Publications

[367]Pelagic Species Identification by using a Probabilistic Neural Network and Echo-sounder Data ( and ), In ICANN (accepted), . [bibtex]
[366] Palindromic Decompositions with Gaps and Errors (), In CoRR, volume abs/1703.08931, . [bibtex] [pdf]
[365]Efficient Enumeration of Non-Equivalent Squares in Partial Words with Few Holes ( and ), In COCOON (accepted), . [bibtex]
[364]Covering Problems for Partial Words and for Indeterminate Strings (, , , , and ), In Theoretical Computer Science, . [bibtex]
[363]On-line pattern matching on a set of similar texts (, , , , , , , and ), Chapter in 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017), Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, . [bibtex]
[362] Global Sequence Alignment with a Bounded Number of Gaps (, , and ), Chapter in Pattern Recognition in Computational Molecular Biology: Techniques and Approaches (Mourad Elloumi, Costas S. Iliopoulos, Jason T. L. Wang, Albert Y. Zomaya, eds.), Wiley, . [bibtex] [pdf]
[361]Dedicated to Professor William F. Smyth on the occasion of his 80th birthday, (Costas S. Iliopoulos, Simon J. Puglisi, eds.), volume , . [bibtex]
[360]Searching And Indexing Circular Patterns (, and ), Chapter in Algorithms for Next-Generation Sequencing (, ed.), Springer, . [bibtex]
[359]Popping Superbubbles and Discovering Clumps: Recent Developments in Biological Sequence Analysis (, , and ), Chapter in WALCOM: Algorithms in Bioinformatics, Springer, . [bibtex]
[358]Statistical Approach towards Malware Classification and Detection ( and ), In SAI Computing Conference 2016, . [bibtex]
[357]Repetitive structures in biological sequences: algorithms and applications (, and ), In Frontiers, . [bibtex]
[356]A Novel Pattern Matching Approach for Fingerprint-based Authentication ( and ), In PATTERNS 2016, IARIA, . [bibtex]
[355]Transcriptome activity of isochores during pre-implantation process in human and mouse (, , and ), In FEBS Letters, . [bibtex]
[354]Truly Subquadratic-Time Extension Queries and Periodicity Detection in Strings with Uncertainties ( and ), In Annual Symposium on Combinatorial Pattern Matching (CPM 2016), . [bibtex]
[353]Detection of URL in Image Steganography ( and ), In International Conference on Internet of things and Cloud Computing (ICC 2016), ACM Digital Library, . [bibtex]
[352] Linear algorithm for conservative degenerate pattern matching (, , , and ), In Engineering Applications of Artificial Intelligence, volume 51, . [bibtex] [pdf] [doi]
[351]Approximate circular pattern matching with a simple and light-weight filter-based algorithm ( and ), In IEEE Transactions on NanoBioscience, . [bibtex]
[350]Text redundancies (, , and ), Chapter in Combinatorics, Words and Symbolic Dynamics (Valerie Berthe, Michel Rigo, eds.), . [bibtex]
[349] Linear-time superbubble identification algorithm for genome assembly (, , , , and ), In Theoretical Computer Science, volume 609, Part 2, . [bibtex] [pdf] [doi]
[348]Smart Meter Data Analysis (, , , and ), In International Conference on Internet of things and Cloud Computing (ICC 2016), ACM Digital Library, . [bibtex]
[347] The longest common substring problem (, , and ), In Mathematical Structures in Computer Science, volume FirstView, . [bibtex] [pdf] [doi]
[346]Fast circular dictionary-matching algorithm (, , , , , and ), In Mathematical Structures in Computer Science, volume FirstView, . [bibtex] [doi]
[345]Generic Algorithms for Factoring Strings (, , and ), In Information Theory, Combinatorics, and Search Theory 2013, . [bibtex]
[344]SimpLiFiCPM: A Simple and Lightweight Filter-based Algorithm for Circular Pattern Matching (, , and ), In International Journal of Genomics, . [bibtex]
