[1] BAJIC V B, CHONG A, SEAH S H, et al. An intelligent system for vertebrate promoter recognition [J]. IEEE Intelligent Systems, 2002, 17(4): 64-70. [2] FICKETT J W, HATZIGEORGIOU A G. Eukaryotic promoter recognition [J]. Genome Research, 1997, 11(5): 861-878. [3] UMESH P, DUBEY J K,KARTHIKA R V, et al. A novel sequence and context based method for promoter recognition [J]. Bioinformation, 2014, 10(4): 175-179. [4] ZENG J, ZHAO X, CAO X, et al. SCS: signal, context, and structure features for genome-wide human promoter recognition [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, 7(3): 550-562. [5] DENG J, LIANG H, ZHANG R, et al. Methylated CpG site count of dapper homolog 1 (DACT1) promoter prediction the poor survival of gastric cancer [J]. American Journal of Cancer Research, 2014, 4(5): 518-527. [6] HUANG W L, TUNG C W, LIAW C, et al. Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species [J]. Scientific World Journal, 2014, 2014(2014): 1-14. [7] FUJII S, KONO H, TAKENAKA S, et al. Sequence-dependent DNA deformability studied using molecular dynamics simulations [J]. Nucleic Acids Research, 2007, 35(18): 6063-6074. [8] GAN Y, GUAN J, ZHOU S. A comparison study on feature selection of DNA structural properties for promoter prediction [J]. BMC Bioinformatics, 2012, 13:4. [9] ANWAR F, BAKER S M, JABID T, et al. Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach [J]. BMC Bioinformatics, 2008, 9(1): 414-418. [10] WU J, XIE J. Hidden Markov model and its applications in motif findings [M]//Statistical Methods in Molecular Biology. New York: Humana Press, 2010: 405-416. [11] ZHAO X, ZHANG J, CHEN Y, et al. Promoter recognition based on the maximum entropy hidden Markov model[J]. Computers in Biology & Medicine, 2014, 51(15):73-81. [12] LI Y, LEE K, WALSH S, et al. Establishing glucose-and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a relevance vector machine [J]. Genome Research, 2008, 16(3):414-427. [13] LIU G, LIU J, CUI X, et al. Sequence-dependent prediction of recombination hotspots in Saccharomyces cerevisiae [J]. Journal of Theoretical Biology, 2012, 293(1): 49-54. [14] LU J, LUO L. Prediction for human transcription start site using diversity measure with quadratic discriminant [J]. Bioinformation, 2008, 2(7): 316-21. [15] WANG J, UNGAR L H, TSENG H, et al. MetaProm: a neural network based meta-predictor for alternative human promoter prediction [J]. BMC Genomics, 2007, 8(1): 374-13. [16] BURDEN S, LIN Y, ZHANG R. Improving promoter prediction for the NNPP2.2 algorithm: a case study using escherichia coli DNA sequences [J]. Bioinformatics, 2005,21(5): 601-607. [17] MEI L. Human promoter recognition algorithm[D]. Dalian: Liaoning Normal University, 2010. (梅丽. 人类启动子识别算法研究[D].大连:辽宁师范大学, 2010.) [18] XU W, YE Z, YU X. The human promoter recognition based on SVMs[J]. Auhui Agricultural Science Bulletin, 2006, 12(13): 64-66. (徐文韬,叶子弘,俞晓平. 基于支持向量机(SVMs)的人类核心启动子的识别[J]. 安徽农学通报, 2006, 12(13): 64-66.) [19] ZHI H, LI T. Applying novel knowledge-based encoding methods and dual SVM to human Pol Ⅱ promoter recognition [J]. Journal of Harbin Medical University, 2012, 46(1): 23-26.(智慧. 李通化. 应用新的基于知识编码方法及双层SVM 识别人类PolⅡ启动子[J]. 哈尔滨医科大学学报,2012,46(1): 23-26.) [20] GODDARD N L, BONNET G, KRICHEVSKY O. Sequence dependent rigidity of single stranded DNA [J]. Physical Review Letters, 2000, 85(11): 2400-3. [21] ZENG J, ZHU S, YAN H. Towards accurate human promoter recognition: a review of currently used sequence features and classification methods [J]. Brief Bioinform, 2009, 10(5): 498-508. [22] BAJIC V B. Comparing the success of different prediction programs in sequence analysis:a review [J]. Brief Bioinform, 2000, 1(3): 214-228. [23] YAMASHITA R, SUZUKI Y, WAKAGURI H, et al. DBTSS: database of human transcription start sites, progress report 2006 [J]. Nucleic Acids Research, 2006, 34(Database issue): 86-89. [24] LI W, KOU Q, WEI L, et al. Plant promoter recognition based on analysis of base bias and SVM [J]. Journal of Liaoning Normal University: Natural Science, 2012, 35(2): 183-187.(李文举,寇秋波,韦丽华,等. 基于碱基偏好分析和SVM的植物启动子识别[J].辽宁师范大学学报:自然科学版,2012, 35(2): 183-187) [25] SAXONOV S, BERG P, BRUTLAG D L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters [J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(5): 1412-1417. [26] VAPNIK V, CORTES C. Support-vector networks [J]. Machine Learning, 1995, 20(3): 273-297. [27] GANGAL R, SHARMA P. Human pol II promoter prediction: time series descriptors and machine learning [J]. Nucleic Acids Research, 2005, 33(4): 1333-6. [28] BAJIC V B. Comparing the success of different prediction programs in sequence analysis:a review [J]. Brief Bioinform, 2000, 1(3): 214-228. |