Bioinformatics and Computation

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Presentation file introducer date paper video
DAVID MAIER. "The Complexity of Some Problems on Subsequences". Journal of the ACM (JACM) Volume 25 Issue 2, April 1978 Pages 322-336  方鈞毅 Jan. 07
Chang-Biau Yang(楊昌彪), R.C.T. Lee(李家同). "Systolic Algorithms for the Longest Common Subsequence Problem". Journal of the Chinese Institute of Engineers Vol. 10, NO 6, pp.691-699(1987) 許竣傑 Jan. 14
PETER H. SELLERS. "An Algorithm for the Distance between Two Finite Sequences". JOURNAL OF COMBINATORIAL THEORY (A) 16, 253-258 (1974) 許哲睿 Jan. 14
Alfred V. Aho, Margaret J. Corasick. "Efficient String Matching: An Aid to Bibliographic Search". Communications of the Association for Computing Machinery, vol. 18, issue 6, p.p. 333-340, June 1975 戴君潔 Jan. 14
Michael L. Fredman. "On computing the length of longest increasing subsequences". Discrete Mathematics vol. 11 pp. 29–35 (1975) 袁信全 Jan. 27
C. Schensted. "Longest Increasing and Decreasing Subsequences". Canadian Journal of Mathematics 13(1961), 179-191 許竣傑 Jan. 27
Maxime Crochemore, Costas S. Iliopoulos, Yoan J. Pinzon3, and James F. Reid. "A Fast and Practical Bit-Vector Algorithm for the Longest Common Subsequence Problem". Information Processing Letters, Volume 80, Issue 6, 31 December 2001, Pages 279–285 陳慶耀 Jan. 27
SAUL B. NEEDLEMAN AND CHRISTIAN D. WUNSCH. "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins". J. Mol. Biol. (1970) 48, 443-453 黃鼎耀 Feb.10
J.F.Collins, A.F.W.Coulson and A.Lyall. "The significance of protein sequence similarities". Computer applications in the biosciences : CABIOS Vol.4, no.1. 1988 PP. 67-71 郭冠呈 Feb.10
Robert A. Wagner. "On the Complexity of the Extended String-to-String Correction Problem". Proceedings of seventh annual ACM symposium on Theory of computing, Pages 218-223, 1975 許哲睿 Feb.10
J. W. Hunt, M. D. McIlroy. "An Algorithm for Differential File Comparison". Bell Laboratories Computing Science Technical Report #41(July 1976) 周展億 Feb.18
D.S. Hirschberg. "A Linear Space Algorithm for Computing Maximal Common Subsequences". Communications of the ACM June 1975 Volume 18 Number 6 詹德勝 Feb.18
Roy Lowrance and Robert A. Wagner. "An Extension of the String-to-String Correction Problem". Journal of the Association for Computing Machinery, vol.22, No.2, pp. 177-183, April 1975 戴君潔 Feb.18
WALTER M. FITCH TEMPLE F. SMITH. "Optimal sequence alignments". Proc. Nati Acad. Sci. USA Vol. 80, pp. 1382-1386, March 1983 方鈞毅 Feb.25
Daniel S. Hirschberg. "An information theoretic lower bound for the longest common subsequence problem". Information Processing Letters; vol. 7 pp. 40–41 (1978) 袁信全 Feb.25
TEMPLE F. SMITH , MICHAEL S. WATERMAN. "Comparison of Biosequences". Advances in Applied Mathematics, December 1981, p482-489 許竣傑 Feb.25
Narao Nakatsu, Yahiko Kambayashi and Shuzo Yajima "A Longest Common Subsequence Algorithm Suitable for Similar Text Strings". Acta Informatica 18, 1982 PP.171 - 179 郭冠呈 Mar.04