[343]Circular Sequence Comparison with q-grams (, , , , , and ), Chapter in Algorithms in Bioinformatics (Pop, Mihai, Touzet, Helene, eds.), Springer Berlin Heidelberg, volume 9289, . [bibtex] [doi]
[342]Order-Preserving Indexing (, , , , , , , and ), In Theoretical Computer Science, volume 638, . [bibtex] [doi]
[341]A note on the longest common compatible prefix problem for partial words (, , , , , , , and ), In Journal of Discrete Algorithms, volume 34, . [bibtex]
[340]A Novel Pattern Matching Approach for Fingerprint-based Authentication (, , , and ), In PATTERNS 2015: The Seventh International Conferences on Pervasive Patterns and Applications, IARIA, . [bibtex]
[339]A Statistical Approach for Discovering Critical Malicious Patterns in Malware Families (, and ), In PATTERNS 2015: The Seventh International Conferences on Pervasive Patterns and Applications, IARIA, . [bibtex]
[338]Using Arabic Microblogs Features in Determining Credibility ( and ), In Fab 2015, Springer, . [bibtex]
[337] Antimagicness of Generalized Corona and Snowflake Graphs (, , and ), In Mathematics in Computer Science, volume 9, . [bibtex] [pdf] [doi]
[336]On the appearance of seeds in words (, , and ), In Journal of Combinatorial Mathematics and Combinatorial Computing, volume 95, . [bibtex]
[335] Average-Case Optimal Approximate Circular String Matching (, and ), In Language and Automata Theory and Applications - 9th International Conference Proceedings, . [bibtex] [pdf] [doi]
[334] Accurate and Efficient Methods to Improve Multiple Circular Sequence Alignment (, , , , and ), In Experimental Algorithms - 14th International Symposium, SEA 2015, . [bibtex] [pdf] [doi]
[333] Global and local sequence alignment with a bounded number of gaps (, , and ), In Theoretical Computer Science, volume 582, . [bibtex] [pdf] [doi]
[332] A Filter-Based Approach for Approximate Circular Pattern Matching (, , and ), In Bioinformatics Research and Applications - 11th International Symposium, . [bibtex] [pdf] [doi]
[331] Algorithms for Longest Common Abelian Factors (, , and ), In CoRR, volume abs/1503.00049, . [bibtex] [pdf]
[330]SimpLiSMS: A Simple, Lightweight and Fast Approach for Structured Motifs Searching (, , , and ), In Bioinformatics and Biomedical Engineering - Third International Conference, . [bibtex]
[329] Proceedings of the 2nd International Conference on Algorithms for Big Data, Palermo, Italy, April 07-09, 2014, (Costas S. Iliopoulos, Alessio Langiu, eds.), CEUR-WS.org, volume 1146, . [bibtex] [pdf]
[328]A Model for Recalibrating Credibility in Different Contexts and Languages-A Twitter Case Study (, and ), In International Journal of Digital Information and Wireless Communications (IJDIWC), The Society of Digital Information and Wireless Communication, volume 4, . [bibtex]
[327] Order-preserving matching (, , , , , , and ), In Theoretical Computer Science, volume 525, . [bibtex] [pdf] [doi]
[326] On-line Minimum Closed Covers ( and ), In Artificial Intelligence Applications and Innovations 2014 Rhodes Greece September Proceedings, . [bibtex] [pdf] [doi]
[325] Detection of Web Spambot in the Presence of Decoy Actions (, and ), In 2014 IEEE Fourth International Conference on Big Data and Cloud Computing, BDCloud 2014 Australia, . [bibtex] [pdf] [doi]
[324] Extracting powers and periods in a word from its runs structure (, , , , and ), In Theoretical Computer Science, volume 521, . [bibtex] [pdf] [doi]
[323] New simple efficient algorithms computing powers and runs in strings (, , , , , and ), In Discrete Applied Mathematics, volume 163, Part 3, . [bibtex] [pdf] [doi]
[322] Abelian borders in binary words (, , and ), In Discrete Applied Mathematics, volume 171, . [bibtex] [pdf] [doi]
[321] Optimal computation of all repetitions in a weighted string ( and ), In International Conference on Algorithms for Big Data (ICABD2014) (Costas S. Iliopoulos, Alessio Langiu, eds.), . [bibtex] [pdf]
