Zheng, Weihua, et al. "A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency." IEEE/ACM Transactions on Computational Biology and Bioinformatics (2016).
Gavarraju, Lakshmi Naga Jayaprada, Jeevana Jyothi Pujari, and K. Karteeka Pavan. "Sequence Alignment by Advanced Differential Evolutionary Algorithm."Computational Intelligence Techniques in Health Care. Springer Singapore, 2016. 69-81.
Brown, Simon. "A bioinformatic perspective on linguistic relatedness." Cultural Anthropology and Ethnosemiotics 1.4 (2015): 43-52.
Yao, Dengfeng, et al. "An algorithm of multiple sequence alignment based on consensus sequence searched by simulated annealing and star alignment." Bioelectronics and Bioinformatics (ISBB), 2015 International Symposium on. IEEE, 2015.
Sundfeld, Daniel, George Teodoro, and Alba Cristina Magalhaes Alves de Melo. "Parallel A-Star Multiple Sequence Alignment with Locality-Sensitive Hash Functions." Complex, Intelligent, and Software Intensive Systems (CISIS), 2015 Ninth International Conference on. IEEE, 2015.
Hung, Che-Lun, et al. "CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs." Computational biology and chemistry 58 (2015): 62-68.
Horiguchi, Yukio, et al. "Comparison of Train Drivers' Eye-Gaze Movement Patterns Using Sequence Alignment." SICE Journal of Control, Measurement, and System Integration 8.2 (2015): 114-121.
Lalwani, Soniya, Rajesh Kumar, and Nilama Gupta. "A novel two-level particle swarm optimization approach for efficient multiple sequence alignment."Memetic Computing 7.2 (2015): 119-133.
Pramanik, Sarah, and S. K. Setua. "A steady state genetic algorithm for multiple sequence alignment." Advances in Computing, Communications and Informatics (ICACCI, 2014 International Conference on. IEEE, 2014.
Šimalová, Mária, and Gabriela Andrejková. "Speeding up simultaneous alignment and folding of RNA sequences." Open Computer Science 4.3 (2014): 141-149.
Li, L., et al. "New support vector machine-based method for microRNA target prediction." Genetics and molecular research: GMR 13.2 (2014): 4165.
Liu, Yulong, et al. "Automated Text Data Extraction Based on Unsupervised Small Sample Learning." Foundations and Applications of Intelligent Systems. Springer Berlin Heidelberg, 2014. 133-150.
Deorowicz, Sebastian, Agnieszka Debudaj-Grabysz, and Adam Gudyś. "Kalign-LCS—A More Accurate and Faster Variant of Kalign2 Algorithm for the Multiple Sequence Alignment Problem." Man-Machine Interactions 3. Springer International Publishing, 2014. 495-502.
Gotoh, Osamu. "Heuristic Alignment Methods." Multiple Sequence Alignment Methods. Humana Press, 2014. 29-43.
Liu, Yulong, et al. "Automated Text Data Extraction Based on Unsupervised Small Sample Learning." Foundations and Applications of Intelligent Systems. Springer Berlin Heidelberg, 2014. 133-150.
Lin, Chun Yuan, and Yu Shiang Lin. "Efficient parallel algorithm for multiple sequence alignments with regular expression constraints on graphics processing units." International Journal of Computational Science and Engineering 9.1 (2014): 11-20.
Czajka, Adam. "Influence of Iris Template Aging on Recognition Reliability." Biomedical Engineering Systems and Technologies. Springer Berlin Heidelberg, 2013. 284-299.
Tahar Ben Othman, Mohamed, and Gamil Abdel-Azim. "Genetic Algorithms with Permutation Coding for Multiple Sequence Alignment." Recent patents on DNA & gene sequences 7.2 (2013): 105-114.
Nguyen, Ken D., and Yi Pan. "A Knowledge-Based Multiple-Sequence Alignment Algorithm." IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 10.4 (2013): 884-896.
