Home | Publications | Activities | Software | Poetry | Contact
  

Book Chapters

  • Costas S. Iliopoulos and Solon P. Pissis. Algorithms for next-generation sequencing data. Handbook of Biological Knowledge Discovery, 2012. Wiley (in press)

    Journal Publications

  • Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler. GapMis: a tool for pairwise sequence alignment with a single gap. Recent Patents on DNA and Gene Sequence Journal: Pattern Finding in Computational Molecular Biology, 2012. Bentham Science (accepted)

  • Tomas Flouri, Costas Iliopoulos, Jan Janousek, Borivoj Melichar, and Solon P. Pissis. Tree template matching in ranked ordered trees by pushdown automata. Journal of Discrete Algorithms, 2012. Elsevier (accepted)

  • Michalis Christou, Maxime Crochemore, Ondrej Guth, Costas S. Iliopoulos, and Solon P. Pissis. On left and rights seeds of a string. Journal of Discrete Algorithms, 2012. Elsevier (accepted)

  • Carl Barton, Mathieu Giraud, Costas S. Iliopoulos, Thierry Lecroq, Laurent Mouchard, and Solon P. Pissis. Querying highly similar sequences. International Journal of Computational Biology and Drug Design, 2012. Inderscience (accepted)

  • Michalis Christou, Maxime Crochemore, Costas S. Iliopoulos, Marcin Kubica, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Bartosz Szreder, and Tomasz Walen. Efficient seed computation revisited. Theoretical Computer Science, 2012. Elsevier (in press)

  • Tomas Flouri, Costas S. Iliopoulos, Solon P. Pissis, and German Tischler. Mapping short reads to a genomic sequence with circular structure. International Journal of Systems Biology and Biomedical Technologies, 1(1):26-34, 2012. IGI Global

  • Costas S. Iliopoulos, Derrick Kourie, Laurent Mouchard, Themba K. Musombuka, Solon P. Pissis, and Corne de Ridder. An algorithm for mapping short reads to a dynamically changing genomic sequence. Journal of Discrete Algorithms, 10:15-22, 2012. Elsevier

  • Stilianos Arhondakis, Kimon Frousios, Costas S. Iliopoulos, Solon P. Pissis, German Tischler, and Sophia Kossida. Transcriptome map of mouse isochores. BMC Genomics, 12:511, 2011. BioMed Central

  • Oudone Phanalasy, Mirka Miller, Costas S. Iliopoulos, Solon P. Pissis, and Elaheh Vaezpour. Construction of Antimagic Labeling for the Cartesian Product of Regular Graphs. Mathematics in Computer Science, 5(1):81-87, 2011. Springer

  • Costas S. Iliopoulos, Mirka Miller, and Solon P. Pissis. Parallel algorithms for mapping short degenerate and weighted sequences to a reference genome. International Journal of Foundations of Computer Science, 23(2):249-259, 2012. World Scientific

  • Maxime Crochemore, Costas S. Iliopoulos, and Solon P. Pissis. A Parallel Algorithm for Fixed-length Approximate String Matching with k-mismatches. Algorithms and Applications, Lecture Notes in Computer Science, 6060:92-101, 2010. Springer

  • Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, and Solon P. Pissis. A fast and efficient algorithm for mapping short sequences to a reference genome. Advances in Experimental Medicine and Biology, 680(4):399-403, 2010. Springer

  • Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, and Solon P. Pissis. Algorithms for mapping short degenerate and weighted sequences to a reference genome. International Journal of Computational Biology and Drug Design, 2(4):385-397, 2010. Inderscience

    Conference Publications

  • Michalis Christou, Maxime Crochemore, Tomas Flouri, Costas S. Iliopoulos, Jan Janousek, Borivoj Melichar and Solon P. Pissis. Computing all subtree repeats in ordered ranked trees. In Proceedings of the 18th International Symposium on String Processing and Information Retrieval (SPIRE 2011), Lecture Notes in Computer Science, 7024:338-343, 2011. Springer

