中国科学院深圳先进技术研究院导师简况表
导师姓名
周丰丰
专业名称
计算机科学/生物信息学
所在单元
性别
医工所医学信息中心
男
职称
研究员
导师类别
■博导 □硕导
是否兼职
□是
■否
□物理化学（含化学物理）□生物化学与分子生物学□信号
招生专业
与信息处理■模式识别与智能系统■计算机应用技术□材料
工程□电子与通信工程□控制工程■计算机技术□生物工程
研究方向
生物信息学，并行化算法优化，高通量基因组测序数据分析，数据挖掘，生理/
生化数据的建模
中国科学院健康信息学重点实验室-临床异构数据源融合及整合性建模；
在研课题
深圳市基础研究项目-人类肝脏功能基因组学研究；
国家自然科学基金-基因组可视化条形码分析技术研究；
具有长期从事理论计算机科学和生物信息学两方面的研究经验。1996 年-2000
年在中国科大少年班系获得计算机软件与理论专业学士学位，2000 年保送攻读
中国科大计算机系，国家高性能计算中心陈国良院士的计算机软件与理论专业
的硕博连读生。于 2005 年获得计算机软件与理论专业博士学位。2005 年赴美国
个人简历
佐治亚大学生物信息研究所所长徐鹰教授的实验室从事博士后研究，并分别于
2008 年和 2009 年获聘为生物能源研究组组长和助理研究科学家。
现任中国科学院深圳先进技术研究院健康信息学研究员，博士研究生导师。广
主要科研
成果及所
获荣誉
东省创新团队核心成员；中国科学院健康信息学重点实验室核心成员。
已发表学术论文 29 篇，其中包括 SCI 索引 26 篇，第一作者或共第一作者 16
篇。影响因子合计为 96.868 分，以及总引用次数 353 次（他引 292 次）。学
术成果多次在包括 Nature Protocols、Nucleic Acids Research、Bioinformatics、
BMC Genomics、PLoS ONE 和 Genetics 等高水平 SCI 索引学术期刊上发表。
应邀担任新杂志 Frontiers in Bioinformatics and Computational Biology 的副主
编(associate editor，大陆唯一)以及 BioEnergy Research(SCI 索引，影响因子
4.019)的唯一生物信息学编委，并多次应邀评审国际项目标书、国际学术期
刊和会议的投稿论文。
其他
联系方式
备注
邮箱
ff.zhou@siat.ac.cn
电话
0755-86392200
个人主页
http://www.HealthInformaticsLab.org/
国 内 学 术 论 坛 丁 香 园 (http://bioinformatics.dxy.cn)
和 生 物 谷
(http://bbs.bioon.net/bbs/forum-57-1.html) 的生物信息学版面版主 cdragon。
Name
Academic
title
Fengfeng Zhou
Professor of
Health
Informatics
Phone
86-755-86392200
Resume
Positions
E-mail
Personal
Website
N/A
ff.zhou@siat.ac.cn
http://www.HealthInformaticsLab.org/
Dr. Fengfeng Zhou has an extensive experience in both theoretical computer
science and bioinformatics. He received his Bachelor degree on theoretical
computer science from the Special Class of Gifted Young (SCGY) of the University
of Science and Technology (USTC) in 2000. Then he was enrolled in the Ph.D.
program on theoretical computer science without test, and studied the optimization
algorithms of all optical networks and wireless networks supervised by the
Academician Prof. Guoliang Chen in the National High Performance Computing
Center (NHPCC), Department of Computer Science in USTC from 2000-2005.
After he got his Ph.D. degree in theoretical computer science in 2005, he joined
Prof. Ying Xu’s lab as a Bioinformatics Postdoc Research Associate, in the Institute
of Bioinformatics of the University of Georgia, USA. He was promoted to the
positions of group leader of the biofuel research group and assistant research
scientist in 2008 and 2009, respectively.
Now he works as a Professor of Health Informatics in the Shenzhen Institutes of
Advanced Technology, Chinese Academy of Sciences, and a Ph.D. advisor. He
serves as the core team members of the Guangdong Creative Research Consortium,
and the Health Informatics Key Laboratory of the Chinese Academy of Sciences.
Bioinformatics,
Direction
parallel
algorithm
optimization,
high-throughput
genome
sequencing analysis, data mining, biochemical and biophysical clinical data
modeling.
Dr. Fengfeng Zhou has published 29 scientific papers, including 26 indexed by the
SCI database, and first-authored or co-first-authored 16. The impact factors sum up
to be 96.868, and the total citation number is 353. The work was published in
top-level journals, including Nature Protocols, Nucleic Acids Research,
Achieveme
Bioinformatics, BMC Genomics, PLoS ONE and Genetics. He served as the only
nts
China mainland associate editor of the journal Frontiers in Bioinformatics and
Computational Biology, and the only bioinformatics editor of the journal
BioEnergy Research (SCI-indexed, impact factor=4.019). He was also invited to
serve as the reviewers of international proposals, journal papers and conference
manuscripts.
Book chapters
1.
Article
2.
Morgan G.I. Langille, Fengfeng Zhou, Amber Fedynak, William W.L. Hsiao,
Ying Xu, Fiona S.L. Brinkman, "Mobile genetic elements and their prediction",
Chapter 5 in “Computational Methods for Understanding Bacterial and Archaeal
Genomes”. Ying Xu and J Peter Gogarten (eds.), Imperial College Press, London,
pp. 113-135, 2008.
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.
Conference papers
* means equal contribution authors, and † means corresponding authors.