Sundfeld, Daniel, and Alba CMA de Melo. "MSA-GPU: Exact Multiple Sequence Alignment Using GPU." Advances in Bioinformatics and Computational Biology. Springer International Publishing, 2013. 47-58.
Banerjee, Sagnik, Tamal Chakrabarti, and Devadatta Sinha. "A Faster Fitness Calculation Method for Genetic Algorithm Based Multiple Protein Sequence Alignment.", International Journal of Scientific & Engineering Research, Volume 4, Issue 7, July-2013
Hatem, Matthew, and Wheeler Ruml. "External memory best-first search for multiple sequence alignment." Submitted to Proceedings of the Twenty-Seventh Conference on Artificial Intelligence (AAAI-2013). 2013.
Hassanien, Aboul Ella, Eiman Tamah Al-Shammari, and Neveen I. Ghali. "Computational intelligence techniques in bioinformatics." Computational biology and chemistry 47 (2013): 37-47.
S. Divakaran, A. Mithal and N. Jain, “A Fast Template Based Heuristic For Global Multiple Sequence Alignment”, arXiv preprint arXiv:1302.6030, 2013.
J. Kececioglu and D. DeBlasio, “Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment”, Journal of Computational Biology, 2013.
S. Lalwani, R. Kumar and N. Gupta, “A Review on Particle Swarm Optimization variants and their applications to Multiple Sequence Alignment”, Journal of Applied Mathematics & Bioinformatics, vol.3, no.2, pp. 87-124, 2013.
O. Okunoye Babatunde, “Resolving the Decision Version of the Directed Hamiltonian Path (Cycle) Problem under Two Special Conditions by Method of Matrix Determinant: An Overview”, World Applied Programming, Vol.3, Issue 5, pp.178-181, 2013.
F. A. Oliehoek, M. T. Spaan, C. Amato and S. Whiteson, “Incremental Clustering and Expansion for Faster Optimal Planning in Decentralized POMDPs”, Journal of Artificial Intelligence Research, vol.46, pp. 449-509, 2013.
Kim Sung, “Alineación de secuencia múltiple utilizando una variante del método de cálculo de la similitud conjunto de cadenas”, Journal of BESO: Software y Aplicaciones. Capítulo 40 No. 1,pp. 53-60, 2013.
L. Sheneman and J. A. Foster, “Eliminating Dynamic Programming Bias in Multiple Sequence Alignment Algorithms”, Retrieved March, vol.24, 2012.
И. Пироженко and А. Сальников, “CLUSTALW2: ПАРАЛЛЕЛЬНАЯ РЕАЛИЗАЦИЯ С ПОМОЩЬЮ ТЕХНОЛОГИИ OPENMP”, 2012.
Hisato TOKUNAGA, Sayaka KANATA, Hiroaki NAKANISHI1, Tetsuo SAWARAGI, “A Method for Behavior Analysis using Change-points Sequences Extracted by Singular Spectrum Transformation”, Journal of Japan Societyfor Fuzzy Theory and Intelligent Informatics, vol.24, no.1, pp.526-535. 2012.
R. Jagadeesh Chandra Bose and W. M. van der Aalst, “Process diagnostics using trace alignment: opportunities, issues, and challenges”, Information Systems, vol.37, issue 2, 2012.
B.-R. Kung, W.-H. Chen and R. Lee, “On the Repeating Group Finding Problem”, The 29th Workshop on Combinatorial Mathematics and Computation Theory, 2012.
G. R. Lakshmi and M. B. N. Swamy, “Web Data Identification and Extraction”, International Journal of Electronics, vol.1, pp. 1862-1869, 2012.
Chih-Chin Liu, 繼正 邱, “Multi-Version Music Performance Comparison Based on the Progressive Multiple Sequence”, Journal of Information Technology and Applications, vol.5, issue 4, pp.157, 2012.
