., Zhao, W.-M.,..., Zhang, Z.,..., Wang, G.-D., and Zhang, Y.-P. (2015) DoGSD: the dog and wolf genome SNP database, Nucleic Acids Research, 43:D777-83. Pubmed.png
  23. Ma, L.N., Li, A., Zou, D., Xu, X.J., Xia, L., Yu, J., Bajic, V.B., and Zhang, Z*. (2015) LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs, Nucleic Acids Research, 43:D187-92. Pubmed.png
  24. Zou, D., Sun, S., Li, R., Liu, J., Zhang, J., Zhang, Z.* (2015) MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data, Nucleic Acids Research, 43:D54-8. Pubmed.png
  25. Kang, Y., Gu, C., Yuan, L., Wang, Y., Zhu, Y., Li, X., Luo, Q., Xiao, J., Jiang, D., Qian, M., Ahmed, K.A., Chen, F., Zhang, Z.*, Yu, J.* (2014) Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks, MBio, 25:5(6), e01867-14. Pubmed.png
  26. Xu, P., Zhang, X., Wang, X., ..., Zhang, Z., Yu, J., and Sun, X. (2014) Genome sequence and genetic diversity of the common carp, Cyprinus carpio, Nature Genetics, 46(11):1212-9. Pubmed.png
  27. Wu, G., Zhu, J., Yu, J., Zhou, L., Huang, J.H., and Zhang, Z.* (2014) Evaluation of five methods for genome-wide circadian gene identification, Journal of Biological Rhythms, 29(4):231-42. Pubmed.png
  28. Zhang, Z.*, Zhu, W.M., and Luo, J.C. (2014) Bringing biocuration to China, Genomics Proteomics Bioinformatics, 12(4):153-5. Pubmed.png
  29. Ma, L.N., Cui, P., Zhu, J., Zhang, Z.H., and Zhang, Z.* (2014) Translational selection in human: more pronounced in housekeeping genes, Biology Direct, 9,17. Pubmed.png
  30. Wu, J.Y., Xiao, J.F., Zhang, Z., Wang, X.M., Hu, S.N., and Yu, J. (2014) Ribogenomics: the science and knowledge of RNA, Genomics, Proteomics & Bioinformatics, 12(2):57-63. Pubmed.png
  31. Zhao, Y.B., Jia, X.M., Yang, J.H., Ling, Y.C., Zhang, Z., Yu, J., Wu, J.Y., and Xiao, J.F. (2014) PanGP: A tool for quickly analyzing bacterial pan-genome profile, Bioinformatics, 30(9):1297-9. Pubmed.png
  32. Wu, H., Fang, Y.J., Yu, J.*, and Zhang, Z.* (2014) The quest for a unified view of bacterial land colonization, The ISME Journal, 8(7),1358-69. Pubmed.png
  33. Zhang, Z.*, Sang, J. Ma, L.N., Wu, G., Wu, H., Huang, D.W., Zou, D., Liu, S.Q., Li, A., Hao, L.L., Tian, M., Xu, C., Wang, X.M., Wu, J.Y., Xiao, J.F., Dai, L., Chen, L.-L., Hu, S.N., and Yu, J. (2014) RiceWiki: a wiki-based database for community curation of rice genes, Nucleic Acids Research, 42(D1),D1222-D1228. Pubmed.png
  34. Wu, J.Y., Xiao, J.F., Wang, L.P., Zhong, J., Yin, H.Y., Wu, S.X., Zhang, Z., Yu, J. (2013) Systematic analysis of intron size and abundance parameters in diverse lineages, Sci China Life Sci, 56(10),968-974. Pubmed.png
  35. Zhang, Z., Wong, G.K. and Yu, J. (2013) Protein coding, In: Encyclopedia of Life Sciences (eLS). John Wiley & Sons Ltd, Chichester. DOI: 10.1002/9780470015902.a0005017.pub2
  36. Dai, L., Tian, M., Wu, J.Y., Xiao, J.F., Wang, X.M., Townsend, J.P. and Zhang, Z.* (2013) AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification, Bioinformatics, 29(14),1837-1839. Pubmed.png