Jesse Eickholt and Jianlin Cheng. "Predicting protein residue–residue contacts using deep networks and boosting". Bioinformatics, Vol. 28, No. 23, 2012, pp. 3066–3072 何秋誼 Mar.04
Alberto Apostolico. "IMPROVING THE WORST-CASE PERFORMANCE OF THE HUNT-SZYMANSKI STRATEGY FOR THE LOGEST COMMON SUBSEQUENCE OF TWO STRINGS". Information Processing Letters 23 (1986) 63-69 陳慶耀 Mar.04
Alberto Apostolico. "IMPROVING THE WORST-CASE PERFORMANCE OF THE HUNT-SZYMANSKI STRATEGY FOR THE LOGEST COMMON SUBSEQUENCE OF TWO STRINGS". Information Processing Letters 23 (1986) 63-69 陳慶耀 Mar.10
P. Hogeweg, B. Hesper. "The alignment of sets of sequences and the construction of phylogenetic trees: An integrated method". Journal of Molecular Evolution 1984; Volume 20,Issue 2;pp. 175-186 黃鼎耀 Mar.10
Che-Jui Hsu. "Flexible Dynamic Time Warping for Time Series". 許哲睿 Mar.10
MICHAEL S. WATERMAN "Sequence Alignments in the Neighborhood of the Optimum with General Application to Dynamic Programming". Proc. NatL. Acad. Sci. USA Vol. 80, May 1983, pp. 3123-3124 羅崇軒 Mar.17
Jyun-Jie Shiu. "The Department Score Forecast and Analysis of the College Entrance Examination". 許竣傑 Mar.17
Jun-Yi Fang. "The Disulfide Connectivity Prediction". 方鈞毅 Mar.17
W. J. Hsu and M. W. Du. "New Algorithms for the LCS Problem". JOURNAL OF COMPUTER AND SYSTEM SCIENCES 29, 1984, pp. 133-152 詹德勝 Mar.24
Hsin-Chuan Yuan. "Protein Backbone Reconstruction with Tool Preference Classification and Feature Selection". 袁信全 Mar.24
Cing-Yao Chen. "Imprving Common Interval Problem". 陳慶耀 Mar.24
Chin Francis Y. L. and Poon C. K. "A Fast Algorithm for Computing Longest Common Subsequences of Small Alphabet Size". Journal of information processing 13(4), 463-469 (Feb, 1991) 周展億 Apr.08
M. S. WATERMAN, T. F. SMITH, W. A. BEYER. "Some Biological Sequence Metrics". Advances in Mathematics Volume 20, Issue 3, June 1976, Pages 367–387
OSAMU GOTOH "An Improved Algorithm for Matching Biological Sequences".Journal of molecular biology, Vol. 162, No. 3. (15 December 1982), Pages 705-708
STEPHAN F. Altschul, Bruce W. Erickson "OPTIMAL SEQUENCE ALIGNMENT USING AFFINE GAP COSTS". Bulletin of Mathematical Biology 1986, Volume 48,Issue 5-6, page 603-616
詹皇廷 Apr.08
Arthur M. Lesk, Michael Levitt and Cyrus Chothia. "Alignment of the Amino Acid Sequences of Distantly Related Proteins Using Variable Gap Penalties". Protein Engineering, Vol. 1 No.1 pp.77-78, 1986 羅崇軒 Apr.22
D.F. Feng, M.S. Johnson, and R.F. Doolittle. "Aligning Amino Acid Sequences: Comparison of Commonly Used Methods". Journal of Molecular Evolution(1985) 21:112-125 黃鼎耀 Apr.22
Michael J. Wise. "YAP3: Improve Detection of Similarities in Computer Program and Other Texts". SIGCSE Proceedings of the twenty-seventh SIGCSE technical symposium on Computer science education 1996 pp. 130-134 郭冠呈 Apr.22
Hung-Hsin Chen, and Chang-Biau Yang. "Stock Investment with Stochastic Programming". Department of Computer Science and Engineering 陳紘昕 Apr.29
F. K. HWANG, S. LIN. "A Simple Algorithm for Merging Two Disjoint Linearly Ordered Sets". JOURNAL OF COMPUTER AND SYSTEM SCIENCES 29, pp. 133-152 (1984) 詹德勝 Apr.29
