Solon P. Pissis

  Senior Lecturer in Computer Science

  Department of Informatics

  King's College London

Publications

2018
[127]	T. Kociumaka, S. P. Pissis, J. Radoszewski, "Pattern Matching and Consensus Problems on Weighted Sequences and Profiles", Theory of Computing Systems, Aug 2018. [bibtex] [pdf] [doi]
[126]	J. A. Carricco, M. Crochemore, A. P. Francisco, S. P. Pissis, B. Ribeiro-Gonccalves, C. Vaz, "Fast phylogenetic inference from typing data", Algorithms for Molecular Biology, vol. 13, no. 1, Feb 2018, pp. 4. [bibtex] [doi]
[125]	S. P. Pissis, A. Retha, "Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line", in 17th International Symposium on Experimental Algorithms (SEA 2018), G. D'Angelo, Ed., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 16:1–16:14. [bibtex] [pdf] [doi]
[124]	T. Kociumaka, R. Kundu, M. Mohamed, S. P. Pissis, "Longest Unbordered Factor in Quasilinear Time", in 29th International Symposium on Algorithms and Computation (ISAAC 2018), W. Hsu, D. Lee, C. Liao, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 70:1–70:13. [bibtex] [pdf] [doi]
[123]	L. A. K. Ayad, S. P. Pissis, D. Polychronopoulos, "CNEFinder: finding conserved non-coding elements in genomes", Bioinformatics, vol. 34, no. 17, 2018, pp. i743-i747. [bibtex] [pdf] [doi]
[122]	P. Charalampopoulos, M. Crochemore, C. S. Iliopoulos, T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Linear-Time Algorithm for Long LCF with k Mismatches", in Annual Symposium on Combinatorial Pattern Matching (CPM 2018), G. Navarro, D. Sankoff, B. Zhu, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 23:1–23:16. [bibtex] [doi]
[121]	M. Alzamel, L. A. K. Ayad, G. Bernardini, R. Grossi, C. S. Iliopoulos, N. Pisanti, S. P. Pissis, G. Rosone, "Degenerate String Comparison and Applications", in 18th International Workshop on Algorithms in Bioinformatics (WABI 2018), L. Parida, E. Ukkonen, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 21:1–21:14. [bibtex] [pdf] [doi]
[120]	P. Charalampopoulos, M. Crochemore, C. S. Iliopoulos, T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Efficient Enumeration of Non-Equivalent Squares in Partial Words with Few Holes", Journal of Combinatorial Optimization, 2018. [bibtex] [doi]
[119]	T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Efficient algorithms for shortest partial seeds in words", Theor. Comput. Sci., vol. 710, 2018, pp. 139–147. [bibtex] [doi]
[118]	M. Crochemore, S. P. Pissis, "Advances in Algorithms & Combinatorics on Strings (Honoring 60th birthday for Prof. Costas S. Iliopoulos)", Theor. Comput. Sci., vol. 710, 2018, pp. 1. [bibtex] [doi]
[117]	P. Charalampopoulos, M. Crochemore, S. P. Pissis, "Preface", Fundam. Inform., vol. 163, no. 3, 2018, pp. i. [bibtex] [doi]
[116]	C. Barton, S. P. Pissis, "Crochemore's Partitioning on Weighted Strings and Applications", Algorithmica, vol. 80, no. 2, 2018, pp. 496–514. [bibtex] [doi]
[115]	C. S. Iliopoulos, M. Mohamed, S. P. Pissis, F. Vayani, "Maximal Motif Discovery in a Sliding Window", in SPIRE, Springer, 2018, pp. 191–205. [bibtex] [doi]
[114]	P. Charalampopoulos, M. Crochemore, S. P. Pissis, "On Extended Special Factors of a Word", in SPIRE, Springer, 2018, pp. 131–138. [bibtex] [doi]
[113]	L. A. K. Ayad, G. Bernardini, R. Grossi, C. S. Iliopoulos, N. Pisanti, S. P. Pissis, G. Rosone, "Longest Property-Preserved Common Factor", in SPIRE, Springer, 2018, pp. 42–49. [bibtex] [doi]
[112]	L. A. K. Ayad, C. Barton, P. Charalampopoulos, C. S. Iliopoulos, S. P. Pissis, "Longest Common Prefixes with k-Errors and Applications", in SPIRE, Springer, 2018, pp. 27–41. [bibtex] [doi]
[111]	M. Alzamel, P. Charalampopoulos, C. S. Iliopoulos, T. Kociumaka, S. P. Pissis, J. Radoszewski, J. Straszynski, "Efficient Computation of Sequence Mappability", in SPIRE, Springer, 2018, pp. 12–26. [bibtex] [doi]
[110]	P. Charalampopoulos, M. Crochemore, G. Fici, R. Mercaş, S. P. Pissis, "Alignment-free sequence comparison using absent words", Information and Computation, vol. 262, 2018, pp. 57–68. [bibtex] [pdf] [doi]