  37. Ma, L.N., Bajic, V.B., and Zhang, Z.* (2013) On the classification of long non-coding RNAs, RNA Biology, 10(6),1-10. Pubmed.png
  38. Tong, X., Yang, Y., Wang, W., Bai, Z., Ma, L., Zheng, X., Sun, H., Zhang, Z., Zhao, M., Yu, J., Ge, R.L.(2013) Expression profiling of abundant genes in pulmonary and cardiac muscle tissues of Tibetan Antelope (Pantholops hodgsonii), Gene, 523(2),187–191. Pubmed.png
  39. Dai, L., Xu, C., Tian, M., Sang, J., Zou, D., Li, A., Liu, G.C., Chen, F., Wu, J.Y., Xiao, J.F., Wang, X.M., Yu, J., and Zhang, Z.* (2013) Community intelligence in knowledge curation: an application to managing scientific nomenclature, PLoS ONE, 8(2), e56961.Pubmed.png
  40. Zhang, Z., and Yu. J. (2013) Does the genetic code have a eukaryotic origin? Genomics Proteomics Bioinformatics, 11(1),41-55.Pubmed.png
  41. Chen, M., Xiao, J.F., Zhang, Z., Liu, J., Wu, J.Y., and Yu, J. (2013) Identification of human HK Genes and gene expression regulation study in cancer from transcriptomics data analysis, PLoS ONE, 8(1), e54082.Pubmed.png
  42. Dai, L., Gao, X., Guo, Y., Xiao, J.F. and Zhang, Z.* (2012) Bioinformatics clouds for big data manipulation, Biology Direct, 7, 43. Highly-accessed.gif [Official Certificate for Highly Accessed] Pubmed.png
  43. Zhang, Z. and Yu, J. (2012) The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids, Genomics Proteomics Bioinformatics, 10(4), 175-180. [Cover story] Pubmed.png
  44. Wu, H., Qu, H.Z, Wan, N., Zhang, Z., Hu, S.N. and Yu, J. (2012) Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition, Genomics Proteomics Bioinformatics, 10(4), 186-196. Pubmed.png
  45. Cui, P., Liu, W., Zhao, Y., Lin, Q., Zhang, D., Ding, F., Xin, C., Zhang, Z., Song, S., Sun F et al (2012) Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis, Genomics Proteomics Bioinformatics, 10(2), 82-93. Pubmed.png
  46. Cui, P., Ding, F., Lin, Q., Zhang, L., Li, A., Zhang, Z., Hu, S. and Yu, J. (2012) Distinct contributions of replication and transcription to mutation rate variation of human genomes, Genomics Proteomics Bioinformatics, 10(1), 4-10. Pubmed.png
  47. Zhang, Z.*, Xiao, J., Wu, J., Zhang, H., Liu, G., Wang, X. and Dai, L. (2012) ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments, Biochem Biophys Res Commun, 419(4), 779-781.Pubmed.png
  48. Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J.P. and Yu, J. (2012) Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance, BMC Bioinformatics, 13, 43. Highly-accessed.gif [Official Certificate for Highly Accessed] Pubmed.png
  49. Wu, H., Zhang, Z., Hu, S. and Yu, J. (2012) On the molecular mechanism of GC content variation among eubacterial genomes, Biology Direct, 7, 2.Pubmed.png
  50. Zhang, Z., Bajic, V.B., Yu, J., Cheung, K.-H. and Townsend, J.P. (2011) Data integration in bioinformatics: current efforts and challenges. In Mahdavi, M.A. (ed), Bioinformatics - Trends and Methodologies. InTech - Open Access Publisher, Rijeka, Croatia. Available from: http://www.intechopen.com/articles/show/title/data-integration-in-bioinformatics-current-efforts-and-challenges.