[320] Fast and Simple Computations Using Prefix Tables Under Hamming and Edit Distance (, , and ), In Combinatorial Algorithms - 25th International Workshop, IWOCA 2014, Duluth, MN, USA, October 15-17, 2014, Revised Selected Papers, . [bibtex] [pdf] [doi]
[319] Fast algorithms for approximate circular string matching (, and ), In Algorithms for Molecular Biology, volume 9, . [bibtex] [pdf] [doi]
[318]On the Average-case Complexity of Pattern Matching with Wildcards ( and ), In CoRR, volume abs/1407.0950, . [bibtex]
[317]Optimal computation of all tandem repeats in a weighted sequence (, and ), In Algorithms for Molecular Biology, volume 9, . [bibtex]
[316]Extending alignments with k-mismatches and $-gaps (, , , , and ), In Theoretical Computer Science, volume 525, . [bibtex] [doi]
[315] Closed Factorization (, , , , , , and ), In Proceedings of the Prague Stringology Conference 2014, . [bibtex] [pdf]
[314] A fast and lightweight filter-based algorithm for circular pattern matching (, , and ), In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 14 California USA 2014, . [bibtex] [pdf] [doi]
[313] Evaluation of credibility assessment for microblogging: models and future directions (, and ), In 14th International Conference on Knowledge Management and Data-driven Business, I-KNOW 14, Graz, Austria, September 16-19, 2014, . [bibtex] [pdf] [doi]
[312] The swap matching problem revisited (, , and ), In Theoretical Computer Science, volume 557, . [bibtex] [pdf] [doi]
[311]Transcriptome map of mouse isochores in embryonic and neonatal cortex (, , , , and ), In Genomics, volume 101, . [bibtex]
[310]Telematics solution for the Teleco industry in the Developing World (, and ), In Proceedings of the First International Conference on Green Computing, Technology and Innovation (ICGCTI 2013), . [bibtex]
[309]Suffix Tree of an Alignment: An Efficient Index for Similar Data (, , , , , and ), In Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA) 2013, . [bibtex]
[308]Overlapping factors in words (, , and ), In Australasian Journal of Combinatorics, volume 57, . [bibtex]
[307]Order Preserving Matching (, , , , , , and ), In Theoretical Computer Science, volume December, . [bibtex]
[306]Identification of all Exact and Approximate Inverted Repeats in Regular and Weighted Sequences ( and ), In Proceedings of the International Conference on Engineering Applications of Neural Networks (EANN) 2013, . [bibtex]
[305]Predicting the functional consequences of non-synonymous DNA sequence variants - evaluation of bioinformatics tools and development of a consensus strategy (, , and ), In Genomics, volume 102, . [bibtex]
[304]Enhanced String Covering (, , , , , and ), In Theoretical Computer Science, volume 506, . [bibtex]
[303]Degree/diameter problem for trees and pseudotrees (, and ), In AKCE International Journal of Graphs and Combinatorics, volume 10(4), . [bibtex]
[302]Algorithms for next-generation sequencing data ( and ), Chapter in Handbook of Biological Knowledge Discovery (, ed.), Wiley, . [bibtex]
[301]Suffix Tree of an Alignment: An Efficient Index for Similar Data (, , , , , and ), In IWOCA 2013, volume 8288, . [bibtex]
[300]Static Analysis and Clustering of Malware Applying Text Based Search ( and ), In The International Conference on Digital Information Processing, E-Business and Cloud Computing, SDIWC, . [bibtex]
[299]Malware Detection using Computational Biology Tools ( and ), In International Journal of Engineering and Technology, . [bibtex]
[298]Verifying an enhanced cover array in linear time ( and ), Chapter in Formal Aspects of Computing, Essays dedicated to Derrick Kourie on the occasion of his 65th birthday (Stefan Gruner, Bruce Watson, eds.), Shaker Verlag, . [bibtex] [doi]
