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Book or book chapters

  • “Health Informatics Data Analysis: Methods and Examples”. Editors: Dong Xu, May Dongmei Wang, Fengfeng Zhou, Yunpeng Cai. Springer, 2017.
  • 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.

Journal papers: 
* equal contribution, and # corresponding author. The supplementary materials and softwares may be found at the section Resources.

  1. Yuting Ye, Ruochi Zhang, Weiwei Zheng, Shuai Liu, Fengfeng Zhou#. “RIFS: a randomly restarted incremental feature selection algorithm”. Accepted by Scientific Reports.
  2. Jiamei Liu, Cheng Xu, Weifeng Yang, Yayun Shu, Weiwei Zheng, Fengfeng Zhou#. “Multiple similarly-well solutions exist for biomedical feature selection and classification problems”. Accepted by Scientific Reports.
  3. Ruiquan Ge, Guoqin Mai, R Zhang, X Wu, Q Wu, Fengfeng Zhou#. “MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs)”. Accepted by Journal of Integrative Bioinformatics, 2017.
  4. Pu Wang, Ruiquan Ge, Xuan Xiao, Yunpeng Cai, Guoqing Wang, Fengfeng Zhou#. “Rectified-Linear-Unit-Based Deep Learning for Biomedical Multi-label Data”. Interdisciplinary Sciences – Computational Life Sciences, 9: 419–422, 2017.
  5. Yan Xu, Li Li, Jun Ding, Ling-Yun Wu, Guoqin Mai, Fengfeng Zhou#. “Gly-PseAAC: Identifying protein lysine glycation through sequences”. Gene, 602: 1-7, 2017.
  6. Pu Wang, Ruiquan Ge, Xuan Xiao, Manli Zhou, Fengfeng Zhou#. “hMuLab: a Biomedical Hybrid MUlti-LABel Classifier Based on Multiple Linear Regression”.  Accepted by IEEE Transactions on Computational Biology and Bioinformatics, 2016.
  7. Yu Wang, Yaonan Zhang, Zhaomin Yao, Ruixue Zhao, Fengfeng Zhou#. “Machine learning based detection of age-related macular degeneration (AMD) and diabetic macular edema (DME) from optical coherence tomography (OCT) images”. BioMedical Optics Express, 7 (12): 4928-4940, 2016.
  8. Ruiquan Ge, Guoqin Mai, Pu Wang, Manli Zhou, Youxi Luo, Yunpeng Cai, Fengfeng Zhou#. “CRISPRdigger: detecting CRISPRs with better direct repeat annotations”. Scientific Reports, 6: 32942, 2016.
  9. Dongli Ma, Shan Zhong, Xiaorong Liu, Huirong Mai, Guoqin Mai, Cheng Xu, Fengfeng Zhou#. “CD3D and PRKCQ work together to discriminate between B-cell and T-cell acute lymphoblastic leukemia”. Computers in Biology and Medicine, 77: 16-22, 2016.
  10. Guoqin Mai, Ruiquan Ge, Guoquan Sun, Qinghan Meng, Fengfeng Zhou#. “A comprehensive curation shows the dynamic evolutionary patterns of prokaryotic CRISPRs”. BioMed Research International, 2016: 7237053, 2016.
  11. Ruiquan Ge, Manli Zhou, Youxi Luo, Qinghan Meng, Guoqin Mai, Dongli Ma, Guoqing Wang, Fengfeng Zhou#. "McTwo: a two-step feature selection algorithm based on maximal information coefficient ". BMC Bioinformatics 17: 142, 2016.
  12. Miaomiao Zhao, Yunpeng Cai, Jiankui He, Guanyu Wang, Dongqing Wei, Yanjie Wei, Caiwan Zhang, Fengfeng Zhou#. “Personalized clinical data screening: Special issue on health informatics”. Computers in Biology and Medicine, 61: 161-162, 2015.
  13. Bin Liu, Jikui Liu, Guoqing Wang, Fan Li, Yang Zheng, Fengfeng Zhou#. "A Novel Electrocardiogram Parameterization Algorithm and its Application in Myocardial Infarction Detection". Computers in Biology and Medicine 61: 178-184, 2015.
  14. Miaomiao Zhao, Zhao Zhang, Guoqin Mai, Youxi Luo, Fengfeng Zhou#. "jEcho: an Evolved weight vector to CHaracterize the protein's post-translational modification mOtifs". Interdisciplinary Sciences: Computational Life Sciences, 7:194-199, 2015.
  15. Wei Du, Zhongbo Cao, Yan Wang, Fengfeng Zhou, Wei Pang, Xin Chen, Yuan Tian, Yanchun Liang. “Specific Biomarkers: Detection of Cancer Biomarkers Through High-Throughput Transcriptomics Data”. Cognitive Computation 7 (6), 652-666, 2015.
  16. Manli Zhou*, Youxi Luo*, Guoquan Sun, Guoqin Mai, Fengfeng Zhou#. "Constraint Programming based Biomarker Optimization". BioMed Research International, 910515, 2015.
  17. Zhao Zhang*, Miaomiao Zhao*, Guoqin Mai, Youxi Luo, Ze Wang, Fengfeng Zhou#. "Evolutionary optimization of transcription factor binding motif detection". Advances in Experimental Medicine and Biology, 827: 261-274, 2015.
