Fengfeng Zhou

Contact:

Address:
120 Green Street, Athens, GA, 30602-7229
Webpage: http://csbl.bmb.uga.edu/~ffzhou/
Work phone: 706-542-9763

• Nature network: http://network.nature.com/profile/ffzhou
• Epernicus: http://www.epernicus.com/users/8124
• Researcher ID: http://www.researcherid.com/rid/A-8932-2008

• Computational Systems Bioinformatics Conference (CSB) 2009, Stanford University, California, USA, August 10-12, 2009.
  Fengfeng Zhou, Victor Olman, Xizeng Mao, Ying Xu. "The intrinsic barcode feature of a genome", Poster.
• 3rd BESC Science Retreat, Asheville, NC, USA, June 22-24, 2009.
  Fengfeng Zhou, Ying Xu. "Comparative glydromics revealed the unexpected diverse distribution of two unconventional glydromes", Poster.
• SMBE 2009, Iowa City, IA, USA, June 3-7, 2009.
  Fengfeng Zhou, Victor Olman, Xizeng Mao, Ying Xu. "The intrinsic barcode feature of a genome and its applications", Poster.
• Invited talk, "Miniature Transposons in Prokaryotes", Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, January 22, 2009.
• 2nd BESC Science Retreat, Chattanooga, TN, USA, December 1-3, 2008.
  Fenglou Mao, Fengfeng Zhou, Wen-chi Chou, Yanbin Yin, Huiling Chen, Chan Zhou, Ying Xu. "pDAWG: plant Database of Annotated cell Wall Genome", Poster.
• Life Science Society - Computational Systems Bioinformatics Conference (CSB), 2006, Stanford University, California, USA, Aug. 14-18, 2006.
  Fengfeng Zhou, Ying Xu, "Proteins' indel mutations tend to reside in the internal regions", Poster.
• Molecular Evolution, 2006, Gordon Conference, Ventura, California, USA, Feb. 5-10, 2006. Attendee.
• International Symposium on Computational and Information Sciences, 2004, Shanghai, China, Dec. 16-18, 2004.
  Bin Song, Fengfeng Zhou, Guoliang Chen, "Algorithms for Loosely Constrained Multiple Sequence Alignment", Lecture Notes in Computer Science (LNCS) 3314 (CIS'2004), pp. 213-218, 2004.

• Reviewers for journals: Acta Biotheoretica; Genome Biology; Nucleic Acid Research; BMC Genomics; BMC Bioinformatics; Trends in Genetics; FEBS Letters; BMC Evolutionary Biology; Science in China - C; Biophysical Chemistry; PLoS ONE; Bioinformatics; Genomics, Proteomics & Bioinformatics; Journal of Molecular Biology.
• Reviewers for conferences: ACBI 2006, ICIC 2006, IEEE-GRC 2006, PRIB 2006, GIW 2006, GIW 2007, ICIC 2007, CSB 2007, LSMS 2007, APBC 2008, CSB 2008, ICIC 2008, IBW 2009, ICIC 2009, CSB 2009.
• Program Committee Member:
1. International Bioinformatics Workshop, 2009, Soochow University, Suzhou, China, June 19-21, 2009.
2. International Conference on Intelligent Computing, 2009, University of Ulsan, Korea, Sept. 16-19, 2009.
3. International Conference on Intelligent Computing, 2008, Shanghai, P.R.China, Sept. 15-18, 2008.
4. International Conference on Intelligent Computing, 2007, Qingdao, Shandong, P.R.China, Aug. 21-24, 2007.
5. Workshop on Intelligent Computing & Bioinformatics of CAS, 2006, Hefei, Anhui, P.R.China, Nov. 12-14, 2006.
6. IEEE International Conference on Granular Computing, 2006. Atlanta, USA, May 10-12, 2006.