[297]A note on efficient computation of all Abelian periods in a string (, , , , , , and ), In Inf. Process. Lett., volume 113, . [bibtex]
[296] Circular string matching revisited (, and ), In Proceedings of the Fourteenth Italian Conference on Theoretical Computer Science (ICTCS 2013), . [bibtex] [pdf]
[295]GapMis: a tool for pairwise sequence alignment with a single gap (, , , , and ), In Recent Patents on DNA and Gene Sequence Journal: Pattern Finding in Computational Molecular Biology, Bentham Science, volume 7(2), . [bibtex]
[294]Computing the Longest Previous Factor (, , , , and ), In The Electronic Journal of Combinatorics, volume 34, . [bibtex]
[293] Tree template matching in unranked ordered trees (, , , , , and ), In Journal of Discrete Algorithms, volume 20, . [bibtex] [pdf] [doi]
[292]Querying Highly Similar Sequences (, , , , and ), In International Journal or Computation Biology and Drug Design, volume 6, . [bibtex]
[291] GapsMis: Flexible Sequence Alignment with a Bounded Number of Gaps (, , and ), In Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM, . [bibtex] [pdf] [doi]
[290]Maximal palindromic factorization ( and ), Chapter in , . [bibtex]
[289]Comparison for the detection of Virus and spam using pattern matching tools (, , , , and ), In Technological Advances in Electrical, Electronics and Computer Engineering (TAEECE), 2013 International Conference on, . [bibtex] [doi]
[288]Minimising processor communication in parallel approximate string matching (, , and ), In Technical Reports, . [bibtex]
[287]Computing all subtree repeats in ordered trees (, , , , , and ), In Information Processing Letters, volume 112, . [bibtex]
[286]Quasiperiodicities in Fibonacci strings (, and ), In Local Proceedings of International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2012), . [bibtex]
[285]New and efficient approaches to the quasiperiodic characterisation of a string (, , , , , and ), In Proceedings of the Prague Stringology Conference (PSC 2012), . [bibtex]
[284]Overlapping Repetitions in Weighted Sequence (, , and ), In Proceedings of the CUBE International Information Technology Conference, . [bibtex]
[283]Querying Highly Similar Structured Sequences via Binary Encoding and Word Level Operations (, , and ), In Artificial Intelligence Applications and Innovations (Iliadis, Lazaros, Maglogiannis, Ilias, Papadopoulos, Harris, Karatzas, Kostas, Sioutas, Spyros, eds.), Springer Berlin Heidelberg, volume 382, . [bibtex]
[282]GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures (, , and ), Chapter in Artificial Intelligence Applications and Innovations (Iliadis, Lazaros, Maglogiannis, Ilias, Papadopoulos, Harris, Karatzas, Kostas, Sioutas, Spyros, eds.), Springer Berlin Heidelberg, volume 382, . [bibtex]
[281]Conceptualization, Significance Study Of a New Application CS-MIR (, , and ), Chapter in Artificial Intelligence Applications and Innovations (Iliadis, Lazaros, Maglogiannis, Ilias, Papadopoulos, Harris, Karatzas, Kostas, Sioutas, Spyros, eds.), Springer Berlin Heidelberg, volume 381, . [bibtex]
[280]Computing the Minimum lambda-Cover in Weighted Sequences (, and ), In ICIC (1) (De-Shuang Huang, Changjun Jiang, Vitoantonio Bevilacqua, Juan Carlos Figueroa Garcia, eds.), Springer, volume 7389, . [bibtex]
[279]Tree template matching in ranked ordered trees by pushdown automata (, , , and ), In Journal of Discrete Algorithms, volume 17, . [bibtex]
[278]Improved Algorithms for the Range Next Value Problem and Applications (, , , , and ), In Theoretical Computer Science, Elsevier, volume 434, . [bibtex]
[277]Parallel algorithms for mapping short degenerate and weighted sequences to a reference genome (, and ), In International Journal of Foundations of Computer Science, volume 23, . [bibtex]