  • Tomas Flouri, Costas S. Iliopoulos, Jan Janousek, Borivoj Melichar, and Solon Pissis. Tree indexing by pushdown automata and repeats of subtrees. In Proceedings of the Federated Conference on Computer Science and Information Systems (FedCSIS 2011), pp. 899-902 , 2011. IEEE Xplore

  • Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler. Approximate string-matching with a single gap for sequence alignment. In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library

  • Tomas Flouri, Costas S. Iliopoulos, and Solon P. Pissis. DynMap : mapping short reads to multiple related genomes. In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 330-334, 2011. ACM Digital Library

  • Tomas Flouri, Costas Iliopoulos, Jan Janousek, Borivoj Melichar, and Solon P. Pissis. Tree template matching in ranked ordered trees by pushdown automata. In Proceedings of the 16th International Conference on Implementation and Application of Automata (CIAA 2011), Lecture Notes in Computer Science, 6807:273-281, 2011. Springer

  • Michalis Christou, Maxime Crochemore, Ondrej Guth, Costas S. Iliopoulos, and Solon P. Pissis. On the right-seed array of a string. In Proceedings of the 17th Annual International Computing and Combinatorics Conference (COCOON 2011), Lecture Notes in Computer Science, 6842:492-502, 2011. Springer

  • Michalis Christou, Maxime Crochemore, Costas S. Iliopoulos, Marcin Kubica, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Bartosz Szreder, and Tomasz Walen. Efficient seed computation revisited. In Proceedings of the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), Lecture Notes in Computer Science, 6661:350-363, 2011. Springer

  • Tomas Flouri, Jan Holub, Costas S. Iliopoulos and Solon P. Pissis. An algorithm for mapping short reads to a dynamically changing genomic sequence. In Proceedings of the International Conference on Bioinformatics & Biomedicine (BIBM 2010), pp.133-136, 2010. IEEE Xplore

  • Kaichun K. Chang, Solon P. Pissis, Jyh-Shing R. Jang and Costas S. Iliopoulos. Sub-Nyquist Audio Fingerprinting for Music Recognition In Proceedings of the 2nd Computer Science and Electronic Engineering Conference (CEEC 2010), 2010. IEEE Xplore

  • Costas S. Iliopoulos, Tewogboye A. Okanlawon, Solon P. Pissis and German Tischler. Mapping short reads to a genomic sequence with circular structure. In Proceedings of the 10th International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), 2010. IEEE Xplore

  • Kimon Frousios, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis and German Tischler. REAL: An efficient REad ALigner for next generation sequencing reads. In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010), pp.154-159, 2010. ACM Digital Library

  • Costas S. Iliopoulos, Maxime Crochemore, Solon P. Pissis and German Tischler. Cover array string reconstruction. In Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching (CPM 2010), Lecture Notes in Computer Science, 6129:251-259, 2010. Springer

  • Costas S. Iliopoulos, Laurent Mouchard, and Solon 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), Advances in Parallel Computing, 19:150-157, 2010. IOS Press

  • Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, and Solon P. Pissis. Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. In Proceedings of the International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS 2009), pp.174-180, 2009. IEEE Xplore

  • Costas S. Iliopoulos, Mirka Miller, and Solon P. Pissis. Parallel algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies. In Proceedings of the Prague Stringology Conference (PSC 2009), pp.129-136, 2009.

  • Pavlos Antoniou, Jackie W. Daykin, Costas S. Iliopoulos, Derrick Kourie, Laurent Mouchard, and Solon P. Pissis. Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome. In Proceedings of the 9th International Conference on Information Technology and Applications in Biomedicine (ITAB 2009), 2009. IEEE Xplore

    Theses

    Solon P. Pissis. Algorithms on strings with applications in molecular biology. Ph.D thesis, 2011. King's College, University of London

    Solon P. Pissis. Parallel Fourier Transformations using shared memory nodes. M.Sc thesis, 2008. University of Edinburgh

    		•