Bioinformatics and Computation

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Presentation file introducer date paper video
H. Abdi, "A Neural Network Primer", Journal of Biological Systems, Vol. 2(3), pp. 247-283, (1994) 王仁暉 Jan. 04
Matthew E. P. Davies and Mark D. Plumbley, "Causal Tempo Tracking of Audio", 5th International Conference on Music Information Retrieval ISMIR 2004 高茂源 Jan. 04
Chris H.Q. Ding and Inna Dubchak, "Multi-Class Protein Fold Recognition Using Support Vector Machines and Neural Networks", Bioinformatics, Vol. 17, No. 4, 2001, Pages 349–358 林俊雄

Jan. 04 

Wenbin Liu, Fengyue Zhang, and Jin Xu, "A DNA Algorithm for the Graph Coloring Problem", J. Chem. Inf. Comput. Sci. 2002, 42, 1176-1178 邱喬偉 Jan. 11
Ilya N. Shindyalov and Philip E. Bourne, "A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm", Nucleic Acids Res. 2001 January 1; 29(1): 228–229 張嘉宏 Jan. 11
Danny Barash, "Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation", BIOINFORMATICS, Vol. 20, no. 12, 2004,pp. 1861–1869 張小燕 Jan. 18
Joseph C. Culberson and Piotr Rudnicki, "A fast algorithm for constructing trees from distance matrices", Information Processing Letters 30 (1989) p.215–p.220 蔣宗翰 Jan. 18
I. Porche, M. Sampath, R. Sengupta, Y.-L. Chen, and S. Lafortune, "A Decentralized Scheme for Real-Time Optimization of Traffic Signals", Proceedings of the 1996 IEEE International Conference on Control Applications Dearborn, pp. 582-589, 1996 陳宣文 Jan. 18
An Introduction to HMM and Its Applications 彭永興 Jan. 26  
Alexandre Lacoste and Douglas Eck, "Onset Detection with Artificial Neural Networks for MIREX 2005", EURASIP Journal on Advances in Signal Processing, Vol. 2007, Article ID 43745, 13 pages 高茂源 Jan. 26
Apostolico, Landau and Skiena, "Matching for Run-Length Encoded Strings", Journal of Complexity, Vol. 15, pp. 4–16, 1999 安興彥 Feb. 01
Pierre Tuffery, Frederic Guyon, Philippe Derreumaux, "Improved Greedy Algorithm for Protein Structure Reconstruction", J Comput Chem 26: 506–513, 2005 王仁暉 Feb. 08
Alexandre Bernardino & Jos�� Santos-Victor, "Fast IIR Isotropic 2-D Complex Gabor Filters with Boundary Initialization", IEEE Transactions on Image Processing, Vol. 15, No. 11, pp. 3338–3348, Nov 2006 何秋誼 Feb. 08
Andrew V. Goldberg, "A Simple Shortest Path Algorithm with Linear Average Time", ESA 2001, LNCS 2161, pp. 230–241, 2001 邱喬偉 Feb. 08
M. Beck, X. Wang, and T. Zaslavsky, "A Unifying Generalization of Sperner’s Theorem", 2001 曾球庭 Feb. 13
Hong-Bin Shen, Kuo-Chen Chou, "Ensemble Classifier for Protein Fold Pattern Recognition", Bioinformatics, Vol.22, no.14, 2006, pages 1717–1722 林俊雄 Mar. 07
Christopher Lee, Catherine Grasso and Mark F. Sharlow, "Multiple sequence alignment using partial order graphs", BIOINFORMATICS, Vol.18, no.3, 2002, pp.452–464 張小燕 Mar. 07
Valerio Freschi, Alessandro Bogliolo, "Longest common subsequence between run-length-encoded strings: a new algorithm with improved parallelism", Information Processing Letter 90 (2004) 167-173 張嘉宏 Mar. 07
Bart De Schutter, "Optimal Traffic Light Control for a Single Intersection", Proceedings of the 1999 American Control Conference, San Diego, California, pp. 2195-2199, June 1999. 陳宣文 Mar. 21
J. Maupetit, R. Gautier and P. Tuffery, "SABBAC: Online Structural Alphabet-Based Protein Backbone Reconstruction from Alpha-Carbon Trace", Nucleic Acids Research, 2006, Vol. 34, Web Server issue W147–W151 王仁暉 Mar. 21
