Bioinformatics and Computation

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

2006年

Presentation file introducer date paper video
Ayelet Butman, Revital Eres, Gad M.Landau, "Scaled and Permuted String Matching",Information Processing Letters 92 (2004) 293-297 王仁暉 Jan. 05
Pavel A. Pevzner, Haixu Tang, "Fragment assembly with double-barreled data",BIOINFORMATICS, Vol. 17, Suppl.1, Pages S225–S233, 2001 高茂源 Jan. 13
Emidio Capriotti, Piero Fariselli, Remo Calabrese and Rita Casadio,"Predicting protein stability changes from sequences using support vector machines", BIOINFORMATICS, Vol. 21, Suppl.2 2005 ,Pages 54–58, 2001 林俊雄 Jan. 13 
J.Y. Guo and F.K. Wang,"An almost linear time and linear space algorithm for the longest common subsequence problem",Information Processing Letters 94 (2005) 131–135 彭永興 Jan. 19
Chang-Biau Yang, Yun-Jaw Yeh,"On the Traffic Light Timing Setting Problem" 董建甫 Feb. 10
Markus Bläser,"An 8/13-approximation algorithm for the asymmetric
maximum TSP",Journal of Algorithms 50 (2004) 23–48
安興彥 Feb. 17
Jeff Abrahamson, Ali Shokoufandeh, Pawel Winter,"Euclidean TSP Between Two Nested Convex Obstacles",Information Processing Letters, (95) 370–375, 2005. 陳宣文 Feb. 17
I-Hsuan Yang a, Chien-Pin Huang a, Kun-Mao Chao a,b,"A fast algorithm for computing a longest common increasing subsequence",Information Processing Letters 93 (2005) 249–253 王仁暉 Feb. 17
Haim Kaplan, Nira Shafrir,"The greedy algorithm for edit distance with moves",Information Processing Letters 97 (2006) 23–27 高茂源 Feb. 24
Walter A. Burkhard,"Double hashing with passbits",Information Processing Letters 96 (2005) 162–166 林俊雄 Feb. 24
Tolga Can, Yuan-Fang Wang,"CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features",Proceedings of the Computational Systems Bioinformatics (CSB’03) 0-7695-2000-6/03 2003 IEEE 羅裕傑 Mar. 03
(Ben) P.C. Li, M. Toulouse, "Variations of the maximum leaf spanning tree problem for bipartite graphs", Information Processing Letters 97 (2006) 129–132 陳宣文 Mar. 10
Kuan-Yu Chen a, Kun-Mao Chao, "Optimal algorithms for locating the longest and shortest segments satisfying a sum or an average constraint", Information Processing Letters 96 (2005) 197–201 王仁暉 Mar. 17
F. Carrabs, R. Cerulli M. Gentili , G. Parlato, "A linear time algorithm for the minimum Weighted Feedback Vertex Set on diamonds", Information Processing Letters 94 (2005) 29–35 林俊雄 Mar. 24
JamesW. Anderson · Keith R. Fox · Graham A. Niblo, "A fast algorithm for the construction of universal footprinting templates in DNA", Journal of Mathematical Biology Volume 52, Number 3, Pages 307-342, 2006 林旭紳 Mar. 24
Mark Weston, "A fixed-parameter tractable algorithm for matrix domination", Information Processing Letters 90 (2004) 267–272 高茂源 Mar. 31
Sung Kwon Kim, "Finding a longest nonnegative path in a constant degree tree", Information Processing Letters 93 (2005) 275–279 陳宣文 Mar. 31
Amir, Apostolico and Lewenstein,"Inverse Pattern Matching", Journal of Algorithms, Vol. 24, pp. 325-339, 1997 安興彥 Apr. 22
Protein Tertiary Structure Prediction(聯合meeting) 邢金良 Apr. 26  
An Efficient Algorithm for Determining Protein Structure Similarity(聯合meeting) 羅裕傑 Apr. 26  
Justin Colannino, Godfried Toussaint,"An algorithm for computing the restriction scaffold assignment problem in computational biology", Information Processing Letters 95 (2005) 466–471 王仁暉 May 04
Udi Manber and Gene Myers,"Suffix arrays: A new method for on-line string searches", SIAM Journal on Computing, vol. 22(5), pp. 935–948, 1993 彭永興 May 04