[109]	H. Alamro, L. A. K. Ayad, P. Charalampopoulos, C. S. Iliopoulos, S. P. Pissis, "Longest Common Prefixes with k-Mismatches and Applications", in SOFSEM 2018: Theory and Practice of Computer Science: 44th International Conference on Current Trends in Theory and Practice of Computer Science, Krems, Austria, January 29 - February 2, 2018, Proceedings, A. M. Tjoa et al., Eds., Cham: Springer International Publishing, pp. 636–649. [bibtex] [doi]
[108]	M. Alzamel, P. Charalampopoulos, C. S. Iliopoulos, S. P. Pissis, "How to Answer a Small Batch of RMQs or LCA Queries in Practice", in Combinatorial Algorithms, L. Brankovic, J. Ryan, W. F. Smyth, Eds., Cham: Springer International Publishing, 2018, pp. 343–355. [bibtex] [doi]
[107]	P. Charalampopoulos, C. S. Iliopoulos, C. Liu, S. P. Pissis, "Property Suffix Array with Applications", in LATIN 2018: Theoretical Informatics, M. A. Bender, M. Farach-Colton, M. A. Mosteiro, Eds., Cham: Springer International Publishing, pp. 290–302. [bibtex] [doi]
2017
[106]	I. Fontana, G. Giacalone, A. Bonanno, S. Mazzola, G. Basilone, S. Genovese, S. Aronica, S. Pissis, C. S. Iliopoulos, R. Kundu, A. Fiannaca, A. Langiu, G. Lo Bosco, M. La Rosa, R. Rizzo, "Pelagic species identification by using a PNN neural network and echo-sounder data", in Artificial Neural Networks and Machine Learning – ICANN 2017 - 26th International Conference on Artificial Neural Networks, Proceedings, Germany: Springer Verlag, pp. 454–455. [bibtex] [pdf]
[105]	R. Grossi, C. S. Iliopoulos, C. Liu, N. Pisanti, S. P. Pissis, A. Retha, G. Rosone, F. Vayani, L. Versari, "On-Line Pattern Matching on Similar Texts", in 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017), J. R. Juha Kärkkäinen, W. Rytter, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 9:1–9:14. [bibtex] [pdf] [doi]
[104]	A. Heliou, S. P. Pissis, S. J. Puglisi, "emMAW: computing minimal absent words in external memory", Bioinformatics, vol. 33, no. 17, 2017, pp. 2746-2749. [bibtex] [doi]
[103]	M. Crochemore, A. P. Francisco, S. P. Pissis, C. Vaz, "Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time", in 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), R. Schwartz, K. Reinert, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 9:1–9:14. [bibtex] [pdf] [doi]
[102]	Y. Almirantis, P. Charalampopoulos, J. Gao, C. S. Iliopoulos, M. Mohamed, S. P. Pissis, D. Polychronopoulos, "Optimal Computation of Overabundant Words", in 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), R. Schwartz, K. Reinert, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 4:1–4:14. [bibtex] [pdf] [doi]
[101]	L. A. K. Ayad, C. Barton, S. P. Pissis, "A faster and more accurate heuristic for cyclic edit distance computation", Pattern Recognition Letters, vol. 88, 2017, pp. 81–87. [bibtex] [doi]
[100]	C. S. Iliopoulos, R. Kundu, S. P. Pissis, "Efficient Pattern Matching in Elastic-Degenerate Texts", in Language and Automata Theory and Applications: 11th International Conference, LATA 2017, Umeå, Sweden, March 6-9, 2017, Proceedings, F. Drewes, C. Martín-Vide, B. Truthe, Eds., Cham: Springer International Publishing, pp. 131–142. [bibtex] [doi]
[99]	C. S. Iliopoulos, S. P. Pissis, M. S. Rahman, Searching and Indexing Circular Patterns, Cham: Springer International Publishing, 2017, pp. 77–90. [bibtex] [doi]
[98]	T. Athar, C. Barton, W. Bland, J. Gao, C. S. Iliopoulos, C. Liu, S. P. Pissis, "Fast circular dictionary-matching algorithm", Mathematical Structures in Computer Science, vol. 27, no. 2, 2017, pp. 143–156. [bibtex] [doi]
[97]	C. S. Iliopoulos et al., Eds., 16th International Symposium on Experimental Algorithms, SEA 2017, June 21-23, 2017, London, UK, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik. [bibtex] [pdf]
[96]	M. Crochemore, A. Heliou, G. Kucherov, L. Mouchard, S. P. Pissis, Y. Ramusat, "Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching", in Fundamentals of Computation Theory: 21st International Symposium, FCT 2017, Bordeaux, France, September 11–13, 2017, Proceedings, R. Klasing, M. Zeitoun, Eds., Berlin, Heidelberg: Springer Berlin Heidelberg, 2017, pp. 164–176. [bibtex] [doi]