[276]Identifying All Abelian Periods Of A String In Quadratic Time And Relevant Problems (, and ), In International Journal of foundations of Computer Science, volume 23, . [bibtex]
[275]On left and right seeds of a string (, , , and ), In Journal of Discrete Algorithms, Elsevier, volume 17, . [bibtex]
[274]Mapping short reads to a genomic sequence with circular structure (, , and ), In International Journal of Systems Biology and Biomedical Technologies, IGI Global, volume 1, . [bibtex]
[273]Exact and approximate rhythm matching algorithms (, , and ), In International Journal on Digital Libraries, Springer, volume 12, . [bibtex]
[272]Detection of fixed length web spambot using REAL (read aligner) (, , , and ), In Proceedings of the CUBE International Information Technology Conference, ACM, . [bibtex]
[271]Efficient algorithms for three variants of the LPF table (, , , and ), In Journal of Discrete Algorithms, volume 11, . [bibtex]
[270]Locating Tandem Repeats in Weighted Biological Sequences (, and ), In ICIC (3) (De-Shuang Huang, Phalguni Gupta, Xiang Zhang, Prashan Premaratne, eds.), Springer, volume 304, . [bibtex]
[269]The Maximum Number of Squares in a Tree (, , , , , , and ), In CPM (Juha Kärkkäinen, Jens Stoye, eds.), Springer, volume 7354, . [bibtex]
[268]Efficient seed computation revisited (, , , , , , , and ), In Theoretical Computer Science, . [bibtex] [doi]
[267]Exact and approximate rhythm matching algorithms (, , and ), In International Journal on Digital Libraries, Springer-Verlag, volume 12, . [bibtex] [doi]
[266]Morphological Anlysis and generation for arabic language ( and ), In International Journal of Wireless Information Networks & Business Information System, volume May/June, . [bibtex]
[265]Melodic String Matching via Interval Consolidation and Fragmentation (, , and ), In Artificial Intelligence Applications and Innovations, volume 382, . [bibtex]
[264]On the repetitive collection indexing problem (, and ), In 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, IEEE Computer Society, volume 0, . [bibtex]
[263]Efficient seed computation revisited (, , , , , , , and ), In Proceedings of the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), Springer, volume 6661, . [bibtex]
[262]Approximate string-matching with a single gap for sequence alignment (, , , , and ), In Proceedings of the 2nd ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), ACM, . [bibtex]
[261]DynMap : mapping short reads to multiple related genomes (, and ), In Proceedings of the 2nd ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), ACM, . [bibtex]
[260]Computing All Subtree Repeats in Ordered Ranked Trees (, , , , , and ), In String Processing and Information Retrieval (Roberto Grossi, Fabrizio Sebastiani, Fabrizio Silvestri, eds.), Springer Berlin / Heidelberg, volume 7024, . [bibtex]
[259]Construction of Antimagic Labeling for the Cartesian Product of Regular Graphs (, , , and ), In Mathematics in Computer Science, Springer, volume 5, . [bibtex]
[258]An algorithm for mapping short reads to a dynamically changing genomic sequence (, , , , and ), In Journal of Discrete Algorithms, Elsevier, volume 10, . [bibtex]
[257]On the Maximal Number of Cubic Runs in a String (, , , , and ), In Journal of Computer and System Sciences, Elsevier, . [bibtex]
[256]Combinatorial Algorithms - 21st International Workshop, IWOCA 2010, London, UK, July 26-28, 2010, Revised Selected Papers, (Costas S. Iliopoulos, William F. Smyth, eds.), Springer, volume 6460, . [bibtex]
[255]New Complexity Results for the k-Covers Problem (, and ), In International Journal of Information Sciences, Elsevier, volume 181, . [bibtex]
[254]Tree Indexing by Pushdown Automata and Repeats of Subtrees (, , , and ), In FedCSIS, . [bibtex]