Kuo-Si Huang, Chang-Biau Yang, Kuo-Tsung Tseng,Yung-Hsing Peng, Hsing-Yen Ann, "Dynamic programming algorithms for the mosaic longest common subsequence problem", Information Processing Letters, Vol. 102, pp. 99-103, 2007 蔣宗翰 Mar. 28
Esko Ukkonen, "On-line Construction of Suffix Trees", Algorithmica, Vol. 14, No. 3, pp. 249-260, 1995 彭永興 Mar. 28
Apostolico, Erdos and Lewenstein, "Parameterized Matching with Mismatches", Journal of Discrete Algorithms, Vol. 5, Issue 1, pp. 135-140, 2007 安興彥 Apr. 19
Benjamin Raphael, Degui Zhi, Haixu Tang, and Pavel Pevzner, "A novel method for multiple alignment of sequences with repeated and shuffled elements", Genome Research, 2004, Vol.14, pp.2336-2346 張小燕 Apr. 19
Joaqu�瀋 Bautista, Jordi Pereira, "A GRASP Algorithm to Solve the Unicost Set Covering Problem", Computers & Operations Research 34 (2007) 3162 – 3173 邱喬偉 Apr. 19
Y. K. Lin, "Reliability of a Flow Network Subject to Budget Constraints", IEEE TRANSACTIONS ON RELIABILITY, Vol. 56, No. 1, pp. 10-16, 2007 曾球庭 May 02
C�翼ine R�聱ia, Carl Fr�翼icotb, Pierre Courtellemontb, "Automatic analysis of the structure of children’s drawing and writing", Pattern recognition , Vol. 35, pp.1059–1069, 2002 何秋誼 May 02
X.-D. Sun and R.-B. Huang, "Prediction of protein structural classes using support vector machines", Amino Acids, Vol. 30, pp. 469–475, 2006 蔣宗翰 May 09
M. Jiang, Y.P. Luo, S.Y. Yang, "Stochastic convergence analysis and parameter selection of the standard particle swarm optimization algorithm", Information Processing Letters 102 (2007) 8-16 蔡宗容 May 09
Martin Farach-Colton, Paolo Ferragina and S. Muthukrishnan, "On the Sorting-Complexity of Suffix Tree Construction", Journal of the ACM, Vol. 47, No. 6, pp. 987-1011, 2000 彭永興 May 09
Jeongah Yoon, Anselm Blumer1 and Kyongbum Lee, "An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality", BIOINFORMATICS Vol. 22 no. 24 2006, pages 3106–3108 邱喬偉 May 16
Jessica Ebert and Douglas Brutlag, "Development and validation of a consistency based multiple structure alignment algorithm", Bioinformatics, Vol.22, no.9, 2006, pp.1080–1087 張小燕 May 16
Kimmo Fredriksson and Maxim Mozgovoy, "Efficient parameterized string matching", Information Processing Letters, Vol. 100, pp. 91-96, 2006 張嘉宏 May 16
A. V. Aho and M. J. Corasick, "Efficient String Matching: An Aid to Bibliographic Search", Communications of the ACM, Vol. 18, No. 6, 1975, pp. 333-340 安興彥 June 14
Karl Krissian, Carl-Fredrik Westin, Ron Kikinis, and Kirby G. Vosburgh, "Oriented Speckle Reducing Anisotropic Diffusion", IEEE TRANSACTIONS ON IMAGE PROCESSING, VOL. 16, NO. 5, MAY 2007 何秋誼 June 14
I.C. Trelea, "The particle swarm optimization algorithm: convergence analysis and parameter selection", Information Processing Letters 85 (2003) 317-325 蔡宗容 June 20
Zhong He Chen and R. C. T. Lee, "The Application of Convolution to Suffix to Prefix Rule for the Exact String Matching Problem", The 24th Workshop on Combinatorial Mathematics and Computation Theory, pp. 393- 399 蔣宗翰 June 20
Yann Hendel , Francis Sourd, "An Improved Earliness-tardiness Timing Algorithm", Computers & Operations Research 34 (2007) 2931 – 2938 邱喬偉 June 27
Peter Clifford and Rapha��l Clifford, "Simple Deterministic Wildcard Matching", Information Processing Letters, Vol. 101, pp. 53-54, 2007 彭永興 June 27
Amit P. Singh and Douglas L. Brutlag, "Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations", Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 284–293, 1997 張小燕 July 11
Wojciech Szpankowski, John Wiley & sons, INC., "Average Case Analysis of Algorithms on Sequences" ISBN: 0-471-24063-X, 2001 Section 2.1~2.3 曾球庭 July 11  