[95]	P. Charalampopoulos, M. Crochemore, C. S. Iliopoulos, T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Efficient Enumeration of Non-Equivalent Squares in Partial Words with Few Holes", in Computing and Combinatorics: 23rd International Conference, COCOON 2017, Hong Kong, China, August 3-5, 2017, Proceedings, Y. Cao, J. Chen, Eds., Cham: Springer International Publishing, pp. 99–111. [bibtex] [doi]
[94]	M. Alzamel, P. Charalampopoulos, C. S. Iliopoulos, S. P. Pissis, J. Radoszewski, W. Sung, "Faster Algorithms for 1-Mappability of a Sequence", in Combinatorial Optimization and Applications: 11th International Conference, COCOA 2017, Shanghai, China, December 16-18, 2017, Proceedings, Part II, X. Gao, H. Du, M. Han, Eds., Cham: Springer International Publishing, pp. 109–121. [bibtex] [doi]
[93]	G. Bernardini, N. Pisanti, S. P. Pissis, G. Rosone, "Pattern Matching on Elastic-Degenerate Text with Errors", in String Processing and Information Retrieval: 24th International Symposium, SPIRE 2017, Palermo, Italy, September 26–29, 2017, Proceedings, G. Fici, M. Sciortino, R. Venturini, Eds., Cham: Springer International Publishing, pp. 74–90. [bibtex] [doi]
[92]	L. A. K. Ayad, S. P. Pissis, "MARS: improving multiple circular sequence alignment using refined sequences", BMC Genomics, vol. 18, no. 1, 2017, pp. 86. [bibtex] [doi]
[91]	A. Amir, P. Charalampopoulos, C. S. Iliopoulos, S. P. Pissis, J. Radoszewski, "Longest Common Factor After One Edit Operation", in String Processing and Information Retrieval: 24th International Symposium, SPIRE 2017, Palermo, Italy, September 26–29, 2017, Proceedings, G. Fici, M. Sciortino, R. Venturini, Eds., Cham: Springer International Publishing, pp. 14–26. [bibtex] [doi]
[90]	M. Alzamel, J. Gao, C. S. Iliopoulos, C. Liu, S. P. Pissis, "Efficient Computation of Palindromes in Sequences with Uncertainties", in Engineering Applications of Neural Networks: 18th International Conference, EANN 2017, Athens, Greece, August 25–27, 2017, Proceedings, G. Boracchi et al., Eds., Cham: Springer International Publishing, 2017, pp. 620–629. [bibtex] [doi]
[89]	H. Alamro, M. Alzamel, C. S. Iliopoulos, S. P. Pissis, S. Watts, W. Sung, "Efficient Identification of k-Closed Strings", in Engineering Applications of Neural Networks: 18th International Conference, EANN 2017, Athens, Greece, August 25–27, 2017, Proceedings, G. Boracchi et al., Eds., Cham: Springer International Publishing, 2017, pp. 583–595. [bibtex] [doi]
[88]	Y. Almirantis, P. Charalampopoulos, J. Gao, C. S. Iliopoulos, M. Mohamed, S. P. Pissis, D. Polychronopoulos, "On avoided words, absent words, and their application to biological sequence analysis", Algorithms for Molecular Biology, vol. 12, no. 1, 2017, pp. 5. [bibtex] [doi]
2016
[87]	C. Barton, T. Flouri, C. S. Iliopoulos, S. P. Pissis, "Global Sequence Alignment with a Bounded Number of Gaps", in Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, M. Elloumi et al., Eds., Wiley, 2016, pp. 83–96. [bibtex] [pdf]
[86]	T. Kociumaka, S. P. Pissis, J. Radoszewski, "Pattern Matching and Consensus Problems on Weighted Sequences and Profiles", in 27th International Symposium on Algorithms and Computation (ISAAC 2016), S. Hong, Ed., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 46:1–46:12. [bibtex] [doi]
[85]	C. Barton, T. Kociumaka, S. P. Pissis, J. Radoszewski, "Efficient Index for Weighted Sequences", in 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), R. Grossi, M. Lewenstein, Eds., Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, pp. 4:1–4:13. [bibtex] [doi]
[84]	M. Crochemore, C. S. Iliopoulos, T. Kociumaka, M. Kubica, A. Langiu, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Order-Preserving Indexing", Theoretical Computer Science, vol. 638, 2016, pp. 122–135. [bibtex] [doi]