Scientific societies:

• International Society for Computational Biology
• Society for Molecular Biology and Evolution
• Sigma Xi - The Scientific Research Society
• Biofuels, Biopwer and Biomaterials Initiative at UGA

Research interests:

• Graduate students: Chunbao Zhou (JLU), Zhongbo Cao (JLU).
• Undergraduate students: Celine Hong (UGA), Hyongsook Kim (UGA), Farres Obeidin (UGA).
• Outreach projects: Dylan Clark (GIFT2009, math teacher of the Clark Central High School).

	Book chapters:
		[1]	Morgan G.I. Langille, Fengfeng Zhou, Amber Fedynak, William W.L. Hsiao, Ying Xu, Fiona S.L. Brinkman, "Mobile genetic elements and their prediction", in Computational Methods for Understanding Bacterial and Archaeal Genomes. Ying Xu and J Peter Gogarten (eds.) Series on Advances in Bioinformatics and Computational Biology, Vol. 7. Imperial College Press, London, 2008. Approx. 496 pp. ISBN-13: 978-1-86094-982-1. ISBN-10: 1-86094-982-7.
	Peer-reviewed journal papers (the last column shows the number of citations of each paper in GoogleScholar) [Total citations: 265, as of November 3, 2009]:   [22] Fenglou Mao, Yanbin Yan, Fengfeng Zhou, Wen-Chi Chou, Chan Zhou, Huiling Chen, Ying Xu, "pDAWG: an Integrated Database for Plant Cell-Wall Genes", Accepted by BioEnergy Research.   [21] Thao Tran, Fengfeng Zhou, Sarah Marshburn, Mark Stead, Sidney Kushner, and Ying Xu, "De novo computational prediction of non-coding RNA genes in prokaryotic genomes", Accepted by Bioinformatics.   [20] Fengfeng Zhou and Ying Xu, "Large scale analyses of glycosylation in cellulases", Accepted by Genomics, Proteomics & Bioinformatics.   [19] Irina A Kataeva, Sung-Jae Yang, Phuongan Dam, Farris L Poole II, Yanbin Yin, Fengfeng Zhou, Wen-chi Chou, Ying Xu, Lynne Goodwin, David R Sims, John C Detter, Loren J Hausser, Janet Westpheling and Michael WW Adams, "Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725", Journal of Bacteriology 2009 191:3760-3761. 1   [18] Yong Chen*, Fengfeng Zhou*, Guojun Li, and Ying Xu, "MUST: a system for identification of miniature inverted repeats transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi", Gene 2009 436:1-7. 0   [17] Bin Liu, Fengfeng Zhou, Suijie Wu, Ying Xu and Xiaobo Zhang, "Genomic and Proteomic Characterization of a Thermophilic Geobacillus Bacteriophage GBSV1", Research in Microbiology 2009 160:166-171. 0   [16] Chan Zhou, Fengfeng Zhou, Ying Xu, "Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice", Genomics 2009 93:383-391. 0   [15] Fengfeng Zhou, Ying Xu, “RepPop: a database for repetitive elements in Populus trichocarpa”, BMC Genomics 2009 10:14. 3   [14] Fengfeng Zhou*, Victor Olman*, Ying Xu, “Barcodes for Genomes and Applications”, BMC Bioinformatics 2008 9:546. 3   [13] Yong Chen*, Fengfeng Zhou*, Guojun Li, and Ying Xu, "A recently active MITE, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4", Genetics 2008 179:2291-2297. Website: http://csbl.bmb.uga.edu/publications/materials/ffzhou/chunjie/ 1   [12] Fengfeng Zhou, Victor Olman, Ying Xu, "Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea", BMC Genomics 2008 9:36. Website: http://csbl.bmb.uga.edu/~ffzhou/isa_web/ 4   [11] Fengfeng Zhou, Thao Tran, Ying Xu, "Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria", Biochemical and Biophysical Research Communications 2008 365(4): 790-794. 