[253]On the right-seed array of a string (, , , and ), In Proceedings of the 17th Annual International Conference on Computing and Combinatorics, Springer-Verlag, . [bibtex]
[252]Tree template matching in ranked ordered trees by pushdown automata (, , , and ), In Proceedings of the 16th international conference on Implementation and application of automata, Springer-Verlag, . [bibtex]
[251]Transcriptome map of mouse isochores (, , , , and ), In BMC Genomics, volume 12, . [bibtex] [doi]
[250]A Note on a priori Estimations of Classification Circuit Complexity (, , , and ), In Fundamenta Informaticae, volume 104, . [bibtex]
[249]Sub-nyquist audio fingerprinting for music recognition (, , and ), In Computer Science and Electronic Engineering Conference (CEEC), 2010 2nd, . [bibtex] [doi]
[248]Recent Advances in Weighted DNA Sequences ( and ), Chapter in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (Mourad Elloumi, Albert Y. Zomaya, eds.), Wiley, . [bibtex] [doi]
[247]A Combinatorial Model for ECG Interpretation ( and ), In International Journal of Biological and Life Sciences (Cemal Ardil, ed.), World Academy of Science, Engineering and Technology, volume 2, . [bibtex]
[246]Advances in Combinatorial Algorithms II (), In Special issue of Mathematics in Computer Science, Birkhauser/Springer, volume 3, . [bibtex]
[245]New developments in processing of degenerate sequences ( and ), Chapter in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (Mourad Elloumi, Albert Y. Zomaya, eds.), Wiley, . [bibtex] [doi]
[244]Algorithms for three versions of the shortest common superstring problem (, , , , , and ), In Proceedings of the 21st Annual Conference on Combinatorial pattern matching, Springer-Verlag, . [bibtex]
[243]Cover array string reconstruction (, , and ), In Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching (CPM 2010), Springer, volume 6129, . [bibtex]
[242]A Fast and Efficient Algorithm for Mapping Short Sequences to a Reference Genome (, , and ), Chapter in Advances in Computational Biology (Hamid R. Arabnia, ed.), Springer New York, volume 680, . [bibtex]
[241]Extracting powers and periods in a string from its runs structure (, , , , and ), In Proceedings of the 17th international conference on String processing and information retrieval, Springer-Verlag, . [bibtex]
[240]Efficient Algorithms for Two Extensions of LPF Table: The Power of Suffix Arrays (, , , and ), In SOFSEM 2010: Theory and Practice of Computer Science (Jan van Leeuwen, Anca Muscholl, David Peleg, Jaroslav Pokorný, Bernhard Rumpe, eds.), Springer Berlin / Heidelberg, volume 5901, . [bibtex]
[239]Loose and Strict Repeats in Weighted Sequences of Proteins (, , and ), In Protein and Peptide Letters, Bentham Science Publishers, volume 17, . [bibtex]
[238]A Parallel Algorithm for the Fixed-length Approximate String Matching Problem for High Throughput Sequencing Technologies (), In Proceedings of the International Conference on Parallel Computing (PARCO 2009), IOS Press, volume 19, . [bibtex]
[237]Combinatorial ECG analysis for mobile devices ( and ), In Proceedings of the international conference on Multimedia information retrieval, ACM, . [bibtex]
[236]A Parallel Algorithm for Fixed-length Approximate String Matching with k-mismatches (, and ), In Algorithms and Applications, Springer-Verlag, volume 6060, . [bibtex]
[235]On the Maximal Number of Cubic Runs in a String (, , , , and ), In Language and Automata Theory and Applications (Adrian-Horia Dediu, Henning Fernau, Carlos Martín-Vide, eds.), Springer Berlin / Heidelberg, volume 6031, . [bibtex]
[234]Finite Automata Based Algorithms on Subsequences and Supersequences of Degenerate Strings (, , and ), In Journal of Discrete Algorithms, volume 8, . [bibtex]