[83]	M. Crochemore, C. S. Iliopoulos, T. Kociumaka, R. Kundu, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Near-Optimal Computation of Runs over General Alphabet via Non-Crossing LCE Queries", in String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings, S. Inenaga, K. Sadakane, T. Sakai, Eds., Cham: Springer International Publishing, 2016, pp. 22–34. [bibtex] [doi]
[82]	C. Barton, C. S. Iliopoulos, S. P. Pissis, S. Arhondakis, "Transcriptome activity of isochores during pre-implantation process in human and mouse", FEBS Letters, vol. 590, no. 14, 2016, pp. 2297–2306. [bibtex] [doi]
[81]	L. A. K. Ayad, S. P. Pissis, A. Retha, "libFLASM: a software library for fixed-length approximate string matching", BMC Bioinformatics, vol. 17, 2016, pp. 454:1–454:12. [bibtex] [doi]
[80]	R. Grossi, C. S. Iliopoulos, R. Mercas, N. Pisanti, S. P. Pissis, A. Retha, F. Vayani, "Circular sequence comparison: algorithms and applications", Algorithms for Molecular Biology, vol. 11, 2016, pp. 12. [bibtex] [doi]
[79]	M. Crochemore, G. Fici, R. Mercas, S. P. Pissis, "Linear-Time Sequence Comparison Using Minimal Absent Words and Applications", in LATIN 2016: Theoretical Informatics: 12th Latin American Symposium, Ensenada, Mexico, April 11-15, 2016, Proceedings, E. Kranakis, G. Navarro, E. Chávez, Eds., Springer Berlin Heidelberg, 2016, pp. 334–346. [bibtex] [doi]
[78]	C. Barton, C. Liu, S. P. Pissis, "On-Line Pattern Matching on Uncertain Sequences and Applications", in Combinatorial Optimization and Applications: 10th International Conference, COCOA 2016, Hong Kong, China, December 16–18, 2016, Proceedings, T. H. Chan, M. Li, L. Wang, Eds., Cham: Springer International Publishing, 2016, pp. 547–562. [bibtex] [doi]
[77]	L. Brankovic, C. S. Iliopoulos, R. Kundu, M. Mohamed, S. P. Pissis, F. Vayani, "Linear-time superbubble identification algorithm for genome assembly", Theoretical Computer Science, vol. 609, Part 2, 2016, pp. 374–383. [bibtex] [doi]
[76]	C. Barton, C. Liu, S. P. Pissis, "Linear-time computation of prefix table for weighted strings and applications", Theoretical Computer Science, vol. 656, Part B, 2016, pp. 160–172. [bibtex] [doi]
[75]	Y. Almirantis, P. Charalampopoulos, J. Gao, C. S. Iliopoulos, M. Mohamed, S. P. Pissis, D. Polychronopoulos, "Optimal Computation of Avoided Words", in Algorithms in Bioinformatics: 16th International Workshop, WABI 2016, Aarhus, Denmark, August 22-24, 2016. Proceedings, M. Frith, N. C. Storm Pedersen, Eds., Springer International Publishing, 2016, pp. 1–13. [bibtex] [doi]
2015
[74]	S. P. Pissis, A. Retha, "Generalised Implementation for Fixed-Length Approximate String Matching under Hamming Distance and Applications", in 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, IPDPS 2015, Hyderabad, India, May 25-29, 2015, IEEE, pp. 367–374. [bibtex] [doi]
[73]	T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Fast Algorithm for Partial Covers in Words", Algorithmica, vol. 73, no. 1, 2015, pp. 217–233. [bibtex] [doi]
[72]	C. Barton, S. P. Pissis, "Linear-Time Computation of Prefix Table for Weighted Strings", in Combinatorics on Words, F. Manea, D. Nowotka, Eds., Springer International Publishing, 2015, pp. 73–84. [bibtex] [doi]
[71]	R. Grossi, C. S. Iliopoulos, R. Mercas, N. Pisanti, S. P. Pissis, A. Retha, F. Vayani, "Circular Sequence Comparison with q-grams", in Algorithms in Bioinformatics, M. Pop, H. Touzet, Eds., Springer Berlin Heidelberg, 2015, pp. 203–216. [bibtex] [doi]
[70]	C. Barton, T. Flouri, C. S. Iliopoulos, S. P. Pissis, "Global and local sequence alignment with a bounded number of gaps", Theoretical Computer Science, vol. 582, 2015, pp. 1–16. [bibtex] [doi]
[69]	C. Barton, C. S. Iliopoulos, R. Kundu, S. P. Pissis, A. Retha, F. Vayani, "Accurate and efficient methods to improve multiple circular sequence alignment", in Experimental Algorithms, E. Bampis, Ed., Springer International Publishing Switzerland, 2015, pp. 247–258. [bibtex] [doi]