Pradipta Prometheus Mitra, Muhammad Arshad Ul Abedin,
Md. Abul Kashem,"Algorithms for solving the symmetry number on trees", Information Processing Letters 91 (2004) 163–169
高茂源 May 04
Abraham P. Punnen, Olena Chapovska,"The Bottleneck k-MST", Information Processing Letters 95(2005) 512-517 林俊雄 May 11
Yangjun Chen, Yibin Chen,"A new tree inclusion algorithm", Information Processing Letters 98 (2006) 253–262 陳宣文 May 11
F. Ergun, S. Muthukrishnan and S. C. Sahinalp,"Comparing Sequences with Segment Rearrangements", FST TCS 2003: Foundations of software technology and theoretical computer science, Vol. 2914 of Lecture Notes in Computer Science, pp. 183-194, 2003 安興彥 May 18
Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir,"The Restriction Scaffold Problem", J. Comput. Biol. 10(2) (2003) 385-398 王仁暉 May 18
Owen Kaser,"Compressing Arrays by Ordering Attribute Values", Information Processing Letters 92 (2004) 253–256 高茂源 May 18
Hélène Touzet,"Tree Edit Distance with Gaps", Information Processing Letters 85 (2003) 123–129 陳宣文 May 25
Daniel Berend, Amir Sapir,"The Diameter of Hanoi Graphs", Information Processing Letters 98(2006) 79-85 林俊雄 May 25
Mohamed Ibrahim Abouelhoda, Enno Ohlebusch, and Stefan Kurtz,"Optimal exact string matching based on suffix arrays", International Symposium on String Processing and Information Retrieval, pp. 31-43, 2002 彭永興 May 25
Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou,"Prediction of protein structural classes by support vector machines", Computers and Chemistry 26 (2002) 293–296 王仁暉 Jun. 15
Kazuhisa Makino, Takashi Takabatake, Satoru Fujishige,"A Simple Matching Algorithm for Regular Bipartite Graphs", Information Processing Letters 84 (2002) 189–193 高茂源 Jun. 15
Haim Kaplan, Nira Shafrir,"The Greedy Algorithm for Edit Distance with Moves", Information Processing Letters, Vol. 97, pp. 23–27, 2006 安興彥 Jun. 22
Mohammad Hosseini Dolama, Éric Sopena,"On the Oriented Chromatic Number of Halin Graphs", Information Processing Letters 98(2006) 247-252 林俊雄 Jun. 22
CHRISTOPHER J.C. BURGES, "A Tutorial on Support Vector Machines for Pattern Recognition", Data Mining and Knowledge Discovery, 2, 121–167 (1998) 陳宣文 Jun. 22
Maxime Crochemore, Costas S. Iliopoulos, Yoan J. Pinzon, James F. Reid,"A Fast and Practical Bit-Vector Algorithm for the Longest Common Subsequence Problem", Information Processing Letters 80 (2001) 279–285 高茂源 Jun. 29
M. Kano, C. Merinob, J. Urrutiab, "On Plane Spanning Trees and Cycles of Multicolored Point Sets with Few Intersections", Information Processing Letters 93(2005) 301-306 林俊雄 Jul. 13
Yu-Dong Cai, Guo-Ping Zhou, Kuo-Chen Chou, "Support Vector Machines for Predicting Membrane Protein Types by Using Functional Domain Composition", Biophysical Journal Volume 84 May 2003 3257–3263 王仁暉 Jul. 13
Graham Cormodc, S. Muthukrishnan, "The String Edit Distance Matching Problem with Moves", Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms, pp. 667-676, 2002 安興彥 Jul. 19
Sebastian Deorowicz,"Speeding up transposition-invariant string matching", Information Processing Letters, In Press, Corrected Proof, Available online 12 June 2006 陳宣文 Jul. 19
Yoriko Iwata, Atsushi Kasuya, Shuichi Miyamoto, "An efficient method for reconstructing protein backbones from α–carbon coordinates",Journal of Molecular Graphics and Modelling 21 (2002) 119–128 王仁暉 Jul. 26
