Fengfeng Zhou

Postdoc research associate
Computational & Systems Biology Laboratory
Institute of Bioinformatics
Univ. of Georgia

Contact:

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

Education:

2000.9. - 2005.7. Ph.D Degree in Computer Science, Dept. of Computer Science, Univ. of Sci. & Tech. of China
1996.9. - 2000.7. Bachelor Degree in Computer Science, Special Class for Gifted Yound (SCGY), Univ. of Sci. & Tech. of China

My profiles on internet:

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

Research experience:

2005.9. - now postdoc research associate, Computational & Systems Biology Laboratory, Univ. of Georgia

Conferences and presentations:

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.

Academic services:

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.
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.
Program Committee Member:

International Conference on Intelligent Computing, 2008, Shanghai, P.R.China, Sept. 15-18, 2008.
International Conference on Intelligent Computing, 2007, Qingdao, Shandong, P.R.China, Aug. 21-24, 2007.
Workshop on Intelligent Computing & Bioinformatics of CAS, 2006, Hefei, Anhui, P.R.China, Nov. 12-14, 2006.
IEEE International Conference on Granular Computing, 2006. Atlanta, USA, May 10-12, 2006.

Scientific societies:

Research interests:

Characterizations of cellulolysis pathway in prokaryotes and fungi.
Characterizations of mobile genetic elements, including transposons and Insertion Sequences, and their influences on the host genomes.
Metagenomic analysis of microbial communities.
Data mining and large-scale analysis of microbiological genomes.
In silico prediction and large-scale analysis of proteins' post-translational modifications, including SUMOylation, phosphorylation, palmitoylation, acetylation, etc.
Designing and analyzing approximation algorithms for combinatorical optimization problems.
Detailed analysis of genomic structures.

My CV is under construction. Please refer to my personal webpage for details now.

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:


	[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* 179: 2291-2297. Website: http://csbl.bmb.uga.edu/publications/materials/ffzhou/chunjie/
	[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/
	[11]	Fengfeng Zhou, Thao Tran, Ying Xu, "Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria", Biochemical and Biophysical Research Communications 365 (4): 790-794 (2008).
	[10]	Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu, "A general user interface for prediction servers of proteins' post-translational modification sites", Nature Protocols 1 (3): 1318-1321 (2006). Web site: http://csbl.bmb.uga.edu/~ffzhou/PTMP-UI/ or http://bioinformatics.lcd-ustc.org/PTMP-UI/
	[9]	Yu Xue, Fengfeng Zhou*, Chuanhai Fu, Ying Xu, Xuebiao Yao, "SUMOsp: a web server for sumoylation site prediction", Nucl Acids Res* 34: W254-W257, 2006. Web site: http://csbl.bmb.uga.edu/~ffzhou/sumosp/ or http://bioinformatics.lcd-ustc.org/sumosp/old1/
	[8]	Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu, "CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)", Bioinformatics 22 (7): 894-896, 2006. Web site: http://csbl.bmb.uga.edu/~ffzhou/css_palm/ or http://bioinformatics.lcd-ustc.org/css_palm/old1/
	[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, 579 (2005): 3369-3375. Web site: http://bioinformatics.lcd-ustc.org/sumo/
	[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*, 33 (2005): W184-W187. Web site: http://csbl.bmb.uga.edu/~ffzhou/gps_web/ or http://bioinformatics.lcd-ustc.org/gps_web/
	[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, 32 (2005): 187-191.
	[4]	Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "No-wait Scheduling in Single-hop Multi-channel LANs", Information Processing Letters, 93 (2005): 19-24.
	[3]	Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "A Scheduling Algorithm on Symmetric Fiber Trees with Tunable ADMs", (in Chinese), Journal of Computer Science, 28 (2005): 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, 325 (2004): 1443-1448. Web site: http://csbl.bmb.uga.edu/~ffzhou/gps_web/ or http://bioinformatics.lcd-ustc.org/gps_web/
	[1]	Fengfeng Zhou, Guoliang Chen, Yinlong Xu, J. Gu, "Minimizing ADMs on WDM Directed Fiber Trees", J. Comput. Sci. & Technol., vol. 18, no. 6, pp.725-731, Nov. 2003.

* 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/