[68]	C. Barton, A. Heliou, L. Mouchard, S. P. Pissis, "Parallelising the Computation of Minimal Absent Words", in Parallel Processing and Applied Mathematics - 11th International Conference, PPAM 2015, Krakow, Poland, September 6-9, 2015. Revised Selected Papers, Part II, R. Wyrzykowski et al., Eds., Springer, 2015, pp. 243–253. [bibtex] [doi]
[67]	M. Aljamea, T. Athar, C. S. Iliopoulos, S. P. Pissis, M. S. Rahman, "A Novel Pattern Matching Approach for Fingerprint-based Authentication", in PATTERNS 2015: The Seventh International Conferences on Pervasive Patterns and Applications, IARIA, pp. 45–49. [bibtex]
[66]	C. Barton, C. S. Iliopoulos, S. P. Pissis, "Average-Case Optimal Approximate Circular String Matching", in Language and Automata Theory and Applications, A. Dediu et al., Eds., Springer Berlin Heidelberg, 2015, pp. 85–96. [bibtex] [doi]
[65]	C. Barton, C. S. Iliopoulos, S. P. Pissis, W. F. Smyth, "Fast and Simple Computations Using Prefix Tables Under Hamming and Edit Distance", in Combinatorial Algorithms, K. Jan, M. Miller, D. Froncek, Eds., Springer International Publishing, 2015, pp. 49–61. [bibtex] [doi]
[64]	H. Bannai, S. P. Pissis, "Editorial", Journal of Discrete Algorithms, vol. 34, 2015, pp. 1. [bibtex] [doi]
2014
[63]	V. Ghanaei, C. S. Iliopoulos, S. P. Pissis, "Detection of Web Spambot in the Presence of Decoy Actions", in Big Data and Cloud Computing (BdCloud), 2014 IEEE Fourth International Conference on, pp. 277–279. [bibtex] [doi]
[62]	T. Flouri, K. Kobert, S. P. Pissis, A. Stamatakis, "An optimal algorithm for computing all subtree repeats in trees", Philosophical Transactions A, vol. 372, no. 2016, 2014. [bibtex] [doi]
[61]	S. P. Pissis, C. Goll, P. Pavlidis, A. Stamatakis, "Accelerating String Matching on MIC Architecture for Motif Extraction", in Parallel Processing and Applied Mathematics, R. Wyrzykowski et al., Eds., Springer Berlin Heidelberg, 2014, pp. 258–267. [bibtex] [doi]
[60]	S. P. Pissis, "MoTeX-II: structured MoTif eXtraction from large-scale datasets", BMC Bioinformatics, vol. 15, 2014, pp. 235. [bibtex] [doi]
[59]	C. Barton, A. Heliou, L. Mouchard, S. P. Pissis, "Linear-time Computation of Minimal Absent Words Using Suffix Array", BMC Bioinformatics, vol. 15, 2014, pp. 388. [bibtex] [doi]
[58]	C. Barton, S. P. Pissis, "Optimal computation of all repetitions in a weighted string", in International Conference on Algorithms for Big Data (ICABD2014), C. S. Iliopoulos, A. Langiu, Eds., pp. 9-15. [bibtex] [pdf]
[57]	T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Efficient Algorithms for Shortest Partial Seeds in Words", in Combinatorial Pattern Matching, A. S. Kulikov, S. O. Kuznetsov, P. Pevzner, Eds., Springer International Publishing, 2014, pp. 192-201. [bibtex] [doi]
[56]	C. Barton, C. S. Iliopoulos, I. Lee, L. Mouchard, K. Park, S. P. Pissis, "Extending alignments with $k$-mismatches and $\ell$-gaps", Theoretical Computer Science, vol. 525, 2014, pp. 80-88. [bibtex] [doi]
[55]	C. Barton, C. S. Iliopoulos, S. P. Pissis, "Optimal Computation of all Tandem Repeats in a Weighted Sequence", Algorithms for Molecular Biology, vol. 9, no. 21, 2014. [bibtex] [doi]
[54]	C. Barton, C. S. Iliopoulos, S. P. Pissis, "Fast Algorithms for Approximate Circular String Matching", Algorithms for Molecular Biology, vol. 9, no. 9, 2014. [bibtex] [doi]
2013
[53]	C. S. Iliopoulos, S. P. Pissis, "Algorithms for next-generation sequencing data", in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, M. Elloumi, A. Y. Zomaya, Eds., Wiley, 2013, pp. 251–279. [bibtex] [pdf]
[52]	Amborella~Genome~Project, "The Amborella Genome and the Evolution of Flowering Plants", Science, vol. 342, no. 6165, 2013. [bibtex] [doi]
[51]	T. Kociumaka, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Fast Algorithm for Partial Covers in Words", in Combinatorial Pattern Matching, J. Fischer, P. Sanders, Eds., Springer Berlin Heidelberg, 2013, pp. 177-188. [bibtex] [doi]
[50]	M. Crochemore, C. S. Iliopoulos, T. Kociumaka, M. Kubica, A. Langiu, S. P. Pissis, J. Radoszewski, W. Rytter, T. Walen, "Order-Preserving Incomplete Suffix Trees and Order-Preserving Indexes", in String Processing and Information Retrieval, O. Kurland, M. Lewenstein, E. Porat, Eds., Springer International Publishing, 2013, pp. 84-95. [bibtex] [doi]