Shisheng Li , Guangzhong Sun, Guoliang Chen, "Improved Algorithm for Finding Next-to-Shortest Paths",Information Processing Letters 99 (2006) 192–194 高茂源 Jul. 26
Amihood Amir, Martin Farach, S. Muthukrishnan, "Alphabet dependence parameterized matching", Information Processing Letters 49, pp. 111-115, 1994 彭永興 Aug. 03
Jie Wu, "Adaptive Fault-Tolerant Routing in Cube-Based Multicomputers Using Safety Vectors", IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, VOL. 9. NO. 4, APRIL 1998 邱喬偉 Aug. 03
J. J. Ward, L. J. McGuffin, B. F. Buxton and D. T. Jones, "Secondary Structure Prediction with Support Vector Machines", BIOINFORMATICS, Vol. 19, no.13 ,Pages 1650–1655, 2003 林俊雄 Aug. 03
T. Kalganova, G.Russell, A. Cumming, "Multiple Traffic Signal Control Using a Genetic Algorithm", Proc. of the Fourth International Conference on Artificial Neural Networks and Genetic Algorithms (ICANNGA'99). Portoroz, Slovenia. pp. 220-228. (1999) 陳宣文 Aug. 17
Saravanan Dayalan, Savitri Bevinakoppa, Heiko Schroder, "A Dihedral Angle Database of Short Sub-Sequences for Protein Structure Prediction", The 2nd Asia-Pacific Bioinformatics Conference Vol. 29 (2004) 131-137 王仁暉 Aug.17
Amihood Amir, Moshe Lewenstin, Ely Porat, "Faster Algorithm for String Matching with k Mismatches", Journal of Algorithms, Vol. 50, 2004, pp. 257-275 安興彥 Aug. 17
Long-Hui Wang, Juan Liu, Yan-Fu Li, Huai-Bei Zhou, "Predicting Protein Secondary Structure by a Support Vector Machine Based on a New Coding Scheme", Genome Informatics 15(2): 181–190 (2004) 林俊雄 Aug. 24
George Tzanetakis, "Tempo Extraction using Beat Histograms", University of Victoria
Computer Science Department (also in Music)
高茂源 Aug. 24
Wojciech Rytter, "On maximal suffixes and constant-space linear-time versions of KMP algorithm", Theoretical Computer Science 299, pp. 763-774, 2003 彭永興 Aug. 31
DING-WEI HUANG and WEI-NENG HUANG, "Optimization of Traffic Lights at Crossroads", International Journal of Modern Physics C Vol. 14, No. 5 (2003) 539-548 陳宣文 Aug. 31
Xiaojing Yu, Jianping Cao, Yudong Cai, Tieliu Shi, Yixue Li, "Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines", Journal of Theoretical Biology, 2005 張小燕 Aug. 31
MARIUSZ MILIK, ANDRZEJ KOLINSKI, and JEFFREY SKOLNICK, "Algorithm for Rapid Reconstruction of Protein Backbone from Alpha Carbon Coordinates", Journal of Computational Chemistry, Vol. 18, No. 1, 80-85 (1997) 王仁暉 Sept. 07
Miguel A. ALONSO, Bertrand DAVID and Gael RICHARD, "Tempo and Beat Estimation of Music Signals", ISMIR 2004 5th International Conference on Music Information Retrieval 高茂源 Sept. 07
Sheng-I Yeh, Chang-Biau Yang, Hon-Chan Chen, Kuo-Si Huang, "The Design of Safety Vectors on the Star Graph" 邱喬偉 Sept. 07
Jian Guo, Hu Chen, Zhirong Sun, and Yuanlie Lin, "A Novel Method for Protein Secondary Structure Prediction Using Dual-Layer SVM and Profiles", PROTEINS: Structure, Function, and Bioinformatics 54:738–743 (2004) 林俊雄 Sept. 14
D. K. Kim, J. C. Na, J. E. Kim and K. Park, “Efficient Implementation of Rank and Select Functions for Succinct Representation," Workshop on Experimental and Efficient Algorithms 2005, pp. 315-327. 曾球庭 Sept. 14
Amir, Aumann, Landau, M. Lewenstein, N. Lewenstein, "Pattern Matching with Swaps", Journal of Algorithms, Vol. 37, 2000, pp. 247-266 安興彥 Sept. 21
M. Ebrahim Fouladvand and Masoud Nematollahi, "Optimization of Green-Times at an Isolated Urban Crossroads", The European Physical Journal B, Vol. 22 pp. 395-401 (2001) 陳宣文 Sept. 21
