Dhany Saputra

PhD candidate
Center for Biological Sequence Analysis, Technical University of Denmark.

Contact: Dhany Saputra

Address:
Center for Biological Sequence Analysis, Building 208, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
Google Scholar
Education:

My profiles on internet:

Nature network http://network.nature.com/profile/ffzhou
Epernicus http://www.epernicus.com/people/FengfengZhou
Researcher ID http://www.researcherid.com/rid/A-8932-2008
LinkedIn http://www.linkedin.com/in/FengfengZhou
Scopus http://www.scopus.com/authid/detail.url?authorId=8718139300
Google My Citations http://scholar.google.com/citations?user=FL2GqPcAAAAJ&hl=en

Research experience:
Invited talks and conference presentations:
  • Talk: "A Fractal Visualization of Genetic Codes and Its Applications", Junior Interdisciplinary Research Forum on Mathematics, Computer Science and Biological Science, Beijing, May 18-19, 2013.
  • Talk: "A Fractal Visualization of Genetic Codes and Its Applications", Department of Systems Engineering and Engineering Management, Hongkong City University, Hongkong, April 17, 2013.
  • Talk: "Barcode: the Genomic Fractal Feature", the Hongkong-Shenzhen Innovation Forum, Shenzhen, December 8, 2012.
  • Talk: "A Stable Disease Classifier by Screening for 2 Genes from 20,000 Ones", the Summit of Biomedical and Health Engineering, Shenzhen, December 3-4, 2012.
  • Talk: "Disease Modeling: Mining Biologically Meaningful Needles from a Haystack", the 7th Asia Pacific Association for Medical Informatics Conference (APAMI 2012), Beijing, October 22-25, 2012.
  • Talk: "A meta-feature-selection strategy to screen for a stable gene expression profile for human disease", International Conference on Computational and Systems Biology (ICCSB2012), Shanghai, October 12-14, 2012.
  • Poster: "Comparative genomics analysis of pathogen's mobilomes", National Conference of Bioinformatics and Systems Biology, Haerbin, July 10-12, 2012.
  • Talk: "Genome visualization and its application in detecting pathogenic genome islands", Peking University Summer School on Biomedical Engineering, Beijing, July 10-20, 2012.
  • Talk: "Large scale detection of foreign genetic elements and its application in reconstruction of common ancestor sequences", Guangxi University, Nanning, April 15, 2012.
  • Talk: "Reconstruction of recent ancestral sequence based on the high-throughput sequencing data", HKU-SIAT Workshop on Experimental/Computational Biology: Gene and Protein, Shenzhen, April 11, 2012.
  • Talk: "Cloud-based bioinformatics problems for low-cost health plan", Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, February 24, 2012.
  • Talk: "Large-scale detection algorithms of foreign elements", Jilin University, Changchun, Jilin, December 9, 2011.
  • Talk: "Large-scale detection algorithms of foreign elements", Tsinghua University, Beijing, China, December 9, 2011.
  • Talk: "In silico Detection of Foreign Elements", University of Georgia, Athens, GA, USA, November 10, 2011.
  • Poster: "Genomic Location is Information: Towards Complete Assignment of Metabolic Pathways by Bacterial Genes", BioEnergy Science Center Annual Retreat, Chattanoogan, TN, USA, July 18-21, 2011.
  • Poster: "A novel method for assigning holes in metabolic pathways with predicted enzyme-encoding genes based on genomic locations", Genomic Sciences Contrator-Grantee Meeting/USDA-DOE Plant Feedstock Genomics for Bioenergy Awardees Meeting 2011, Arlington, VA, USA, April 10-13, 2011.
  • Talk: "Transposable elements are actively involved in the evolution of prokaryotic genomes", BioConference Live: Life Scienes, March 21-22, 2011.