  51. Zhang, Z. and Yu, J. (2011) On the organizational dynamics of the genetic code, Genomics Proteomics Bioinformatics, 9(1-2), 21-29.Pubmed.png
  52. Zhang, Z. and Yu, J. (2010) Modeling compositional dynamics based on GC and purine contents of protein-coding sequences, Biology Direct, 5, 63.Pubmed.png
  53. Zhang, Z. and Townsend, J.P. (2010) The filamentous fungal gene expression database (FFGED), Fungal Genetics Biology, 47(3), 199-204.Pubmed.png
  54. Zhang, Z., Lopez-Giraldez, F. and Townsend, J.P. (2010) LOX: inferring Level Of eXpression from diverse methods of census sequencing, Bioinformatics, 26(15), 1918-1919.Pubmed.png
  55. Wang, D., Zhang, Y., Zhang, Z., Zhu, J. and Yu, J. (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies, Genomics Proteomics Bioinformatics, 8(1), 77-80.Pubmed.png
  56. Qu, H., Wu, H., Zhang, T., Zhang, Z., Hu, S. and Yu, J. (2010) Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes, Res Microbiol, 161(10), 838-846.Pubmed.png
  57. Zhang, Z. and Townsend, J.P. (2009) Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences, PLoS Comput Biol, 5(6), e1000421.Pubmed.png
  58. Zhang, Z., Cheung, K.H. and Townsend, J.P. (2009) Bringing Web 2.0 to bioinformatics, Briefings in Bioinformatics, 10(1), 1-10.Pubmed.png
  59. Li, J., Zhang, Z.#, Vang, S., Yu, J., Wong, G.K. and Wang, J. (2009) Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage, J Mol Evol, 68(4), 414-423.Pubmed.png
  60. Zheng, H., Shi, J., Fang, X., Li, Y., Vang, S., Fan, W., Wang, J., Zhang, Z., Wang, W. and Kristiansen, K. (2007) FGF: a web tool for Fishing Gene Family in a whole genome database, Nucleic Acids Res, 35, W121-125.Pubmed.png
  61. Zhao, X., Zhang, Z.#, Yan, J. and Yu, J. (2007) GC content variability of eubacteria is governed by the pol III alpha subunit, Biochem Biophys Res Commun, 356, 20-25.Pubmed.png
  62. Hu, J., Zhao, X., Zhang, Z.# and Yu, J. (2007) Compositional dynamics of guanine and cytosine content in prokaryotic genomes, Res Microbiol, 158, 363-370.Pubmed.png
  63. Zhang, Z. and Yu, J. (2006) Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates, Genomics Proteomics Bioinformatics, 4, 173-181.Pubmed.png
  64. Zhang, Z., Li, J., Zhao, X.Q., Wang, J., Wong, G.K. and Yu, J. (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging, Genomics Proteomics Bioinformatics, 4, 259-263. [Highly cited in GPB] Pubmed.png
  65. Zhang, Z., Li, J. and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions, BMC Evolutionary Biology, 6, 44. Highly-accessed.gifPubmed.png
  66. Li, H., Coghlan, A., Ruan, J., Coin, L.J., Hériché, J.-K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., Wong, G.K.-S., Zheng, W., Dehal, P., Wang, J. and Durbin, R. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families, Nucleic Acids Res, 34, D572-D580.Pubmed.png

INVITED TALKS

  1. Database Resources of the BIG Data Center in 2018. International Conference on Precision Medicine, Bangkok, Thailand, 19-20 July 2018.
  2. 基因大数据汇交共享与多组学数据资源体系建设, 北京生物信息学系列论坛, 北京大学, 2018年1月19日
  3. Big Data Deposition, Integration and Sharing. The Functional Genomics Summit IV(第四界全国功能基因组学高峰论坛), Beijing, 23-24 October 2017.
  4. The BIG Data Center: from deposition to integration to translation. The 2017 Conference on Science Data in China(第四届科学数据大会), Kunming, 2-4 August 2017.
  5. The BIG Data Center: from deposition to integration to translation. The Sino-ASEAN Conference on Precision Medicine, Burapha University, Thailand, 17-18 June 2017.
  6. The BIG Data Center’s database resources: towards precision medicine . The 10th International Biocuration Conference, Stanford University, United States, 26-29 March 2017.
  7. The BIG Data Center: from deposition to integration to translation. The Conference of Computational Biology for Big Data, Shanghai, 23-24 March 2017.