G. Abdel-Azim, Z. Abo-Eleneen and M. T. B. Othman, “Proteins Sequence Alignment with Progressive Strategy based on mutual information”, Journal of Selected Areas in Bioinformatics (JBIO), 2012.
B. Akgun, M. Cakmak, K. Jiang and A. L. Thomaz, “Keyframe-based learning from demonstration”, International Journal of Social Robotics, issue 4, vol. 4, pp. 343-355, 2012.
B. Akgun, M. Cakmak, K. Jiang and A. L. Thomaz, “Keyframe-based Learning from Demonstration Method and Evaluation” Springer, 2012.
A. S. BABUI, S. NAUREEN, M. U. RAO and G. SIRISHA, “Web Information Extraction Using Depta”, International Journal for Research and Development in Engineering, vol.1, issue 1, pp. 58-64.
S. Banerjee, D. Sensarma, K. Basuli, S. Naskar and S. S. Sarma, “FROM RECONSTRUCTION CONJECTURE TOWARDS A LEMMA”, Computer Science & Engineering, vol.2, issue 1, 2012.
W. Frohmberg, M. Kierzynka, J. Błażewicz and P. Wojciechowski, “G-MSA-a powerful GPU-based tool for multiple sequence alignment”, 2012.
A. D. Goldman, J. A. Horst, L. H. Hung and R. Samudrala, “Evolution of the Protein Repertoire”, Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2012.
K. D. Nguyen, “On the edge of web-based multiple sequence alignment services”, Tsinghua Science and Technology, vol.17, issue 6, 2012.
Cutello, G. Nicosia, M. Pavone and I. Prizzi, “Protein multiple sequence alignment by hybrid bio-inspired algorithms”, Nucleic acids research, vol.39, issue 6, pp. 1980-1992, 2011.
G. Abdel-Azim, A. Hamdi-Cherif, M. B. Othman and Z. Aboeleneen, “Protein Progressive MSA Using 2-Opt Method”, Systems and Computational Biology - Bioinformatics and Computational Modeling, 2011.
Z. ABO-ELENEEN, “Modified Progressive Strategy for Multiple Proteins Sequence Alignment”, INTERNATIONAL JOURNAL OF COMPUTERS, Issue 2, Volume 5, 2011.
M. E. Helal and V. Sintchenko, “Dynamic programming algorithms for discovery of antibiotic resistance in microbial genomes”, Electronic Journal of Health Informatics, vol. 6, issue 1, pp. e10, 2011.
M. Kessentini, H. Sahraoui and M. Boukadoum, “Example-based model-transformation testing”, Automated Software Engineering, vol.18, issue 2, pp. 199-224, 2011.
C.-L. Hung, C.-Y. Lin, S.-C. Chang, Y.-C. Chung, S. Hsieh, C. Tang and Y.-L. Lin, “Multiple genome sequences alignment algorithm based on coding regions”, International Journal of Computational Biology and Drug Design, vol.4, issue 2, 2011.
A.-S. Malaspinas, N. Eriksson and P. Huggins, “Parametric analysis of alignment and phylogenetic uncertainty”, Bulletin of mathematical biology, vol.73, issue 4, pp. 795-810, 2011.
A. Mokaddem and M. Elloumi, “Algorithms for the Alignment of Biological Sequences”, Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, pp. 241-260. 2011.
K. D. Nguyen and Y. Pan, “Multiple sequence alignment based on dynamic weighted guidance tree”, International Journal of Bioinformatics Research and Applications, vol.7, issue 2, pp. 168-182, 2011.
K. D. Nguyen and Y. Pan, “An improved scoring method for protein residue conservation and multiple sequence alignment”, NanoBioscience, IEEE Transactions on, vol.10, issue 4, pp. 275-285, 2011.
K. D. Nguyen, Y. Pan and G. Nong, “Parallel progressive multiple sequence alignment on reconfigurable meshes”, BMC genomics, vol.12, issue suppl 5, pp.s4, 2011.