[49]	N. Alachiotis, S. Berger, T. Flouri, S. P. Pissis, A. Stamatakis, "libgapmis: extending short-read alignments", BMC Bioinformatics, vol. 14, no. (Suppl 11), 2013, pp. S4. [bibtex] [doi]
[48]	S. P. Pissis, A. Stamatakis, P. Pavlidis, "MoTeX: A word-based HPC tool for MoTif eXtraction", in Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, New York, NY, USA: ACM, 2013, pp. 13–22. [bibtex] [doi]
[47]	C. S. Iliopoulos, S. P. Pissis, "Verifying an enhanced cover array in linear time", in Formal Aspects of Computing, Essays dedicated to Derrick Kourie on the occasion of his 65th birthday, S. Gruner, B. Watson, Eds., Shaker Verlag, 2013, pp. 111 - 123. [bibtex] [doi]
[46]	F. Izquierdo-Carrasco, N. Alachiotis, S. Berger, T. Flouri, S. P. Pissis, A. Stamatakis, "A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library", in Proceedings of the 2013 IEEE 27th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Washington, DC, USA: IEEE Computer Society, pp. 530–538. [bibtex] [doi]
[45]	T. Flouri, K. Kobert, S. P. Pissis, A. Stamatakis, "An Optimal Algorithm for Computing All Subtree Repeats in Trees", in Combinatorial Algorithms, T. Lecroq, L. Mouchard, Eds., Springer Berlin Heidelberg, 2013, pp. 269-282. [bibtex] [doi]
[44]	C. Barton, C. S. Iliopoulos, S. P. Pissis, "Circular string matching revisited", in Proceedings of the Fourteenth Italian Conference on Theoretical Computer Science (ICTCS 2013), pp. 200-205. [bibtex] [pdf]
[43]	T. Flouri, K. Frousios, C. S. Iliopoulos, K. Park, S. P. Pissis, G. Tischler, "GapMis: a tool for pairwise sequence alignment with a single gap", Recent Patents on DNA & Gene Sequences, vol. 7, no. 2, 2013, pp. 84 - 95. [bibtex] [doi]
[42]	K. Frousios, C. S. Iliopoulos, G. Tischler, S. Kossida, S. P. Pissis, S. Arhondakis, "Transcriptome map of mouse isochores in embryonic and neonatal cortex", Genomics, vol. 101, no. 2, 2013, pp. 120 - 124. [bibtex] [doi]
[41]	T. Flouri, C. S. Iliopoulos, T. Kociumaka, S. P. Pissis, S. J. Puglisi, W. Smyth, W. Tyczynski, "Enhanced string covering", Theoretical Computer Science, vol. 506, 2013, pp. 102 - 114. [bibtex] [doi]
[40]	M. Christou, T. Flouri, C. S. Iliopoulos, J. Janousek, B. Melichar, S. P. Pissis, J. Zdarek, "Tree template matching in unranked ordered trees", Journal of Discrete Algorithms, vol. 20, 2013, pp. 51 - 60. [bibtex] [doi]
[39]	M. Christou, M. Crochemore, C. S. Iliopoulos, M. Kubica, S. P. Pissis, J. Radoszewski, W. Rytter, B. Szreder, T. Walen, "Efficient seed computation revisited", Theoretical Computer Science, vol. 483, 2013, pp. 171 - 181. [bibtex] [doi]
[38]	C. Barton, T. Flouri, C. S. Iliopoulos, S. P. Pissis, "GapsMis: flexible sequence alignment with a bounded number of gaps", in Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, New York, NY, USA: ACM, 2013, pp. 402–411. [bibtex] [doi]
[37]	C. Barton, M. Giraud, C. S. Iliopoulos, T. Lecroq, L. Mouchard, S. P. Pissis, "Querying highly similar sequences", International Journal of Computational Biology and Drug Design, vol. 6, no. 1, 2013, pp. 119 - 130. [bibtex] [doi]
[36]	M. Elloumi, P. Hayati, C. S. Iliopoulos, J. A. Mirza, S. P. Pissis, A. Shah, "Comparison for the detection of Virus and spam using pattern matching tools", in Technological Advances in Electrical, Electronics and Computer Engineering (TAEECE), 2013 International Conference on, pp. 304-311. [bibtex] [doi]
2012
[35]	M. Elloumi, P. Hayati, C. S. Iliopoulos, S. P. Pissis, A. Shah, "Detection of fixed length web spambot using REAL (read aligner)", in Proceedings of the CUBE International Information Technology Conference, New York, NY, USA: ACM, 2012, pp. 820–825. [bibtex] [doi]
[34]	C. Hadjinikolis, C. S. Iliopoulos, S. P. Pissis, A. Stamatakis, "Minimising processor communication in parallel approximate string matching", Heidelberg Institute for Theoretical Studies, Rep. Exelixis-RRDR-2012-8. [bibtex]