  8. The BIG Data Center: from deposition to integration to translation. The 1st National Forum on Biological Systems (首届全国生物系统学学术论坛), Beijing, China, December 10-11, 2016. http://blog.sciencenet.cn/blog-536560-1017089.html
  9. The BIG Data Center: from deposition to integration to translation. The 2nd Scientific Annual Meeting of Committee on Precision Medicine and Tumor Rehabilitation (精准医学与肿瘤康复专业委员会第二届学术年会), Beijing, China, November 5-6, 2016. http://www.carttp.org/index.php?a=shows&catid=17&id=174
  10. The BIG Data Center: from deposition to integration to translation. The 7th National Conference on Bioinformatics & System Biology (第七届全国生物信息学与系统生物学学术大会), Chengdu, China, October 6-9, 2016. http://ccbsb.uestc.edu.cn/2016/
  11. The BIG Data Center for Life and Health Sciences. The 2016 Conference on Science Data in China (2016中国科学数据大会), Shanghai, China, August 25-26, 2016. http://dc2016.codata.cn/dct/page/70021
  12. The BIG Data Center: from deposition to integration to translation. The 4th Youth Forum for Computer & Life Sciences Interdisciplinary Research (第四届数学、计算机与生命科学交叉研究青年学者论坛), Beijing, China, May 21-22, 2016. http://yf2016.csp.escience.cn/dct/page/70006
  13. The BIG Data Center for Life and Health Sciences. The Phoenix City Forum for Genome Informatics (基因组信息学凤凰城论坛), Tangshan, China, May 13-15, 2016. http://www.ncst.edu.cn/col/1374811047971/2016/05/11/1462970939504.html
  14. The BIG Data Center: from deposition to integration to translation. The 9th International Biocuration Conference, Geneva, Switzerland, April 10-14, 2016. http://www.isb-sib.ch/events/biocuration2016/scientific-program
  15. Big Data integration: scalability and sustainability. KAUST Research Conference on Computational and Experimental Interfaces of Big Data and Biotechnology, Thuwal, Saudi Arabia, Jan. 25-27, 2016. [Keynoted speaker] http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php
  16. Toward Sustainability and Scalability for Big Data Integration. 2015 Functional Genomics Summit II, Beijing, China, Nov. 11-12, 2015.
  17. Community integration of big data. The 2015 International Conference of Genomics, Xi'an, China, Oct. 22-25, 2015.
  18. Big data integration, curation, and analysis. The 2014 Next-Generation Sequencing Workshop, Hefei, China, Oct. 17-20, 2014.
  19. Bringing biocuration to China. The 1st International Coastal Biology Congress, Yantai, China, Sept. 26-30, 2014.
  20. Big data integration, curation, and analysis. The 3rd Young Bioinformatics PI Workshop, Guangzhou, China, Sept. 19-21, 2014.
  21. Big biological data integration and curation. The 2014 Conference on Science Data in China (2014中国科学数据大会—科研大数据和数据科学), Beijing, China, Feb. 24-25, 2014.
  22. Biocuration in the era of big data. The Workshop on Statistical and Computational Theory and Methodology for Big Data Analysis, Banff, Canada, Feb. 9-14, 2014. [Video]
  23. Biological databases: wikify or die. The 2013 International Conference of Genomics, Qingdao, China, Oct. 28-30, 2013.
  24. Community curation in biological knowledge wikis. The 6th International Biocuration Conference, Churchill College, Cambridge, United Kingdom, April 7-10, 2013.
  25. Rewarding community-curated contributions in biological knowledge wikis. The High-throughput Sequencing Data Analysis and Approaches Workshop, Beijing, China, Dec. 5-7, 2012.
  26. Next-Generation Bioinformatics: harnessing collective resources for large-scale data manipulation, in workshop “Challenges and future of Bioinformatics: sharing insights from the Dutch and Chinese perspective”, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China, March 19, 2012.
  27. Estimating codon usage bias and its statistical significance by accounting for background nucleotide composition. 2011 International Conference of Genomics, Changchun, China, October 22-24, 2011.

SOFTWARE & WEB SYSTEMS

  1. AuthorReward: a wiki extension to reward community-curated efforts in bio-wikis through automated authorship quantification.
  2. ParaAT (Parallel Alignment & back-Translation): a parallel tool for constructing multiple proteincoding DNA alignments.
  3. CAT (Composition Analysis Toolkit): a toolkit for estimating codon usage bias and its statistical significance.
  4. LOX (Level Of eXpression): a program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.
  5. FFGED (Filamentous Fungal Gene Expression Database): a database for managing filamentous fungal gene expression data and correlating diverse gene expression levels under multiple experimental designs within different experiments.
  6. MACML (Model Averaging Clustering by Maximum Likelihood): a program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
  7. FGF (Fishing Gene Family): a web server that finds gene family in a genome by a protein sequence and provides the phylogenetic tree of the family.
  8. KaKs_Calculator: a program that adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates.
  9. TreeFam (Tree Families Database): a database of phylogenetic trees of animal genes that provides reliable information about ortholog and paralog assignments and evolutionary history of various gene families.
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