L. Steiner, P. F. Stadler and M. Cysouw, “A pipeline for computational historical linguistics”, Language Dynamics and Change, vol.1, issue 1, pp. 89-127, 2011.
H. Willy, L. Q. Xiang, P. S. Wasan and V. B. V. SN, “CS5238 Project Stochastic Algorithms for Multiple Sequence Alignment”.
X. Ye, G. Wang and S. F. Altschul, “An assessment of substitution scores for protein profile–profile comparison”, Bioinformatics, vol.27, issue 24, 2011.
Axelson-Fisk, M. (2010). "Sequence Alignment." Comparative Gene Finding: Computational Biology, 2010, Volume 11, 89-155 .
Cutello, V., G. Nicosia, et al. (2010). "Protein multiple sequence alignment by hybrid bio-inspired algorithms." Nucleic Acids Research, Nov. Pages 1-13.
Dubbs, A., B. Seiler, et al. "A fast Lp spike alignment metric." Neural Computation November 2010, Vol. 22, No. 11, Pages 2785-2808 2010 Massachusetts Institute of Technology
Penn, O., E. Privman, (2010). "GUIDANCE: A Web Server for Assessing Alignment Confidence Scores" Nucleic Acids Research, May, Pages 1-13.
Penn, O., E. Privman, et al. (2010). "An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty." Molecular Biology and evolution 27(8): 1759–1767.
Szabo, A., A. Novak, et al. (2010). "Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment." BMC Bioinformatics 11(1): 570.
Zamora, V., J. Hernández, et al. "Implementación de un metódo híbrido usando secuencias de ADN, para la obtención de probabilidades de enfermedades (diabetes tipo2, hipertensión e insuficiencia renal)." Advances in Intelligent and Information Technologies. Research in Computing Science 50, 2010, pp. 275-288.
Domazet-Loso, M. and B. Haubold (2009). "Efficient estimation of pairwise distances between genomes." Bioinformatics 25(24): 3221-3227.
Jantschi, L., S. Bolboaca, et al. (2009). "Hard Problems in Gene Sequence Analysis: Classical Approaches and Suitability of Genetic Algorithms." Biotechnology & Biotechnological Equipment 23(2): 1275-1280.
LAI, C., C. WU, et al. "Using Genetic Algorithm to Solve Multiple Sequence Alignment Problem" International Journal of Software Engineering and Knowledge Engineering (IJSEKE) Volume: 19, Issue: 6(2009) pp. 871-888.
Sahoo, B., A. Kumar, et al. (2009). "Parallel Implementation of Centre Star Method in SMP Cluster for Multiple Sequence Alignment." International Journal of Recent Trends in Engineering, Vol 2, No. 1, November 2009.
Siva Sathya, S., S. Kuppuswami, et al. (2009). "Nomadic genetic algorithm for multiple sequence alignment (MSANGA)." International Journal of Adaptive and Innovative Systems 1(1): 44-59.
Kazutaka Katoh. “Recent developments in the MAFFT multiple sequence alignment program” Briefings in Bioinformatics Vol. 9 Num. 4 Pp. 286-298, 2008.
Benedict Paten, Javier Herrero, Kathryn Beal, Stephen Fitzgerald, and Ewan Birney “Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs” Genome Res. 2008. 18: 1814-1828.
Zne-Jung Leea , Shun-Feng Sub, Chen-Chia Chuangc and Kuan-Hung Liub “Genetic algorithm with ant colony optimization (GA-ACO) for multiple sequence alignment” Applied Soft Computing Volume 8, Issue 1, January 2008, Pages 55-78.
K Joo, J Lee, I Kim, SJ Lee “Multiple sequence alignment by conformational space annealing” Biophysical Journal Volume 95, Issue 10, 15 November 2008, Pages 4813-4819.