T.F. Smith, M.S. Waterman, and W.M. Fitch. "Comparative Biosequence Metrics". Journal of Molecular Evolution 1981, pp.38-46 郭冠呈 May.06
J.Y. Guo and F.K. Hwang. "An almost-linear time and linear space algorithm for the longest common subsequence problem". Information Processing Letters 94(2005), pp. 131-135 周展億 May.06
Temple F.Smith, Michael S.Waterman and Christian Burks. "The statistical distribution of nucleic acid similarities". Nucleic Acids Research Volume 13 Number 2 1985, pp. 645–656 方鈞毅 May.06
SAUL B. NEEDLEMAN AND CHRISTIAN D. WUNSCH. "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins". Journal of Molecular Biology(1970) 48, pp. 443-453
Peter H. Sellers "ON THE THEORY AND COMPUTATION OF EVOLUTIONARY DISTANCES".SIAM J. APPL. MATH. Vol. 26, No. 4, June 1974, pp. 787-793
T.F. Smith, M.S. Waterman, and W.M. Fitch. "Comparative Biosequence Metrics". Journal of Molecular Evolution 1981, pp.38-46
郭冠呈 May.14
Nan Xiao [蕭南], Qingsong Xu [徐青松], Dongsheng Cao [曹東升], Yizeng Liang [梁逸曾]. "protr: Protein Sequence Descriptor Calculation and Similarity Computation with R". Central South University 何秋誼 May.19
D.F. Feng, M.S. Johnson, and R.F. DoolittleGeoffrey J. Barton and Michael J. E. Sternberg "A Strategy for the Rapid Multiple Alignment of Protein Sequences Confidence Levels from Tertiary Structure Comparisons". J. Mol. Biol. (1987)198,327-337 黃鼎耀 May.19
Jyun-Jie Shiu. "The Department Score Forecast and Analysis of the College Entrance Examination". 許竣傑 May.26
A. Apostolico. "Remark on Hsu-Du New Algorithm for the LCS Problem". Information Processing Letters, Volume 25, Issue 4, 17 June 1987, pp. 235–236 周展億 May.26
Che-Jui Hsu. "Flexible Dynamic Time Warping for Time Series Classification". 許哲睿 June 10
吳哲賢、王志倫. "生物序列比對問題上考慮凸形間隔處罰函數的一些O(nm)演算法". Proc.of the 19th Workshop on Combinatorial Mathematics and Computation Theory 黃鼎耀 June 10
Chun-Yi Fang (方鈞毅). "The Disulfide Connectivity Prediction". 方鈞毅 June 16
S. Kiran Kumar and C. Pandu Rangan. "A Linear Space Algorithm for the LCS Problem". Acta Informatica 24, pp. 353-362 (1987) 詹德勝 June 16
Reed A. Cartwright. "Ngila: global pairwise alignments with logarithmic and affine gap costs". Bioinformatics Applications Note Vol. 23 no. 11 2007, pp. 1427–1428 郭冠呈 June 16
Hsin-Chuan Yuan(袁信全). "Protein Backbone Reconstruction with Tool Preference Classification and Feature Selection". 袁信全 July 01
C. K. Wong AND Ashok K. Chandra. "Bounds for the String Editing Problem". Journal of the ACM (JACM) Volume 23 Issue 1, Jan. 1976 pp. 13-16  詹皇廷 July 01
Maxime Crochemore, Costas S. Iliopoulos, and Yoan J. Pinzon. "Speeding-up Hirschberg and Hunt-Szymanski LCS Algorithms". Fundamental Informaticae, Vol. 56, No. 1-2, pp. 89-103, 2003 周展億 July 08
Jiaoyun Yang, Yun Xu, Yi Shang. "An Efficient Parallel Algorithm for Longest Common Subsequence Problem on GPUs". Proceedings of the World Congress on Engineering 2010 Vol I WCE 2010, June 30 - July 2, 2010, London, U.K. pp. 499-504 詹德勝 July 08
Xiaoqiu Huang, Ross C.Hardison and Webb Miller. "A space-efficient algorithm for local similarities". CABIOS Vol 6. no.4. 1990 Pages 373 – 381 黃鼎耀 July 15
