Epernicus: Fengfeng Zhou, Ph.D.

Fengfeng Zhou, Ph.D.

Position:
Research Scientist and Group Leader

Biochemistry and Molecular Biology

Institute of Bioinformatics

University of Georgia (Athens, GA)
Advisor:
Ying Xu
Degrees:

Ph.D., Computer Science, University of Science and Technology of China (Hefei, China)

B.Sc., Computer Science, University of Science and Technology of China (Hefei, China)
Past Advisors:

Ying Xu (as Post Doctoral Fellow)

Guoliang Chen (as Graduate Student - Ph.D.)
Research:
I'm working on computational genomics and metagenomics on transposons, biofuel-related enzymes and alternative splicing.

*) Cancer biomarker characterization based on microarray and sequencing data.
*) 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.
Other Experience:
2008 Judges for ISEF and GSEF

Communities:

Fengfeng Zhou's Genealogy

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Fengfeng Zhou's Publications (24)

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.
Zhou F, Xu Y

Bioinformatics (Oxford, England). 2010 Aug 15;26(16):2051-2
Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes.
Wang G, Zhou F, Olman V, Li F, Xu Y

FEBS letters. 2010 Jan 4;584(1):194-8
GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems.
Zhou F, Chen H, Xu Y

BMC microbiology. 2010;10:69
Large-scale analyses of glycosylation in cellulases.
Zhou F, Olman V, Xu Y

Genomics, proteomics & bioinformatics / Beijing Genomics Institute. 2009 Dec;7(4):194-9
De novo computational prediction of non-coding RNA genes in prokaryotic genomes.
Tran TT, Zhou F, Marshburn S, Stead M, Kushner SR, Xu Y

Bioinformatics (Oxford, England). 2009 Nov 15;25(22):2897-905
Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725.
Kataeva IA, Yang SJ, Dam P, Poole FL, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW

Journal of bacteriology. 2009 Jun;191(11):3760-1
MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi.
Chen Y, Zhou F, Li G, Xu Y

Gene. 2009 May 1;436(1-2):1-7
Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice.
Zhou C, Zhou F, Xu Y

Genomics. 2009 Apr;93(4):383-91
Genomic and proteomic characterization of a thermophilic Geobacillus bacteriophage GBSV1.
Liu B, Zhou F, Wu S, Xu Y, Zhang X

Research in microbiology. 2009 Mar;160(2):166-71
RepPop: a database for repetitive elements in Populus trichocarpa.
Zhou F, Xu Y

BMC genomics. 2009;10:14
A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4.
Chen Y, Zhou F, Li G, Xu Y

Genetics. 2008 Aug;179(4):2291-7
Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria.
Zhou F, Tran T, Xu Y

Biochemical and biophysical research communications. 2008 Jan 25;365(4):790-4
Barcodes for genomes and applications.
Zhou F, Olman V, Xu Y

BMC bioinformatics. 2008;9:546
Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.
Zhou F, Olman V, Xu Y

BMC genomics. 2008;9:36
SUMOsp: a web server for sumoylation site prediction.
Xue Y, Zhou F, Fu C, Xu Y, Yao X

Nucleic acids research. 2006 Jul 1;34(Web Server issue):W254-7
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).
Zhou F, Xue Y, Yao X, Xu Y

Bioinformatics (Oxford, England). 2006 Apr 1;22(7):894-6
A general user interface for prediction servers of proteins' post-translational modification sites.
Zhou F, Xue Y, Yao X, Xu Y

Nature protocols. 2006;1(3):1318-21
GPS: a comprehensive www server for phosphorylation sites prediction.
Xue Y, Zhou F, Zhu M, Ahmed K, Chen G, Yao X

Nucleic acids research. 2005 Jul 1;33(Web Server issue):W184-7
A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus.
Zhou F, Xue Y, Lu H, Chen G, Yao X

FEBS letters. 2005 Jun 20;579(16):3369-75
A Scheduling Algorithm on Symmetric Fiber Trees with Tunable ADMs
Fengfeng Zhou, Yinlong Xu, Guoliang Chen

Journal of Computer Science (in Chinese). 2005;28:774-781
GoPipe: Streamlined Gene Ontology Annotation for Batch Anonymous Sequences with Statistics
Zuozhou Chen, Chenghai Xue, Sheng Zhu, Fengfeng Zhou, Xuefeng Bruce Ling, Guoping Liu, Liangbiao Chen

Progress in Biochemistry and Biophysics. 2005;32:187-191
No-wait Scheduling in Single-hop Multi-channel LANs
Fengfeng Zhou, Yinlong Xu, Guoliang Chen

Information Processing Letters. 2005;93:19-24
GPS: a novel group-based phosphorylation predicting and scoring method.
Zhou FF, Xue Y, Chen GL, Yao X

Biochemical and biophysical research communications. 2004 Dec 24;325(4):1443-8
Minimizing ADMs on WDM Directed Fiber Trees
Fengfeng Zhou, Guoliang Chen, Yinlong Xu, J Gu

J. Comput. Sci. & Technol. 2003;18(6):725-731

Fengfeng Zhou's Posters and Presentations (1)

Proteins' indel mutations tend to reside in the internal regions (poster)
Fengfeng Zhou, Ying Xu

Computational Systems Bioinformatics Conference (CSB); 08/2006

One Figure

Fengfeng Zhou

Websites

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