Eagu Kim, J Kececioglu “Learning Scoring Schemes for Sequence Alignment from Partial Examples” Computational Biology and Bioinformatics, Volume: 5 Issue:4 On page(s): 546 – 556.
Do, C. and K. Katoh (2008). "Protein Multiple Sequence Alignment." Methods in Molecular Biology, Vo. 484, Pages 379-413.
Glass, M., M. Evens, "Extracting Information from Natural Language Input to an Intelligent Tutoring System." East Journal of Experimental and Theoretical Artificial Intelligence Volume 1, Issue 2, Pages 87 - 125 (May 2008).
Wang-Sheng Juang and Shun-Feng Su "Incorporating Random Pairwise Dynamic Programming with Particle Swarm Optimization in Solving Multiple Sequence Alignment" Far East Journal of Experimental and Theoretical Artificial Intelligence Volume 1, Issue 2, Pages 137 - 150 (May 2008).
Juang, W. and S. Su (2008). "Multiple sequence alignment using modified dynamic programming and particle swarm optimization." Journal of the Chinese Institute of Engineers 31(4): 659-673.
Kim, E. and J. Kececioglu (2008). "Learning scoring schemes for sequence alignment from partial examples." Computational Biology and Bioinformatics, IEEE/ACM Transactions on 5(4): 546-556.
Levasseur, A., P. Pontarotti, et al. (2008). "Strategies for reliable exploitation of evolutionary concepts in high throughput biology" Evolutionary Bioinformatics Online 2008; 4: 121–137.
Madeira, P., R. Pemberton, et al. (2008). "A molecular phylogeny of the genus Lygodium (Schizaeaceae) with special reference to the biological control and host range testing of Lygodium microphyllum" Biological Control 45(3): 308-318.
Ingolf Sommer, “Protein Fold Recognition Based on Distant Homologs” Bioinformatics - From Genomes to Therapies, Pages: 351–388, 2008 Published Online : 5 FEB 2008.
Zhang, Z., H. Lin, et al. "MANGO: multiple alignment with n gapped oligos." Journal of Bioinformatics and Computational Biology (JBCB), Volume: 6, Issue: 3(2008) pp. 521-541.
Hemaspaandra, Edith, Hemaspaandra, Lane A. Radziszowski, Stanislaw P. Tripathi, Rahul. “Complexity Results In Graph Reconstruction”, en Discrete Applied Mathematics, Volume 155, Pages 103-118, 2007.
R. Mulet, M. Hernández-Guía And S. Rodríguez-Pérez, “A New Simulated Annealing Algorithm For The Multiple Sequence Alignment”, en Journal Of Software, Vol.18, No.2, Pages 185−195 2007.
Eric A. Hansen “Anytime heuristic search” Journal of Artificial Intelligence Research 28 (2007) 267-297.
H Kiryu, Y Tabei, T Kin “Murlet: a practical multiple alignment tool for structural RNA sequences” Bioinformatics (2007) 23 (13): 1588-1598.
Azzedine Boukerche, Jan Mendonca Correa, Alba Cristina Magalhaes Alves de Melo, Ricardo Pezzuol Jacobi and Adson Ferreira Rocha “An FPGA-Based Accelerator for Multiple Biological Sequence Alignment with Dialign” High Performance Computing – Hipc 2007 Lecture Notes in Computer Science, 2007, Volume 4873/2007, 71-82.
Kupis, P. and J. Mandziuk (2007). "Multiple Sequence Alignment with Evolutionary-Progressive Method" Adaptive and Natural Computing Algorithms, Lecture Notes in Computer Science, 2007, Volume 4431/2007, 23-30.
Liu, W., L. Chen, et al. (2007). "An efficient algorithm for multiple sequence alignment based on ant colony optimization and divide-and-conquer method" New Zealand Journal of Agricultural Research 50(5): 617-626.