Wen-Jing Hsu. "New Algorithms for Comparing Symbol Sequences". Proceeding ACM '87 Proceedings of the 1987 Fall Joint Computer Conference on Exploring technology: today and tomorrow pp. 381-389 郭冠呈 July 15
Jyun-Jie Shiu. "The Department Score Forecast and Analysis of the College Entrance Examination". 許竣傑 July 22
Francis Y.L. Chin, Alfredo De Santis, Anna Lisa Ferrara, N.L. Hoa, S.K. Kim. "A Simple Algorithm for the Constrained Sequence Problems". Information Processing Letters 90 pp.175-179(2004) 周展億 July 22
Sebastian Deorowicz, Szymon Grabowski. "Efficient algorithms for the longest common subsequence in k-length substrings". Information Processing Letters, Volume 114, Issue 11, November 2013, Pages 634–638 詹皇廷 July 22
Che-Jui Hsu. "Flexible Dynamic Time Warping for Time Series Classification". 許哲睿 July 29
Göbel U, Sander C, Schneider R, Valencia A.. "Correlated Mutations and Residue Contacts in Proteins". Proteins. 1994 Apr;18(4): pp.309-17 黃鼎耀 July 29
Heikki Hyyro. "Bit-Parallel LCS-length Computation Revisited". PR In Proc. 15th Australasian Workshop on Combinatorial Algorithms (AWOCA) 2004 詹德勝 July 29
Wen-Chen Hu, Gerhard X. Ritter, Mark S. Schmalz. "Approximating the Longest Approximate Common Subsequence Problem". Proceeding ACM-SE 36 Proceedings of the 36th annual Southeast regional conference pp. 166-172 (1998) 郭冠呈 Aug. 05
Chun-Yi Fang (方鈞毅). "The Disulfide Connectivity Prediction". 方鈞毅 Aug. 19
Mauro Castelli, Stefano Beretta, Leonardo Vanneschi. "A hybrid genetic algorithm for the repetition free longest common subsequence problem". Operations Research Letters Volume 41, Issue 6, November 2013, Pages 644–649 詹皇廷 Aug. 19
Lasse Bergroth, Harri Hakonen, and Timo Raita. "New Approximation Algorithms for Longest Common Subsequences". String Processing and Information Retrieval: A South American Symposium, 1998. Proceedings pp. 32-40 周展億 Aug. 19
Arindam Banerjee and Joydeep Ghosh. "Clickstream Clustering using Weighted Longest Common Subsequences". In Proceedings of the Web Mining Workshop at the 1st SIAM Conference on Data Mining 黃鼎耀 Aug. 26
Sebastian deorowicz and Agnieszka Danek. "Bit-Parallel Algorithms for the Merged Longest Common Subsequence Problem". International Journal of Foundations of Computer Science Vol. 24, No. 8 (2013) pp. 1281-1298 詹德勝 Aug. 26
Cing-Yao Chen. "Imprving Common Interval Problem". 陳慶耀 Aug.26
Maurice Maes. "On a Cyclic String-to-String Correction Problem". Information Processing Letters Volume 35, Issue 2, 29 June 1990, pp. 73-78 郭冠呈 Sept. 24
Hsin-Chuan Yuan(袁信全). "Protein Backbone Reconstruction with Tool Preference Classification and Feature Selection". 袁信全 Sept. 24
Costas S. Iliopoulos and M. Sohel Rahman. "A New Efficient Algorithm for Computing the Longest Common Subsequence". Theory of Computing Systems, Volume 45, Issue 2, pp 355-371(2009) 周展億 Sept. 24
A. Apostolico and C. Guerra. "The Longest Common Subsequence Problem Revisited". Algorithmica,Volume 2,Issue 1-4,pp. 315-336 (1987) 徐子強 Oct. 01