Areej Zuhily, Alan Burns, "Optimal (D-J)-monotonic priority assignment", Information Processing Letters 103 (2007) 247–250 張嘉宏 July 18
Thierry Lecroq, "Fast exact string matching algorithms", Information Processing Letters, Vol. 102, pp. 229–235, 2007 蔣宗翰 July 18
Jung-Hwan Chang, "Ring Embedding in Faulty (n, k)-star Graphs", ICPADS, Proceedings of the Eighth International Conference on Parallel and Distributed Systems, Page: 99, Year of Publication: 2001 邱喬偉 July 18
Xiaochun Cao and Hassan Foroosh, "Camera Calibration Using Symmetric Objects", IEEE TRANSACTIONS ON IMAGE PROCESSING, VOL. 15, NO. 11, MAY 2006 何秋誼 July 27
A. D. McLachlan, "Rapid Comparison of Protein Structures", Acta Crystallographica Section A , pp.871-873, 1982 張小燕 Aug. 01
Wojciech Szpankowski, John Wiley & sons, INC., "Average Case Analysis of Algorithms on Sequences", ISBN: 0-471-24063-X, 2001 Chapter 3, pp. 51-56 安興彥 Aug. 08  
Amihood Amir, Gad M. Landau and Uzi Vishkin, "Efficient Pattern Matching with Scaling", Journal of Algorithms, Vol. 13, pp. 2-32, 1992 彭永興 Aug. 15
Pufeng Du, Tao He, Yanda Li, "Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features", Biochemical and Biophysical Research Communications 358 (2007) 336–341 張嘉宏 Aug. 15
Wei-Kuo Chiang, Rong-Jaye Chen, "The (n, k)-star graph: A generalized star graph", Information Processing Letters 56 ( 1995) 259-264 邱喬偉 Aug. 22
Wojciech Szpankowski, John Wiley & sons, "Average Case Analysis of Algorithms on Sequences Section 2.4", INC., ISBN: 0-471-24063-X, 2001 曾球庭 Aug. 31  
Shinichiro Omachi and Masako Omachi, "Fast Template Matching With Polynomials", IEEE TRANSACTIONS ON IMAGE PROCESSING, VOL. 16, NO. 08, MAY 2007 何秋誼 Sept. 05
Michael Feig, Piotr Rotkiewicz, Andrzej Kolinski, Jeffrey Skolnick, and Charles L. Brooks III, "Accurate Reconstruction of All-Atom Protein Representations From Side-Chain-Based Low-Resolution Models", PROTEINS: Structure, Function, and Genetics 41:86–97 (2000) 張小燕 Sept. 05
Kimmo Fredriksson and Maxim Mozgovoy, "Efficient parameterized string matching", Information Processing Letters, Vol. 100, pp. 91-96, 2006 陳俊仁 Sept. 19
Tzung-Shi Chen, Nen-Chung Wang, "Optimal broadcasting on incomplete star graph interconnection networks", Journal of Systems Architecture 51 (2005) 143–150 邱喬偉 Sept. 19
Elena Rivas and Sean R. Eddy, "A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots", J. Mol. Biol. (1999) 285, 2053-2068 張嘉宏 Sept. 19
Ivan Y. Torshin, Irene T. Weber and Robert W. Harrison, "Geometric criteria of hydrogen bonds in proteins and identification of `bifurcated' hydrogen bonds", Protein Engineering, Vol. 15, No. 5, 359-363, May 2002 蔡宗容 Sept. 26
Jean-Christophe Novelli, Igor Pak and Alexander V. Stoyanovskii, "A direct bijective proof of the hook-length formula", Discrete Mathematics and Theoretical Computer Science, Vol. 1, pp.53-67, 1997 蔣宗翰 Sept. 26
A. Amir, Y. Aumann, R. Cole, M. Lewenstein and E. Porat, "Function Matching: Algorithms, Applications and a Lower Bound", In Proceedings of the 30th International Colloquium on Automata, Languages and Programming (ICALP), pp. 929-942, 2003 安興彥 Sept. 26
Philip W. Payne, "Reconstruction of protein conformations from estimated positions of the Cα coordinates", Protein Science, pp.315-324, 1993 張小燕 Oct. 03
Michael A. Bender, Mart�滱 Farach-Colton and Miguel A. Mosteiro, "Insertion Sort is O(nlogn)", Theory of Computing Systems, Vol. 39, pp. 391-397, 2006 彭永興 Oct. 03