4   [10] Fengfeng Zhou*, Yu Xue*, Xuebiao Yao, Ying Xu, "A general user interface for prediction servers of proteins' post-translational modification sites", Nature Protocols 2006 1(3):1318-1321. Web site: http://csbl.bmb.uga.edu/~ffzhou/PTMP-UI/ or http://bioinformatics.lcd-ustc.org/PTMP-UI/ 11   [9] Yu Xue*, Fengfeng Zhou*, Chuanhai Fu, Ying Xu, Xuebiao Yao, "SUMOsp: a web server for sumoylation site prediction", Nucl Acids Res 2006 34:W254-W257. Web site: http://csbl.bmb.uga.edu/~ffzhou/sumosp/ or http://bioinformatics.lcd-ustc.org/sumosp/old1/ 40   [8] Fengfeng Zhou*, Yu Xue*, Xuebiao Yao, Ying Xu, "CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)", Bioinformatics 2006 22(7):894-896. Web site: http://csbl.bmb.uga.edu/~ffzhou/css_palm/ or http://bioinformatics.lcd-ustc.org/css_palm/old1/ 38   [7] Fengfeng Zhou*, Yu Xue*, Hualei Lu, Guoliang Chen, Xuebiao Yao, "A genome-scale analysis of sumoylation-related biological processes and functions in human nucleus", FEBS Letters 2005 579:3369-3375. Web site: http://bioinformatics.lcd-ustc.org/sumo/ 24   [6] Yu Xue*, Fengfeng Zhou*, Minjie Zhu, Kashif Ahmed, Guoliang Chen, Xuebiao Yao, "GPS: A comprehensive www server for phosphorylation sites prediction", Nucleic Acids Research 2005 33:W184-W187. Web site: http://csbl.bmb.uga.edu/~ffzhou/gps_web/ or http://bioinformatics.lcd-ustc.org/gps_web/ 67   [5] Zuozhou Chen, Chenghai Xue, Sheng Zhu, Fengfeng Zhou, Xuefeng Bruce Ling, Guoping Liu, Liangbiao Chen, "GoPipe: Streamlined Gene Ontology Annotation for Batch Anonymous Sequences with Statistics", Progress in Biochemistry and Biophysics 2005 32:187-191. 10   [4] Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "No-wait Scheduling in Single-hop Multi-channel LANs", Information Processing Letters 2005 93:19-24. 0   [3] Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "A Scheduling Algorithm on Symmetric Fiber Trees with Tunable ADMs", (in Chinese), Journal of Computer Science 2005 28:774-781.   [2] Fengfeng Zhou*, Yu Xue*, Guoliang Chen, Xuebiao Yao, "GPS: A Novel Group-based Phosphorylation Prediction and Scoring Method", Biochemical and Biophysical Research Communications 2004 325:1443-1448. Web site: http://csbl.bmb.uga.edu/~ffzhou/gps_web/ or http://bioinformatics.lcd-ustc.org/gps_web/ 55   [1] Fengfeng Zhou, Guoliang Chen, Yinlong Xu, J. Gu, "Minimizing ADMs on WDM Directed Fiber Trees", J. Comput. Sci. & Technol. 2003 18(6):725-731. 4   * means that the indicated authors contribute equally to that paper.   Non-peer-reviewed papers:   [3] Yu Xue, Fengfeng Zhou, Ying Xu and Xuebiao Yao, "GPS: A computational protocol for kinase-specific phosphorylation site prediction", Nature Protocol, 2007.   [2] Yu Xue*, Fengfeng Zhou*, Hualei Lu, Guoliang Chen, Xuebiao Yao, "SUMO Substrates and Sites Prediction Combining Pattern Recognition and Phylogenetic Conservation", arXiv:q-bio.GN/0409011   [1] Fengfeng Zhou, Guoliang Chen, Yinlong Xu, "Construction of Small Worlds in the Physical Topology of Wireless Networks", arXiv:cs.NI/0503051   * means that the indicated authors contribute equally to that paper.   Favorite links: Ding Xiang Yuan: http://www.dxy.cn/bbs My research space: http://www.myresearchspace.cn/ UGA: http://www.uga.edu/ Science Board: http://www.scienceboard.net/ HighWire: http://intl.highwire.org/