  • Poster: "Horizontally transferred cazyme islands in the genus Clostridium", Bioenergy Systems Research Initiative (BSRI) Annual Retreat 2010, Athens, GA, USA, November 15, 2010.
  • Poster: "Recent gain and loss of CAZyme components in Clostridium perfringens", BESC Science Retreat 2010, Ashville, NC, USA, June 21-23, 2010.
  • Poster: "Insights into Plant Biomass to Biofuel Conversion from the Genome Sequence, Proteomics and Transcriptomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor bescii", BESC Science Retreat 2010, Ashville, NC, USA, June 21-23, 2010.
  • Poster: "Comparative glydromics in genomes and metagenomes produced by the high-throughput sequencing technique", Earth Day 2010, Atlanta, GA, USA, April 22, 2010.
  • Poster: "The intrinsic barcode feature of a genome". Computational Systems Bioinformatics Conference (CSB) 2009, Stanford University, California, USA, August 10-12, 2009.
  • Poster: "Comparative glydromics revealed the unexpected diverse distribution of two unconventional glydromes. 3rd BESC Science Retreat, Asheville, NC, USA, June 22-24, 2009.
  • Poster: The intrinsic barcode feature of a genome and its applications". SMBE 2009, Iowa City, IA, USA, June 3-7, 2009.
  • Talk: "Miniature Transposons in Prokaryotes", Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, January 22, 2009.
  • Poster: "pDAWG: plant Database of Annotated cell Wall Genome". 2nd BESC Science Retreat, Chattanooga, TN, USA, December 1-3, 2008.
  • Poster: "Proteins' indel mutations tend to reside in the internal regions". Life Science Society - Computational Systems Bioinformatics Conference (CSB), 2006, Stanford University, California, USA, Aug. 14-18, 2006.
  • Attendee. Molecular Evolution, 2006, Gordon Conference, Ventura, California, USA, Feb. 5-10, 2006.
  • Talk: "Algorithms for Loosely Constrained Multiple Sequence Alignment". International Symposium on Computational and Information Sciences, 2004, Shanghai, China, Dec. 16-18, 2004.
Academic services:
  • Editorial services:
    1. Member of editorial board (2013-now): Computers in Biology and Medicine.
    2. Associate editor (2012-now): Interdisciplinary Sciences: Computational Life Sciences.
    3. Member of editorial board (2011-now): Genomics, Proteomics and Bioinformatics.
    4. Associate editor (2011-now): Frontiers in Bioinformatics and Computational Biology.
    5. Member of editorial board (2009-now): BioEnergy Research.
    6. Member of editorial board (2011-2011): Interdisciplinary Sciences: Computational Life Sciences.
    7. Associate editor (2009-2011): Sequencing.
  • Reviewers for funding agencies:
    1. National Science Foundation of China (NSFC), 2012-2013.
    2. Guangdong Science and Technology Award, 2012.Austrian Science Fund (FWF), 2011.
    3. Netherlands Organization for Scientific Research (NOW), the Netherlands Genomics Initiative (NGI), 2011.
    4. US NSF and Louisiana Board of Regents, Louisana Experimental Program to Stimulate Competitive Research (EPSCoR), 2011.
    5. US NSF, Bio-DEB, Evolutionary Process, 2010.
    6. UK Natural Environmental Research Council, 2009.
    7. North Carolina Biotechnology Center, Science and Technology Development Program, 2008.
  • Reviewers for journals: Advances in Bioinformatics; Acta Biotheoretica; African Journal of Microbiology Research; Applied and Environmental Microbiology; BioEnergy Research; Bioinformatics; Bioinformatics and Biology Insights; Biophysical Chemistry; Biotechnology Letters; BMC Bioinformatics; BMC Evolutionary Biology; BMC Genomics; BMC Systems Biology; Briefings in Bioinformatics; Cancer Informatics; Computers in Biology and Medicine; FEBS Letters; Gene; Genome Biology; Genomics; Genomics, Proteomics & Bioinformatics; Indian Journal of Biochemistry & Biophysics; IEEE