C. E. R. Alves, E. N. C'aceres, S. W. Song. "A BSP/CGM Algorithm for the All-Substrings Longest Common Subsequence Problem". Proceedings of the International Parallel and Distributed Processing Symposium(2003) 黃鼎耀 Oct. 01
Sebastian Deorowicz. "Bit-Parallel Algorithm for the Constrained Longest Common Subsequence Problem". Fundamenta Informaticae 99 (2010) pp. 409-433 409 DOI 10.3233/FI-2010-256 詹德勝 Oct. 07
Ronald I. Greenberg. "Fast and Simple Computation of All Longest Common Subsequences". Loyola University March 2011 詹皇廷 Oct. 07
Zvi Gotthilf, Danny Hermelin and Moshe Lewenstein. "Constrained LCS: Hardness and Approximation". Combinatorial Pattern Matching Lecture Notes in Computer Science Volume 5029, 2008, pp. 255-262 郭冠呈 Oct. 14
C.E.R. Alves, E.N. Caceres, S.W. Song. "An all-substrings common subsequence algorithm". Discrete Applied Mathematics 156 (2008) 1025-1035 黃鼎耀 Oct. 14
Chun-Yi Fang (方鈞毅). "The Disulfide Connectivity Prediction". 方鈞毅 Oct. 14
M. Sanjeev Arulampalam, Simon Maskell, Neil Gordon, and Tim Clapp. "A Tutorial on Particle Filters for Online Nonlinear/Non-Gaussian Bayesian Tracking". IEEE Transactions on Signal Processing, Vol. 50, No. 2, pp.174-188, 2002 陳紘昕 Oct. 21
Cing-Yao Chen. "Efficient Algorithm for Common Combination Interval Problem". 陳慶耀 Oct. 21
Eric A. Breimer, Mark K. Goldberg and Darren T. Lim. "A Learning Algorithm for the Longest Common Subsequence Problem". Journal of Experimental Algorithmics, Volume 8, 2003 Article No. 2.1 周展億 Oct. 28
Ora Arbell , Gad M. Landau , Joseph S.B. Mitchell. "Edit distance of run-length encoded strings". Information Processing Letters 83 (2002) pp.307-314 何文娟 Oct. 28
Eamonn J. Keogh , Michael J. Pazzani. "Derivative Dynamic Time Warping". First SIAM International Conference on Data Mining (2001) 郭冠呈 Nov. 04
Carlos E. Ferreira and Christian Tjandraatmadja. "A branch-and-cut approach to the repetition-free longest common subsequence problem". International Symposium on Combinatorial Optimization Volume 36, 1 August 2010, pp. 527-534 蔡曜州 Nov. 04
Goeman.Heiko,Clausen.Michael. "A New Practical Linear Space Algorithm for the Longest Common Subsequence Problem". Kybernetika,vol.38 (2002), issue 1,pp.45-66 林憲良 Nov. 04
Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson. "Sparse LCS Common Substring Alignment". Combinatorial Pattern Matching, Lecture Notes in Computer Science Volume 2676, 2003, pp. 225-236 (2003) 徐子強 Nov. 11
Agnieszka Danek and Sebastian Deorowicz . "Bit-Parallel Algorithm for the Block Variant of the Merged Longest Common Subsequence Problem". Man-Machine Interactions 3 Advances in Intelligent Systems and Computing Volume 242, 2014, pp. 173-181 詹德勝 Nov. 11
Shuangyin Liu, Haijiang Tai , Qisheng Ding ,Daoliang Li, Longqin Xu, Yaoguang Wei. "A hybrid approach of support vector regression with genetic algorithm optimization for aquaculture water quality prediction". Mathematical and Computer Modelling 58 (2013) pp. 458 - 465 黃鼎耀 Nov. 18