[33]	T. Flouri, C. S. Iliopoulos, K. Park, S. P. Pissis, "GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures", in Artificial Intelligence Applications and Innovations, L. Iliadis et al., Eds., Springer Berlin Heidelberg, 2012, pp. 593-601. [bibtex] [doi]
[32]	C. S. Iliopoulos, M. Miller, S. P. Pissis, "Parallel algorithms for mapping short degenerate and weighted sequences to a reference genome", International Journal of Foundations of Computer Science, vol. 23, no. 02, 2012, pp. 249-259. [bibtex] [doi]
[31]	T. Flouri, K. Kobert, S. P. Pissis, A. Stamatakis, "A simple method for computing all subtree repeats in unordered trees in linear time", in Festschrift for Borivoj Melichar, J. Holub, B. W. Watson, J. Zdarek, Eds., Czech Technical University in Prague, 2012, pp. 145-152. [bibtex]
[30]	T. Flouri, C. S. Iliopoulos, T. Kociumaka, S. P. Pissis, S. J. Puglisi, W. F. Smyth, W. Tyczynski, "New and efficient approaches to the quasiperiodic characterisation of a string", in Proceedings of the Prague Stringology Conference (PSC 2012), J. Holub, J. Zdarek, Eds., Czech Technical University in Prague, pp. 75–88. [bibtex]
[29]	C. S. Iliopoulos, D. Kourie, L. Mouchard, T. K. Musombuka, S. P. Pissis, C. d. Ridder, "An algorithm for mapping short reads to a dynamically changing genomic sequence", Journal of Discrete Algorithms, vol. 10, 2012, pp. 15 - 22. [bibtex] [doi]
[28]	T. Flouri, C. S. Iliopoulos, J. Janousek, B. Melichar, S. P. Pissis, "Tree template matching in ranked ordered trees by pushdown automata", Journal of Discrete Algorithms, vol. 17, 2012, pp. 15 - 23. [bibtex] [doi]
[27]	T. Flouri, C. S. Iliopoulos, S. P. Pissis, G. Tischler, "Mapping Short Reads to a Genomic Sequence with Circular Structure", International Journal of Systems Biology and Biomedical Technologies, vol. 1, no. 1, 2012, pp. 26 - 34. [bibtex] [doi]
[26]	M. Christou, M. Crochemore, T. Flouri, C. S. Iliopoulos, J. Janousek, B. Melichar, S. P. Pissis, "Computing all subtree repeats in ordered trees", Information Processing Letters, vol. 112, no. 24, 2012, pp. 958 - 962. [bibtex] [doi]
[25]	M. Christou, M. Crochemore, O. Guth, C. S. Iliopoulos, S. P. Pissis, "On left and right seeds of a string", Journal of Discrete Algorithms, vol. 17, 2012, pp. 31 - 44. [bibtex] [doi]
[24]	N. Alachiotis, S. Berger, T. Flouri, S. P. Pissis, A. Stamatakis, "Libgapmis: An ultrafast library for short-read single-gap alignment", 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012, pp. 688-695. [bibtex] [doi]
2011
[23]	S. P. Pissis, "Algorithms on strings with applications in molecular biology", Ph.D. dissertation, King's College London, London, 2011. [bibtex]
[22]	M. Christou, M. Crochemore, T. Flouri, C. Iliopoulos, J. Janousek, B. Melichar, S. Pissis, "Computing All Subtree Repeats in Ordered Ranked Trees", in String Processing and Information Retrieval, R. Grossi, F. Sebastiani, F. Silvestri, Eds., Springer Berlin / Heidelberg, 2011, pp. 338-343. [bibtex] [doi]
[21]	T. Flouri, J. Janousek, B. Melichar, C. Iliopoulos, S. Pissis, "Tree Template Matching in Ranked Ordered Trees by Pushdown Automata", in Implementation and Application of Automata, B. Bouchou-Markhoff et al., Eds., Springer Berlin / Heidelberg, 2011, pp. 273-281. [bibtex] [doi]
[20]	M. Christou, M. Crochemore, C. Iliopoulos, M. Kubica, S. Pissis, J. Radoszewski, W. Rytter, B. Szreder, T. Waleń, "Efficient Seeds Computation Revisited", in Combinatorial Pattern Matching, R. Giancarlo, G. Manzini, Eds., Springer Berlin / Heidelberg, 2011, pp. 350-363. [bibtex] [doi]
[19]	M. Christou, M. Crochemore, O. Guth, C. S. Iliopoulos, S. P. Pissis, "On the Right-Seed Array of a String", in Computing and Combinatorics, B. Fu, D. Du, Eds., Springer Berlin Heidelberg, 2011, pp. 492-502. [bibtex] [doi]
[18]	O. Phanalasy, M. Miller, C. Iliopoulos, S. P. Pissis, E. Vaezpour, "Construction of Antimagic Labeling for the Cartesian Product of Regular Graphs", Mathematics in Computer Science, vol. 5, no. 1, 2011, pp. 81-87. [bibtex] [doi]