  18. Jiao Xie, Fengfeng Zhou, Guangyu Xu, Guoqin Mai, Jie Hu, Guoqing Wang, Fan Li. “Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization”. Molecular Biology Reports 41(9):5883-5889, 2014.
  19. Weihua Pan, Yanan Zhao, Yun Xu# and Fengfeng Zhou#. "WinHAP2: an extremely fast haplotype phasing program for long genotype sequences". BMC Bioinformatics 15(1):164, 2014.
  20. Bin Liu, Xiaotian Zhang, Honglan Huang, Ying Zhang, Fengfeng Zhou#, Guoqing Wang#. "A novel molecular typing method of Mycobacteria based on DNA barcoding visualization". Journal of Clinical Bioinformatics 4 (1), 4, 2014.
  21. Pi Guo*, Youxi Luo*, Guoqin Mai, Ming Zhang, Guoqing Wang#, Miaomiao Zhao, Liming Gao, Fan Li, Fengfeng Zhou#. "Gene Expression Profile based Classification Models of Psoriasis". Genomics, 103 (1), 48-55, 2014.
  22. Adi L. Tarca, Mario Lauria, Michael Unger, Erhan Bilal, Stephanie Boue, Kushal Kumar Dey, Julia Hoeng, Heinz Koeppl, Florian Martin, Pablo Meyer, Preetam Nandy, Raquel Norel, Manuel Peitsch, Jeremy J. Rice, Roberto Romero, Gustavo Stolovitzky, Marja Talikka, Yang Xiang, Christoph Zechner and IMPROVER DSC Collaborators. "Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge". Bioinformatics 29(22), 2892-2899, 2013.
  23. Meixue Yang, Bin Liu, Fan Li, Guoqing Wang#, Fengfeng Zhou#. "Normalizing electrocardiograms of both healthy persons and cardiovascular disease patients for biometric authentication". PLoS ONE, 8 (8), e71523, 2013.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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, 2012.
  29. 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, 17(14):1910-1914, 2011.
  30. 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.
  31. 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.
  32. 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.
  33. 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>
  34. Fengfeng Zhou and Ying Xu, "Large scale analyses of glycosylation in cellulases", Genomics, Proteomics & Bioinformatics 2009 7(4):194-199.
  35. 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.
  36. 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.
  37. 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.
  38. Yong Chen*, Fengfeng Zhou*, Guojun Li, and Ying Xu, " MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi", Gene 2009 436:1-7.
  39. 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.
  40. Chan Zhou, Fengfeng Zhou, Ying Xu, "Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice", Genomics 2009 93:383-391.
  41. Fengfeng Zhou, Ying Xu, “RepPop: a database for repetitive elements in Populus trichocarpa”, BMC Genomics 2009 10:14.
  42. Fengfeng Zhou*, Victor Olman*, Ying Xu, “Barcodes for Genomes and Applications”, BMC Bioinformatics 2008 9:546. <Highly accessed>
  43. 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.
  44. Fengfeng Zhou, Victor Olman, Ying Xu, "Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea", BMC Genomics, 2008 9:36.
  45. 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.
  46. 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.
  47. Yu Xue*, Fengfeng Zhou*, Chuanhai Fu, Ying Xu, Xuebiao Yao, "SUMOsp: a web server for sumoylation site prediction", Nucleic Acids Research 2006 34:W254-W257.
  48. 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.
  49. 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.
  50. 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.
  51. 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. 
  52. Fengfeng Zhou, Yinlong Xu, Guoliang Chen, "No-wait Scheduling in Single-hop Multi-channel LANs", Information Processing Letters 2005 93:19-24. 
  53. 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.
  54. Fengfeng Zhou, Guoliang Chen, Yinlong Xu, J. Gu, "Minimizing ADMs on WDM Directed Fiber Trees", J. Comput. Sci. & Technol. 2003 18(6):725-731.


© Fengfeng Zhou, Health Informatics Lab, College of Computer Science and Technology, Jilin University.
Last update: September 22, 2017.