Ali Sezgin, Ganesh Gopalakrishnan, "On the Definition of Sequential Consistency", Information Processing Letters 96 (2005) 193–196 張嘉宏 Sept. 21
RAJMUND KAZ´ MIERKIEWICZ, ADAM LIWO, HAROLD A. SCHERAGA, "Energy-Based Reconstruction of a Protein Backbone from its α-Carbon Trace by a Monte-Carlo Method", J Comput Chem 23: 715–723, 2002 王仁暉 Sept. 28
Geoffroy Peeters, "Tempo Detection and Beat Marking for Perceptual Tempo Induction", MIREX 2005 高茂源 Sept. 28
Adam Zemla, Ceslovas Venclovas, Krzysztof Fidelis, and Burkhard Rost, "A Modified Definition of Sov, a Segment-Based Measure for Protein Secondary Structure Prediction Assessment", Structure, Function, and Genetics 34:220–223 (1999) 蔣宗翰 Sept. 28
Wolfgang Kabsch, Christian Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features", BIOINFORMATICS, Vol. 22, no.12 ,Pages 2577–2637, 1983 林俊雄 Oct. 12
INNA DUBCHAK, ILYA MUCHNIK, STEPHEN R. HOLBROOK,AND SUNG-HOU KIM, "Prediction of protein folding class using global description of amino acid sequence", Proc. Natl. Acad. Sci. USA Vol. 92, pp. 8700-8704, September 1995 張小燕 Oct. 12
Wun-Tat Chan, Yong Zhang, Stanley P. Y. Fung, Deshi Ye, Hong Zhu, "Efficient Algorithms for Finding a Longest Common Increasing Subsequence", ISAAC, pp. 665-674, 2005 曾球庭 Oct. 19
M. Ebrahim Fouladvand ,Nima Hamedani Radja, "Optimized Traffic Flow at a Single Urban Crossroads: Dynamical Symmetry Breaking", Technical Report: IPM/P-2001/039, 
Institute for Studies in Theoretical Physics and Mathematics (IPM), 2001
陳宣文 Oct. 19
Haim Kaplen, Nira Shafrir, "The Greedy Algorithm for Shortest Superstrings", Information Processing Letters 93(2005) 13-17 邱喬偉 Oct. 19
A.C.Camproux, P.Tuffery, J.P.Chevrolat, J.F.Boisvieux, S.Hazout, "Hidden Markov model approach for identifying the modular framework of the protein backbone", Protein Engineering vol.12 no.12 pp.1063–1073, 1999 王仁暉 Oct. 27
Martin F. McKinney, Dirk Moelants, "Deviations from the resonance theory of tempo induction", CIM04 - Conference on Interdisciplinary Musicology - Proceedings 高茂源 Oct. 27
Xuehou Tan, "A 2-approximation algorithm for the zookeeper’s problem", Information Processing Letters 100 (2006) 183–187 蔣宗翰 Nov. 02
Xuehou Tan, "Shortest zookeeper’s routes in simple polygons", Information Processing Letters 77 (2001) 23–26 張嘉宏 Nov. 02
Qidong Zhang, Sukjoon Yoon and William J. Welsh, "Improved Method for Predicting ß-turn Using Support Vector Machine", Bioinformatics Vol.21 no.10 2005, pages 2370-2374 林俊雄 Nov. 02
Peter Lackner, Walter A. Koppensteiner, Manfred J. Sippl and Francisco S. Domingues, "ProSup: a Refined Tool for Protein Structure Alignment ", Protein Engineering, Vol. 13, No. 11, 745-752, November 2000 陳宣文 Nov. 09
Liisa Holm, Chris Sander, "Protein Structure Comparison by Alignment of Distance Matrices", Journal of molecular biology 233: 123-138, 1993 高茂源 Nov. 09
Classification of protein structure 王仁暉 Nov. 09
Protein Secondary Structure and Paper Comparison 林俊雄 Nov. 09
Jakob Hull Havgaard, Rune B. Lyngso, Gary D. Stormo and Jan Gorodkin, "Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%", Bioinformatics, Vol. 21 no. 9 2005, pages 1815–1824 張小燕 Nov. 16
O. Dror ,H. Benyamini ,R. Nussinov ,and H. Wolfson, "MASS: multiple structural alignment by secondary structures", Bioinformatics (2003), 19:i94-i104 蔣宗翰 Nov. 16
VALENTIN A. ILYIN, ALEXEJ ABYZOV, AND CHESLEY M. LESLIN, "Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point", Protein Science (2004), 13:1865–1874. 張嘉宏 Nov. 16