Sushila Aghav, Ankit Kumar, Ganesh Gadakar, Aditya Mehta, and Amey Mhaisane. "Mitigation of Rotational Constraints in Image Based Plagiarism Detection Using Perceptual Hash". International Journal of Computer Science Trends and Technology (IJCST), Volume 2 Issue 1, pp. 28-32, Mar-Apr 2014. 孫才洺 Nov. 18
Apostolico, A., Landau, G.M. and Skiena, S. "Matching for Run-Length Encoded Strings". Compression and Complexity of Sequences 1997. Proceedings pp. 348 - 356 周展億 Nov. 18
Apostolico, A., Landau, G.M. and Skiena, S. "Matching for Run-Length Encoded Strings". Compression and Complexity of Sequences 1997. Proceedings pp. 348 - 356 周展億 Nov. 25
Xiaopeng Xi, Eamonn Keogh, Christian Shelton, Li Wei and Chotirat Ann Ratanamahatana. "Fast Time Series Classification Using Numerosity Reduction". Proceeding ICML '06 Proceedings of the 23rd international conference on Machine learning Pages 1033-1040 (2006). 郭冠呈 Nov. 25
L. Bergroth, H. Hakonen, T. Raita. "A Survey of Longest Common Subsequence Algorithms". String Processing and Information Retrieval, 2000. SPIRE 2000. Proceedings. Seventh International Symposium on Pages 39-48 詹皇廷 Nov. 25
J.J. Liu, G.S. Huang, Y.L. Wang and R.C.T. Lee . "Edit distance for a run-length-encoded string and an uncompressed string". Information Processing Letters 105 (2007) pp. 12-16 何文娟 Dec.02
Sebastian Deorowicz. "Fast algorithm for constrained longest common subsequence problem". Theoretical and Applied Informatics Vol. 19 (2007), no. 2 pp. 91–102 詹德勝 Dec.02
Dana Shapira and James A. Storer. "Edit Distance with Move Operations". Brandeis University, Waltham, MA Journal of Discrete Algorithms Volume 5 Issue 2, June, 2007 Pages 380-392 蔡曜州 Dec.15
Marios A. Gavrielides, Elena ˇSikudová, and Ioannis Pitas. "Color-Based Descriptors for Image Fingerprinting". IEEE TRANSACTIONS ON MULTIMEDIA, VOL. 8, NO. 4, pp. 740-748, AUGUST, 2006 孫才洺 Dec.15
Yuya Suzukia, Hirofumi Ibayashia, Yukimasa Kanedab, Hiroshi Minenoa. "Proposal to sliding window-based support vector regression". Procedia Computer Science 35 (2014) pp. 1615-1624 黃鼎耀 Dec.15
I-Hsuan Yang , Chien-Pin Huang Kun-Mao Chao. "A fast algorithm for computing a longest common increasing subsequence". Information Processing Letters 93 (2005) pp. 249-253 林憲良 Dec.22
Wang, Y.P. and Pavlidis, T. "Optimal Correspondence of String Subsequences". Pattern Analysis and Machine Intelligence, IEEE Transactions on Volume:12, Issue:11 pp. 1080-1087 (1990) 詹皇廷 Dec.22
Krisztian Buza, Alexandros Nanopoulos, Lars Schmidt-Thieme. "Time-Series Classification Based on Individualised Error Prediction". Computational Science and Engineering (CSE), 2010 IEEE 13th International Conference on pp.48-54 郭冠呈 Dec.30
Gad M. Landau, Eugene Myers, Michal Ziv-Ukelson. "Two algorithms for LCS Consecutive Suffix Alignment". Journal of Computer and System Sciences Volume 73, Issue 7, pp. 1095–1117 (2007) 徐子強 Dec.30
Hsing-Yen Ann, Chang-Biau Yang, Chiou-Ting Tseng, Chiou-Yi Hor. "A Fast and Simple Algorithm for Computing the Longest Common Subsequence of Run-length Encoded Strings". Information Processing Letters 108 (2008) pp. 360-364 周展億 Dec.30
         

 

1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018