[233]Mapping short reads to a genomic sequence with circular structure (, , and ), In Proceedings of the 10th IEEE Internation Conference on Information Technology and Applications in Biomedicine (ITAB 2010), . [bibtex]
[232]Music genre classification via compressive sampling (, and ), In Proceedings of the Eleventh International Society for Music Information Retrieval Conference (ISMIR 2010) (J. Stephen Downie, Remco C. Veltkamp, eds.), . [bibtex]
[231]Number of Occurrences of powers in Strings (, , and ), In Int. J. Found. Comput. Sci., volume 21, . [bibtex]
[230]Algorithms for mapping short degenerate and weighted sequences to a reference genome (, , and ), In Internation Journal of Computational Biology and Drug Design, volume 2, . [bibtex]
[229]Finding patterns in given intervals (, , , and ), In Fundamenta Informaticae, IOS Press, volume 101, . [bibtex]
[228]An Algorithmic Framework for Motif Discovery Problems in Weighted Sequences (, and ), In Algorithms and Complexity (Tiziana Calamoneri, Josep Diaz, eds.), Springer Berlin / Heidelberg, volume 6078, . [bibtex]
[227]Varieties of Regularities in Weighted Sequences (, and ), In Algorithmic Aspects in Information and Management (Bo Chen, ed.), Springer Berlin / Heidelberg, volume 6124, . [bibtex]
[226]Combinatorial detection of arrhythmia (, , and ), In Proceedings of the 3rd International Conference on Bio-inspired Systems and Signal Processing (BIOSIGNALS 2010), . [bibtex]
[225]An algorithm for mapping short reads to a dynamically changing genomic sequence (, , and ), In Proceedings of the International Conference on Bioinformatics & Biomedicine (BIBM 2010), . [bibtex]
[224]REAL: An efficient REad ALigner for next generation sequencing reads (, , , and ), In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010), . [bibtex]
[223]String Algorithms: Dedicated to Professor Maxime Crochemore on the occasion of his 60th birthday, (Costas S. Iliopoulos, Wojciech Rytter, eds.), Elsevier, . [bibtex]
[222]LPF computation revisited (, , , , and ), In Proceedings of the International Workshop on Combinatorial Algorithms (IWOCA 2009) (J. Fiala, J. Kratochvil, M. Miller, eds.), Springer, volume 5874, . [bibtex]
[221]A Combinatorial Model for ECG Interpretation (), In Proceedings of the International Conference on Medical Informatics and Biomedical Engineering (ICMIBE 2009) (Cemal Ardil, ed.), World Academy of Science, Engineering and Technology, . [bibtex]
[220]Overlay Problems for Music and Combinatorics (), In Proceedings of the International Conference on Auditory Display / Computer Music Modeling and Retrieval (ICAD/CMMR 2009) (Mitsuko Aramaki, Richard Kronland-Martinet, Solvi Ystad, Kristoffer Jensen, eds.), Re:New - Digital Arts Forum, . [bibtex]
[219]On the maximal number of highly periodic runs in a string (, , , , and ), In CoRR, volume abs/0907.2157, . [bibtex]
[218]Parallel algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies (), In Proceedings of the Prague Stringology Conference (PSC 2009) (Jan Holub, Jan Zdarek, eds.), . [bibtex]
[217]Mapping uniquely occuring short sequences derived from high throughput technologies to a reference genome (, , , , and ), In Proceedings of the 9th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2009), . [bibtex] [doi]
[216]Faster Algorithms for Computing Maximal Multirepeats in Multiple Sequences (), In Fundamenta Informaticae, volume , . [bibtex]
[215]Algorithms for two versions of LCS problem for indeterminate strings (, and ), In Journal of Combinatorial Mathematics and Combinatorial Computing, volume 71, . [bibtex]
[214]Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies (), In Proceedings of the Bioinformatics, Systems Biology and Intelligent Computing, International Joint Conference (IJCBS 2009), . [bibtex]