[17]	T. Flouri, C. S. Iliopoulos, S. P. Pissis, "DynMap: mapping short reads to multiple related genomes", in Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, New York, NY, USA: ACM, 2011, pp. 330–334. [bibtex] [doi]
[16]	T. Flouri, K. Park, K. Frousios, S. P. Pissis, C. S. Iliopoulos, G. Tischler, "Approximate string-matching with a single gap for sequence alignment", in Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, New York, NY, USA: ACM, 2011, pp. 490–492. [bibtex] [doi]
[15]	"Tree Indexing by Pushdown Automata and Repeats of Subtrees", in Federated Conference on Computer Science and Information Systems - FedCSIS 2011, Szczecin, Poland, 18-21 September 2011, Proceedings, M. Ganzha, L. A. Maciaszek, M. Paprzycki, Eds., IEEE, pp. 899–902. [bibtex] [pdf]
[14]	S. Arhondakis, K. Frousios, C. S. Iliopoulos, S. Pissis, G. Tischler, S. Kossida, "Transcriptome map of mouse isochores", BMC Genomics, vol. 12, no. 1, 2011, pp. 511. [bibtex] [doi]
2010
[13]	M. Crochemore, C. Iliopoulos, S. Pissis, G. Tischler, "Cover Array String Reconstruction", in Combinatorial Pattern Matching, A. Amir, L. Parida, Eds., Springer Berlin / Heidelberg, 2010, pp. 251-259. [bibtex] [doi]
[12]	P. Antoniou, C. S. Iliopoulos, L. Mouchard, S. P. Pissis, "A Fast and Efficient Algorithm for Mapping Short Sequences to a Reference Genome", in Advances in Computational Biology, H. R. Arabnia, Ed., Springer New York, 2010, pp. 399-403. [bibtex] [doi]
[11]	M. Crochemore, C. S. Iliopoulos, S. P. Pissis, "A Parallel Algorithm for Fixed-Length Approximate String-Matching with k-mismatches", in Algorithms and Applications, T. Elomaa, H. Mannila, P. Orponen, Eds., Springer Berlin Heidelberg, 2010, pp. 92-101. [bibtex] [doi]
[10]	C. S. Iliopoulos, L. Mouchard, S. P. Pissis, "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, 2010, pp. 150-157. [bibtex] [doi]
[9]	K. Frousios, C. S. Iliopoulos, L. Mouchard, S. P. Pissis, G. Tischler, "REAL: an efficient REad ALigner for next generation sequencing reads", in Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, New York, NY, USA: ACM, 2010, pp. 154-159. [bibtex] [doi]
[8]	P. Antoniou, C. S. Iliopoulos, L. Mouchard, S. P. Pissis, "Algorithms for mapping short degenerate and weighted sequences to a reference genome", International Journal of Computational Biology and Drug Design, vol. 2, no. 4, 2010, pp. 385 - 397. [bibtex] [doi]
[7]	K. K. Chang, S. P. Pissis, J. R. Jang, C. Iliopoulos, "Sub-nyquist audio fingerprinting for music recognition", in Computer Science and Electronic Engineering Conference (CEEC), 2010 2nd, pp. 1-5. [bibtex] [doi]
[6]	T. Flouri, J. Holub, C. S. Iliopoulos, S. P. Pissis, "An algorithm for mapping short reads to a dynamically changing genomic sequence", in Bioinformatics and Biomedicine (BIBM), 2010 IEEE International Conference on, pp. 133-136. [bibtex] [doi]
[5]	C. S. Iliopoulos, T. A. Okanlawon, S. P. Pissis, G. Tischler, "Mapping short reads to a genomic sequence with circular structure", in Information Technology and Applications in Biomedicine (ITAB), 2010 10th IEEE International Conference on, pp. 1-4. [bibtex] [doi]
2009
[4]	C. S. Iliopoulos, M. Miller, S. P. Pissis, "Parallel algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies", in Proceedings of the Prague Stringology Conference 2009, J. Holub, J. Zdarek, Eds., pp. 249–262. [bibtex]
[3]	P. Antoniou, J. W. Daykin, C. S. Iliopoulos, D. Kourie, L. Mouchard, S. P. Pissis, "Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome", in Information Technology and Applications in Biomedicine, 2009. ITAB 2009. 9th International Conference on, pp. 1-4. [bibtex] [doi]
[2]	P. Antoniou, C. S. Iliopoulos, L. Mouchard, S. P. Pissis, "Practical and Efficient Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing Technologies", in Bioinformatics, Systems Biology and Intelligent Computing, 2009. IJCBS '09. International Joint Conference on, pp. 174 -180. [bibtex] [doi]
2008
[1]	S. P. Pissis, "Parallel Fourier Transformations using shared memory nodes", Master's thesis, University of Edinburgh, Edinburgh, 2008. [bibtex]