Transactions on Biomedical Engineering; Infection, Genetics and Evolution; ?Infection, Genetics and Microbiology; Insect Science; International Journal of Data Mining and Bioinformatics; International Nano Letters; Journal of Bioinformatics and Computational Biology; Journal of Molecular Biology; Journal of Molecular Modeling; Journal of Theoretical Biology; Mathematical Biosciences; Mobile Genetic Elements; Neural Computing and Applications; Nucleic Acid Research; OMICS PUBLISHING GROUP - Clinical; PLoS ONE; Proteomics & Bioinformatics; Science in China - C; Trends in Genetics.
  • 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; IBW 2010; CSB 2010; Bioinformatics 2010; ISBRA 2010; ACM BCB 2010; IEEE-GrC 2010; IJDMB 2010; BIOINFORMATICS 2011; ICCABS 2011; ISBRA 2011; ICIC 2011; BIBE 2011; BIBM 2011; ICIC 2012; EMBC 2012; ICIC 2013; EMBC 2013.
  • Scientific conferences :
    1. Organizing Committee Member, International Workshop on Cancer Systems Biology (ICSB), 2013, Zhuhai, China, July 4-5, 2013.
    2. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2013, Nanning, China, July 28-31, 2013.
    3. Program Committee Member, IEEE International Conference on Systems Biology (ISB), 2012, Xi'an, China, August 18-20, 2012.
    4. Organizing Committee Member, International Workshop on Cancer Systems Biology (ICSB), 2012, Changchun, China, July 5-6, 2012.
    5. Organizing Committee Member, The 10th International Bioinformatics Workshop (IBW), 2012, Changchun, China, July 7-8, 2012.
    6. Poster Session Chair, Session of Telemedicine and Hospital Information, World Congress in Medical Physics and Biomedical Engineering, 2012, Beijing, China, May 26-31, 2012.
    7. Program Committee Member, International Symposium on Foundations and Frontiers of Data mining (FFDM), 2012, Hangzhou, China, August 11-13, 2012.
    8. Program Committee Member, IEEE Conference on Granular Computing (IEEE GrC), 2012, Hangzhou, China, August 11-13, 2012.
    9. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2012, Huangshan, China, July 25-28.
    10. Program Committee Member, IEEE Conference on Granular Computing (IEEE GrC), 2011, Kaohsiung, Taiwan, November 8-10, 2011.
    11. Program Committee Member, International Conference on Bioinformatics and Biomedical Engineering (iCBBE), 2011, Wuhan, China, May 10-12, 2011.
    12. Organizing Committee Member, International Workshop on Cancer Systems Biology (ICSB), 2011, Changchun, China, July 2-3, 2011.
    13. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2011, Zhengzhou, China, August 11-14, 2011.
    14. Program Committee Member, International Bioinformatics Workshop (IBW), 2010, Wuhan University, Wuhan, China, June 4-6, 2010.
    15. Program Committee Member, IEEE Conference on Granular Computing (IEEE GrC), 2010, Silicon Valley, USA, August 14-16, 2010.
    16. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2010, Changsha, China, August 18-21, 2010.
    17. Program Committee Member, International Bioinformatics Workshop (IBW), 2009, Soochow University, Suzhou, China, June 19-21, 2009.
    18. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2009, University of Ulsan, Korea, Sept. 16-19, 2009.
    19. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2008, Shanghai, P.R.China, Sept. 15-18, 2008.
    20. Program Committee Member, International Conference on Intelligent Computing (ICIC), 2007, Qingdao, Shandong, P.R.China, Aug. 21-24, 2007.
    21. Program Committee Member, Workshop on Intelligent Computing & Bioinformatics of CAS (WICB), 2006, Hefei, Anhui, P.R.China, Nov. 12-14, 2006.
    22. Program Committee Member, IEEE International Conference on Granular Computing (IEEE GrC), 2006. Atlanta, USA, May 10-12, 2006.