Uren, P., R. Cameron-Jones, et al. (2007). "MAUSA: using simulated annealing for guide tree construction in multiple sequence alignment." AI 2007: Advances in Artificial Intelligence, Vol. 4830 Pages 599-608.
Ernst Althaus, Alberto Caprara , Hans-Peter Lenhof And Knut Reinert, “A Branch-And-Cut Algorithm for Multiple Sequence Alignment”, en Mathematical Programming, Vol. 105. Pages 387–425, 2006.
Elena Zaslavsky And Mona Singh, “A Combinatorial Optimization Approach For Diverse Motif Finding” en Algorithms For Molecular Biology. Vol 1, Page 13, 2006.
Virpi Ahola, Tero Aittokallio, Mauno Vihinen And Esa Uusipaikka, “A Statistical Score For Assessing The Quality Of Multiple Sequence Alignments”, en BMC Bioinformatics. Vol 7, Page 484, 2006.
Yonatan Bilu, Pankaj K. And Agarwalrachel Kolodny, “Faster Algorithms For Optimal Multiple Sequence Alignment Based On Pairwise Comparisons”, en Computational Biology And Bioinformatics, Vol. 3, No. 4, Pages 408-422, 2006.
Ke Liu, M. H. Samadzadeh, “Pac: Progressive Alignment With Consensus Sequences”, en Biocomp, Pages 518-524, 2006.
Arun S. Konagurthu, “Optimal Sum-Of-Pairs Multiple Sequence Alignment Using Incremental Carrillo and Lipman Bounds”, en Computational Biology, Vol. 13, No. 3, Pages 668 -685, 2006.
Sing-Hoi Sze, Yue Lu, Qingwu Yang, “A Polynomial Time Solvable Formulation of Multiple Sequence Alignment”, en Journal of Computational Biology, Vol. 13, No. 2: Pages 309 -319. 2006.
Liu, Li-Fang; Huo, Hong-Wei; Wang, Bao-Shu, “Phga-Coffee: Aligning Multiple Sequences By Parallel Hybrid Genetic Algorithm” En Jisuanji Xuebao (Chinese Journal Of Computers). Vol. 29, No. 5, Pages 727-733, 2006.
S Kirsch, B Weiß, TL Miner, RH Waterston “Interchromosomal Segmental Duplications of The Pericentromeric Region on The Human Y Chromosome” Genome Res. 2005. 15: 195-204.
M. Hernández-Guía, R. Mulet, S. Rodríguez-Pérez “Simulated annealing algorithm for the multiple sequence alignment problem: The approach of polymers in a random medium” Phys. Rev. Vol. 72, Issue 3, 2005.
Armano, G., L. Milanesi, et al. (2005). "Using Secondary Structure Information to Perform Multiple Alignment." Lecture Notes in Computer Science, Transactions on computational systems biology III, Vol. 3737, Pages 78-88.
Liu, L., H. Huo, et al. (2005). "HGA-COFFEE: Aligning Multiple Sequences by Hybrid Genetic Algorithm" Advanced Data Mining and Applications: Lecture Notes in Computer Science, 2005, Volume 3584/2005, 464-473.
Stefan Schroedl, “An Improved Search Algorithm for Optimal Multiple-Sequence Alignment”, En Journal of Artificial Intelligence Research. Vol 23 Pages 587-623, 20.
Serafim Batzoglou, “The Many Faces Of Sequence Alignment”, En Briefings In Bioinformatics. Vol 6. No 1. 6–22 2005.
Agarwal, P., Y. Bilu, et al. (2005). "Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons" Algorithms in Bioinformatics, Vol. 3692, Pages 315-327.
Robert G. Beiko, Cheong Xin Chan And Mark A. Ragan, “A Word-Oriented Approach To Alignment Validation”, En Bioinformatics, Volume 21, Pages: 2230-2239, 2005.
C.B. Do, M.S.P. Mahabhashyam, M. Brudno, and S. Batzoglou, “PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment,” Genome Research 15: 330-340, 2005.