Yang Zhang and Jeffrey Skolnick, "TM-align: a protein structure alignment algorithm based on the TM-score", 2302–2309 Nucleic Acids Research, 2005, Vol. 33, No. 7 邱喬偉 Nov. 16
Scott Montgomerie, Shan Sundararaj, Warren J Gallin and David S Wishart, "Improving the accuracy of protein secondary structure prediction using structural alignment", BMC Bioinformatics 2006, Vol. 7, Num. 301  彭永興 Nov. 23
D. Zhi, S. S. Krishna, H. Cao, P. Pevzner, and A. Godzik, "Representing and Comparing Protein Structures as Paths in Three-dimensional Space", BMC Bioinformatics, Vol. 7, pp. 460-474, 2006 曾球庭 Nov. 23
Kengo Sato and Yasubumi Sakakibara, "RNA Secondary Structural Alignment with Conditional Random Fields", Bioinformatics, Vol. 21, Suppl. 2, pp. ii237–ii242, 2005 安興彥 Nov. 23
Daron M Standley, Hiroyuki Toh, and Haruki Naka, "GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures", BMC Bioinformatics, Vol. 6:221, Sept. 8, 2005 黃國璽 Nov. 23
Krzysztof Ginalski, Arne Elofsson, Daniel Fischer and Leszek Rychlewski, 3D-Jury: A Simple Approach to Improve Protein Structure Predictions, Bioinformatics, Vol. 19, No.8, pp. 1015–1018, 2003 陳宣文 Nov. 30
Weizhong Li , Lukasz Jaroszewski and Adam Godzik, "Clustering of Highly Homologous Sequences to Reduce the Size of Large Protein Databases", BIOINFORMATICS,Vol. 17, no. 3 2001, Pages 282–283 高茂源 Nov. 30
David T. Jones, "Protein Secondary Structure Prediction Based on Position-Specific Scoring Matrices", J. Mol. Biol. (1999) 292, pages 195-202 林俊雄 Nov. 30
James A. Cuff and Geoffrey J. Barton, "Application of Multiple Sequence Alignment Profiles to Improve Protein Secondary Structure Prediction", Structure, Function, and Genetics 40:502–511 (2000) 王仁暉 Nov. 30
Ilya N. Shindyalov and Philip E. Bourne, "Protein Structure Alignment by Incremental Combinatorial Extension (CE) of the Optimal Path", Protein Engineering vol.11 no.9 pp.739-747, 1998 張小燕 Dec. 14
Tatsuya Akutsu, Kim Lan Sim, "Protein Threading Based on Multiple Protein Structure Alignment", Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
蔣宗翰 Dec. 14
Raj K. Singh, Alexander Tropsha and Iosif I. Vaisman, "Delaunay Tessellation of Proteins:Four Body Nearest Neighbor Propensities of Amino Acid Residues", J. Comput. Biol. 1996, 3, 2, 213-222 張嘉宏 Dec. 14
H. Bunke and J. Csirik, "An Improved Algorithm for Computing the Edit Distance of Run-Length Coded Strings", Information Processing Letters, Vol. 54, 1995, pp. 93–96 安興彥 Dec. 21
Emad Elbeltagi, Tarek Hegazy and Donald Grierson, "Comparison among five evolutionary-based optimization algorithms", Advanced Engineering Informatics, vol. 19, pp. 43-53, 2005 彭永興 Dec. 21
Long Lu, Hui Lu, and Jeffrey Skolnick, "MULTIPROSPECTOR: An Algorithm for the Prediction of Protein-protein Interactions by Multimeric Threading", PROTEINS: Structure, Function, and Genetics 49:350–364 (2002) 邱喬偉 Dec. 21
Fangting Sun, David Fernandez-Baca and Wei Yu, "Inverse Parametric Sequence Alignment", J. Algorithms, Vol. 53, No. 1, pp. 36-54, 2004 曾球庭 Dec. 28
Elmar Brockfeld, Robert Barlovic, Andreas Schadschneider and Michael Schreckenberg, "Optimizing Traffic Lights in a Cellular Automaton Model for City Traffic", Physical Review E, Vol. 64, No. 056132, 2001 陳宣文 Dec. 28
H. Abdi, "A Neural Network Primer", Journal of Biological Systems, Vol. 2(3), pp. 247-283, (1994) 王仁暉 Dec. 28

 

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