[213]On Diregularity of Digraphs of Defect at Most Two (, and ), In Journal of Combinatorial Mathematics and Combinatorial Computing, volume 71, . [bibtex]
[212]Bounds on powers in strings (, , and ), In International Conference on Developments in Language Theory (DLT'09) (Ito, Masami, Toyama, Masafumi, eds.), Springer-Verlag, volume 5257, . [bibtex]
[211]Toward a General Framework for Polyphonic Comparison (, , , and ), In Fundamenta Informaticae, volume 97, . [bibtex]
[210]Efficient ($\delta$, $\gamma$)-pattern-matching with don't cares (, , and ), In Journal of Combinatorial Mathematics and Combinatorial Computing, volume 70, . [bibtex]
[209]Validation and Decomposition of Partially Occluded Images with Holes (), In Proceedings of the Prague Stringology Conference (PSC 2009) (Jan Holub, Jan Zdarek, eds.), . [bibtex]
[208]Computing Repetitive Structures in Indeterminate Strings (, , and ), In Proceedings of the 3rd IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008), . [bibtex]
[207]Conservative string covering of indeterminate strings (, , , and ), In Proceedings of the 13th Prague Stringology Conference (PSC 2008) (Jan Holub, Jan Zdarek, eds.), Czech Technical University, . [bibtex]
[206]Erratic Dancing (, , and ), In Proceedings of the 5th International Symposium on Computer Music Modeling and Retrieval (CMMR 2008) (Kristoffer Jensen, ed.), Re:New - Digital Arts Forum, . [bibtex]
[205]Indexing Circular Patterns ( and ), In Proceedings of the Workshop on Algorithms and Computation, . [bibtex]
[204]A New Model to Solve Swap Matching Problem and Efficient Algorithms for Short Patterns ( and ), In Proceedings of the 34th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM '08), . [bibtex]
[203]Identifying Rhythms in Musical Texts (, , and ), In International Journal of Foundations of Computer Science, volume 19, . [bibtex]
[202]Special Issue of the Sixteenth Australasian Workshop on Combinatorial Algorithms (AWOCA 2005) September 18-21, 2005, Ballarat, Australia ( and ), In Journal of Discrete Algorithms, volume 6, . [bibtex]
[201]New efficient algorithms for the LCS and constrained LCS problems ( and ), In Information Processing Letters, volume 106, . [bibtex]
[200]Faster index for property matching ( and ), In Information Processing Letters, volume 105, . [bibtex]
[199]Algorithms for computing variants of the longest common subsequence problem ( and ), In Theoretical Computer Science, volume 395, . [bibtex]
[198]A New Approach to Pattern Matching in Degenerate DNA/RNA Sequences and Distributed Pattern Matching (, and ), In Mathematics in Computer Science, volume 1, . [bibtex]
[197]Generalized approximate regularities in strings (, and ), In International Journal of Computer Mathematics, volume 85, . [bibtex]
[196]Algorithms for Computing the $\lambda$-regularities in Strings (, and ), In Fundamenta Informaticae, volume 84, . [bibtex]
[195]Indexing Factors in DNA/RNA Sequences (, , , and ), In Bioinformatics Research and Development, . [bibtex]
[194]Optimal prefix and suffix queries on texts (, and ), In Information Processing Letters, Elsevier North-Holland, Inc., volume 108, . [bibtex] [doi]
[193]External memory algorithms for string problems (, , and ), In Fundamenta Informaticae, volume 84, . [bibtex]
[192]Necklace Swap Problem for Rhythmic Similarity Measures (, , , and ), In International Journal of Computational Methods, volume 5, . [bibtex]
[191]Improved algorithms for the range next value problem and applications (, , , and ), In International Symposium on Theoretical Aspects of Computer Science (STACS'08) (S. Albers, P. Weil, eds.), IBFI Schloss Dagstuhl, . [bibtex]
[190]Implementation of a Swap Matching Algorithm Using a Graph Theoretic Model (, , and ), In Bioinformatics Research and Development, . [bibtex]
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