Jonathan Richard Shewchuk, "An Introduction to the Conjugate Gradient Method without the Agonizing Pain", 1994 曾球庭 Oct. 17
Tseng-Kuei Li, "Cycle embedding in star graphs with edge faults", Applied Mathematics and Computation 167 (2005) 891–900 邱喬偉 Oct. 17
Rune B. Lyngso, Michael Zuker and Christian N. S. Pedersen, "Fast evaluation of internal loops in RNA secondary structure prediction", BIOINFORMATICS Vol. 15 no. 6 1999 Pages 440-445 張嘉宏 Oct. 17
"Moving averages", Source: >> Chart School >> Technical Indicators and Overlays >> Moving average 蔡宗容 Oct. 24
Wun-Tat Chan · Yong Zhang · Stanley P. Y. Fung · Deshi Ye · Hong Zhu "Efficient algorithms for finding a longest common increasing subsequence", Journal of Combinatorial Optimization, Vol. 13, pp. 277–288, 2007 蔣宗翰 Oct. 24
Kuo-Tsung Tseng,"Near-optimal Block Alignments" 曾國尊 Oct. 24
Ken A. Dill, Andrew T. Phillips, J. Ben Rosen, "Protein Structure and Energy Landscape Dependence on Sequence using a Continuous Energy Function", Journal of Computational Biology, 1997, pp.227-239 張小燕 Oct. 31
Costas S. Iliopoulos and M. Sohel Rahman, "New Efficient Algorithms for the LCS and Constrained LCS Problems", Information Processing Letters (2007), doi: 10.1016/j.ipl.2007.09.008 陳俊仁 Oct. 31
A heuristic approach for detecting RNA H-type pseudoknots 張嘉宏 Nov. 07
Min Xu, Xiao-Dong Hu, Qiang Zhu, "Edge-bipancyclicity of star graphs under edge-fault tolerant", Applied Mathematics and Computation 183 (2006) 972–979 邱喬偉 Nov. 14
Yuhui Shi and Russell C. Eberhart, "Parameter Selection in Particle Swarm Optimization" 蔡宗容 Nov. 14
Sarmad Abbasi , Anirvan Sengupta, "An O( n log n) algorithm for finding dissimilar strings", Information Processing Letters 62 (1997) 135-139 翁祥益 Nov. 14
Irit Katriel and Martin Kutz "A Faster Algorithm for Computing a Longest Common Increasing Subsequence", Research Report MPI-I-I2005-1-007 蔣宗翰 Nov. 21
A. Amir, Y. Aumann, R. Cole, M. Lewenstein and E. Porat "Function Matching: Algorithms, Applications and a Lower Bound", In Proceedings of the 30th International Colloquium on Automata, Languages and Programming (ICALP), pp. 929-942, 2003 安興彥 Nov. 21
Benoit Roux, "The Calculation of the Potential of Mean Force Using Computer Simulations", Computer Physics Communications, vol. 91, pp. 275-282, 1995 張小燕 Nov. 30
Wei Shi, Pradip K. Srimani, "Hierarchical star: a new two level interconnection network", Journal of Systems Architecture 51 (2005) 1–14 邱喬偉 Dec. 05
Christian Brauer-Burchardt and Klaus Voss, "A NEW ALGORITHM TO CORRECT FISH-EYE- AND STRONG WIDE-ANGLELENS-DISTORTION FROM SINGLE IMAGES", Proceedings of International Conference on Image Processing, 2001. pp. 225-228, vol.1 蔣宗翰 Dec. 05
Ajmal S. Mian, Mohammed Bennamoun, and Robyn Owens, "An Efficient Multi-modal 2D-3D Hybrid Approach to Automatic Face Recognition", IEEE TRANSACTIONS ON IMAGE PROCESSING, Vol. 29, No. 11, Nov. 2007 何秋誼 Dec. 12
Automatic RNA secondary structure prediction 張嘉宏 Dec. 12
Edit DistanceRLE 曾球庭 Dec. 19
Jian Pei, Jiawei Han, Jianyong Wang, Helen, Qiming Chen, Umeshwar Dayal and MeiChun Hsu , "Mining Sequenctial Patterns by Pattern-Growth", IEEE Transactions on knowledge and data engineering, Vol. 16, No. 11, November 2004 蔡宗容 Dec. 26
J. Arunachalam, V. Kanagasabai and N. Gautham, "Protein Structure Prediction Using Mutually Orthogonal Latin Squares and a Genetic Algorithm", Biochemical and Biophysical Research Communications, Vol. 342, pp. 424~433, 2006 張小燕 Dec. 26


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