Research interests:

  • Computational characterization of genome variations, including SNPs and genome structural variations, based on the high-throughput sequenced genomes and transcriptomes.
  • Biomarker characterization of mammalian genetic diseases, including cardiovascular diseases, hypertension and cancer, etc.
  • 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.
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", Chapter 5 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.
  2. 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.
 
     

Journal papers:
* equal contribution, and # corresponding author.

 
  1. Qilin Ma, Youxi Luo, Pi Guo, Gan Gao, Meixue Yang, Fengfeng Zhou #. “Clinical effects of Xinmailong therapy in patients with chronic heart failure”. International Journal of Medical Sciences, 10(5):624-633, 2013.
  2. Gaurav Sablok, XianMing Wu, Kinshuk Chandra Nayak, Jimmy Kuo, Vesselin Baev, Fengfeng Zhou. “Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom”. Genomics, 101(5):290-295, 2013.
  3. Kaishi Li, Meixue Yang, Gaurav Sablok, Jianping Fan #, Fengfeng Zhou #. “Screening features to improve the class prediction of acute myeloid leukemia and myelodysplastic syndrome”, Gene, 512:348-354, 2013.
  4. Yun Xu #, Wenhua Cheng, Pengyu Nie, Fengfeng Zhou #. “WinHAP: an Efficient Haplotype Phasing Algorithm based on Scalable Sliding Windows”. PLoS ONE, 7(8):e43163, 2012.
  5. Fengfeng Zhou *, Qin Ma*, Guojun Li, Ying Xu. " QServer: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters",PLoS ONE, 2012 7(3):e32660.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Fengfeng Zhou, Huiling Chen, Ying Xu, "GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems", BMC Microbiology 2010 10:69. <Highly accessed>
  11. Fengfeng Zhou and Ying Xu, "Large-scale analyses of glycosylation in cellulases", Genomics, Proteomics & Bioinformatics 2009 7(4):194-199.
  12. Fenglou Mao, Yanbin Yan, 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. Chan Zhou, Fengfeng Zhou, Ying Xu, "Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice", Genomics 2009 93:383-391.
  18. Fengfeng Zhou, Ying Xu, "RepPop: a database for repetitive elements in Populus trichocarpa", BMC Genomics 2009 10:14.
  19. Fengfeng Zhou*, Victor Olman*, Ying Xu, "Barcodes for Genomes and Applications", BMC Bioinformatics 2008 9:546. <Highly accessed>
  20. 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/
  21. 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/
  22. 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.
  23. 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/
  24. 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/
  25. 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/
  26. 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/
  27. 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/
  28. 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.
  29. Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "No-wait Scheduling in Single-hop Multi-channel LANs", Information Processing Letters 2005 93:19-24.
  30. 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/
  31. Fengfeng Zhou, Guoliang Chen, Yinlong Xu, J. Gu, "Minimizing ADMs on WDM Directed Fiber Trees", J. Comput. Sci. & Technol. 2003 18(6):725-731.
     

Journal papers in Chinese:
* equal contribution, and # corresponding author.

 
  1. Kaishi Li, Jianping Fan #, Fengfeng Zhou #. "Early Diagnosis Algorithms for ICU Emergencies" (in Chinese), Integrative Technology, Special Issue on Health Informatics, 2012, 1(2):13-19.
  2. 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.
     

Preprints:
* equal contribution, and # corresponding author.

 
  1. Yu Xue, Fengfeng Zhou, Ying Xu and Xuebiao Yao, "GPS: A computational protocol for kinase-specific phosphorylation site prediction", Nature Protocol, 2007 (invited).
  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
  3. Fengfeng Zhou, Guoliang Chen, Yinlong Xu, "Construction of Small Worlds in the Physical Topology of Wireless Networks", arXiv:cs.NI/0503051

   
   
 

© Fengfeng Zhou, Health Informatics Lab, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences
Last update: July 1, 2013.
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