1.
Po-Yen Wu, John H Phan, Fengfeng Zhou, May D Wang, “Evaluation of
normalization methods for RNA-Seq gene expression estimation”, IEEE
International Conference on Bioinformatics and Biomedicine Workshops
(BIBMW), 2011:50-57.
Journal papers
* means equal contribution authors, and † means corresponding authors.
1.
2.
3.
4.
5.
6.
Fengfeng Zhou*, Qin Ma*, Guojun Li, Ying Xu. “QServer: A Biclustering
Server for Prediction and Assessment of Co-Expressed Gene Clusters”, PLoS
ONE 7(3):e32660.
Guoqing Wang, Fengfeng Zhou, Victor Olman, Yingying Su, Ying Xu, Fan Li,
“Computational prediction and experimental validation of novel markers for
detection of STEC O157:H7”, World Journal of Gastroenterology, 2011
17(14):1910-1914.
Phuongan Dam, Irina Kataeva, Sung-Jae Yang, Fengfeng Zhou, Yanbin Yin,
Wenchi Chou, Farris L., Poole II, Janet Westpheling, Robert Hettich, Richard
Giannone, Derrick L. Lewis, Robert Kelly, Harry J. Gilbert, Bernard Henrissat,
Ying Xu and Michael W.W. Adams, "Insights into Plant Biomass Conversion
from the Genome of the Anaerobic Thermophilic Bacterium Caldicellulosiruptor
bescii DSM 6725", Nucleic Acids Research, 2011 39(8):3240-3254.
Fengfeng Zhou, Ying Xu, “cBar: a computer program to distinguish
plasmid-derived from chromosome-derived sequence fragments in metagenomics
data”, Bioinformatics 2010 26: 2051-2052.
Guoqing Wang, Fengfeng Zhou, Victor Olman, Fan Li, Ying Xu, “Prediction of
pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using
genomic barcodes”, FEBS Letters 2010 584(1):194-198.
Fengfeng Zhou, Huiling Chen, Ying Xu, "GASdb: a large-scale and comparative
exploration database of glycosyl hydrolysis systems", BMC Microbiology 2010
10:69.
Fengfeng Zhou and Ying Xu, "Large scale analyses of glycosylation in
cellulases", Genomics, Proteomics & Bioinformatics 2009 7(4):194-199.
8. Fenglou Mao, Yanbin Yin, Fengfeng Zhou, Wen-Chi Chou, Chan Zhou, Huiling
Chen, Ying Xu, "pDAWG: An Integrated Database for Plant Cell Wall Genes",
BioEnergy Research 2009 2(4):209-216.
9. 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", Bioinformatics 2009 25(22):2897-2905.
10. 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.
11. Yong Chen*, Fengfeng Zhou*, Guojun Li, and Ying Xu, " MUST: A system for
7.
12.
13.
14.
15.
identification of miniature inverted-repeat transposable elements and applications
to Anabaena variabilis and Haloquadratum walsbyi", Gene 2009 436:1-7.
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.
Chan Zhou, Fengfeng Zhou, Ying Xu, "Comparative analyses of distributions
and functions of Z-DNA in Arabidopsis and rice", Genomics 2009 93:383-391.
Fengfeng Zhou, Ying Xu, “RepPop: a database for repetitive elements in Populus
trichocarpa”, BMC Genomics 2009 10:14.
Fengfeng Zhou*, Victor Olman*, Ying Xu, “Barcodes for Genomes and
Applications”, BMC Bioinformatics 2008 9:546.
16. Yong Chen*, Fengfeng Zhou*, Guojun Li, and Ying Xu, "A recently active
miniature inverted-repeat transposable element, Chunjie, inserted into an operon
without disturbing the operon structure in Geobacter uraniireducens Rf4",
Genetics 2008 179: 2291-2297.
17. Fengfeng Zhou, Victor Olman, Ying Xu, "Insertion Sequences show diverse
recent activities in Cyanobacteria and Archaea", BMC Genomics, 2008 9:36.
18. 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.
19. 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.
20. 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.
21. 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.
22. Fengfeng Zhou*, Yu Xue*, Hualei Lu, Guoliang Chen, Xuebiao Yao, "A
genome-wide analysis of sumoylation-related biological processes and functions
in human nucleus", FEBS Letters 2005 579: 3369-3375.
23. 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.
24. 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.
25. Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "No-wait Scheduling in Single-hop
Multi-channel LANs", Information Processing Letters 2005 93:19-24.
26. 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.
27. Fengfeng Zhou*, Yu Xue*, Guoliang Chen, Xuebiao Yao, "GPS: A Novel
Group-based Phosphorylation Predicting and Scoring Method", Biochemical and
Biophysical Research Communications 2004 325:1443-1448.
28. Fengfeng Zhou, Guoliang Chen, Yinlong Xu, J. Gu, "Minimizing ADMs on
WDM Directed Fiber Trees", J. Comput. Sci. & Technol. 2003 18(6):725-731.
Non-peer-reviewed papers
* means equal contribution authors, and † means corresponding authors.
1.
2.
3.
Yu Xue, Fengfeng Zhou, Ying Xu and Xuebiao Yao, "GPS: A computational
protocol for kinase-specific phosphorylation site prediction", Nature Protocols,
2007 (invited).
Fengfeng Zhou, Guoliang Chen, Yinlong Xu, "Construction of Small Worlds in
the Physical Topology of Wireless Networks", arXiv:cs.NI/0503051, 2005.
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, 2004.