Jesper Jansson's Publications

Books:
  1. J. Jansson, C. Martín-Vide, and M. A. Vega-Rodríguez (Eds.). Proceedings of the Fifth International Conference on Algorithms for Computational Biology (AlCoB 2018), LNBI, Vol. 10849, Springer International Publishing AG, 2018. ISBN 978-3-319-91937-9. Preface.


  2. L. A. Gąsieniec, J. Jansson, and C. Levcopoulos (Eds.). Proceedings of the Twenty-Second International Symposium on Fundamentals of Computation Theory (FCT 2019), LNCS, Vol. 11651, Springer Nature Switzerland AG, 2019. ISBN: 978-3-030-25026-3. Preface.



Book chapters:

  1. J. Jansson and W.-K. Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. Chapter 4 of New Topics in Theoretical Computer Science, pp. 119-141, Nova Science Publishers, Inc., New York, 2008. ISBN: 978-1-60456-100-5.


  2. J. Jansson and K. Sadakane. Succinct Representation of Bit Vectors Supporting Efficient rank and select Queries. Commentary in Software Engineering and Development, pp. 3-12, Nova Science Publishers, Inc., New York, 2009. ISBN: 978-1-60692-146-3.


  3. J. Jansson. J. Jansson and W.-K. Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. Invited chapter in Encyclopedia of Algorithms, Second Edition, edited by Ming-Yang Kao, pp. 48-52, Springer Science+Business Media New York, 2016. ISBN: 978-1-4939-2863-7.


  4. J. Jansson. Directed Perfect Phylogeny (Binary Characters). Invited chapter in Encyclopedia of Algorithms, Second Edition, edited by Ming-Yang Kao, pp. 553-556, Springer Science+Business Media New York, 2016. ISBN: 978-1-4939-2863-7. (Also appeared in Encyclopedia of Algorithms, First Edition, edited by Ming-Yang Kao, pp. 246-248, Springer Science+Business Media, LLC., New York, 2008. ISBN: 978-0-387-36061-4.)


  5. J. Jansson. J. Jansson and W.-K. Sung. Maximum Agreement Supertree. Invited chapter in Encyclopedia of Algorithms, Second Edition, edited by Ming-Yang Kao, pp. 1224-1227, Springer Science+Business Media New York, 2016. ISBN: 978-1-4939-2863-7.


  6. J. Jansson. Perfect Phylogeny (Bounded Number of States). Invited chapter in Encyclopedia of Algorithms, Second Edition, edited by Ming-Yang Kao, pp. 1550-1553, Springer Science+Business Media New York, 2016. ISBN: 978-1-4939-2863-7. (Also appeared in Encyclopedia of Algorithms, First Edition, edited by Ming-Yang Kao, pp. 644-647, Springer Science+Business Media, LLC., New York, 2008. ISBN: 978-0-387-36061-4.)


  7. J. Jansson. Phylogenetic Tree Construction from a Distance Matrix. Invited chapter in Encyclopedia of Algorithms, Second Edition, edited by Ming-Yang Kao, pp. 1564-1567, Springer Science+Business Media New York, 2016. ISBN: 978-1-4939-2863-7. (Also appeared in Encyclopedia of Algorithms, First Edition, edited by Ming-Yang Kao, pp. 651-653, Springer Science+Business Media, LLC., New York, 2008. ISBN: 978-0-387-36061-4.)



Journal editorials:

  1. J. Jansson. Editorial: Special Issue on Graph Algorithms. Algorithms, Vol. 6, Number 3, pp. 457-458, Multidisciplinary Digital Publishing Institute (MDPI), 2013.


  2. J. Jansson. Editorial: Special Issue on Efficient Data Structures. Algorithms, Vol. 12, Number 7, Article 136, Multidisciplinary Digital Publishing Institute (MDPI), 2019.


  3. L. Gąsieniec, J. Jansson, and C. Levcopoulos. Foreword: Selected papers from the 22nd International Symposium on Fundamentals of Computation Theory (FCT 2019). Journal of Computer and System Sciences (JCSS), Vol. 120, pp. 177-178, Elsevier Inc., 2021.


  4. J. Jansson. Editorial: Surveys in Algorithm Analysis and Complexity Theory (Special Issue). Algorithms, Vol. 16, Number 4, Article 188, Multidisciplinary Digital Publishing Institute (MDPI), 2023.



Refereed journal articles and refereed international conference papers:

  1. L. Gąsieniec, J. Jansson, A. Lingas, and A. Östlin. On the Complexity of Constructing Evolutionary Trees. Journal of Combinatorial Optimization (JOCO), Vol. 3, Number 2/3, pp. 183-197, Kluwer Academic Publishers, 1999. A preliminary version appeared in Proceedings of the Third Annual International Computing and Combinatorics Conference (COCOON'97), LNCS, Vol. 1276, pp. 134-145, Springer-Verlag Berlin Heidelberg, 1997.
    [See Chapters 2 and 4 of my Ph.D. thesis Consensus Algorithms for Trees and Strings for the final version.]


  2. L. Gąsieniec, J. Jansson, A. Lingas, and A. Östlin. Inferring Ordered Trees from Local Constraints. Proceedings of Computing: the Fourth Australasian Theory Symposium (CATS'98), special issue of Australian Computer Science Communications, Vol. 20, Number 3, pp. 67-76, Springer-Verlag Singapore Pte. Ltd., 1998.
    [See Chapter 3 of my Ph.D. thesis Consensus Algorithms for Trees and Strings for the final version.]


  3. L. Gąsieniec, J. Jansson, and A. Lingas. Efficient Approximation Algorithms for the Hamming Center Problem. Technical Report LU-CS-TR:99-211, Department of Computer Science, Lund University, 1999. A short form version of this article was published in Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'99), pp. 905-906, Society for Industrial and Applied Mathematics (SIAM), 1999.
    [See Chapter 6 of my Ph.D. thesis Consensus Algorithms for Trees and Strings for the final version.]


  4. L. Gąsieniec, J. Jansson, and A. Lingas. Approximation Algorithms for Hamming Clustering Problems. Journal of Discrete Algorithms (JDA), Vol. 2, Number 2, pp. 289-301, Elsevier B.V., 2004 (special issue containing selected papers from CPM 2000). A preliminary version appeared in Proceedings of the Eleventh Annual Symposium on Combinatorial Pattern Matching (CPM 2000), LNCS, Vol. 1848, pp. 108-118, Springer-Verlag Berlin Heidelberg, 2000.
    [See Chapter 7 of my Ph.D. thesis Consensus Algorithms for Trees and Strings for the final version.]


  5. J. Jansson. On the Complexity of Inferring Rooted Evolutionary Trees. Proceedings of the Brazilian Symposium on Graphs, Algorithms, and Combinatorics (GRACO 2001), Electronic Notes in Discrete Mathematics Vol. 7, pp. 50-53, Elsevier B.V., 2001.
    [See Chapter 2 of my Ph.D. thesis Consensus Algorithms for Trees and Strings for the final version.]


  6. J. Jansson and A. Lingas. A Fast Algorithm for Optimal Alignment between Similar Ordered Trees. Fundamenta Informaticae (FI), Vol. 56, Number 1/2, pp. 105-120, IOS Press, 2003. A preliminary version appeared in Proceedings of the Twelfth Annual Symposium on Combinatorial Pattern Matching (CPM 2001), LNCS, Vol. 2089, pp. 232-240, Springer-Verlag Berlin Heidelberg, 2001.
    [See Chapter 5 of my Ph.D. thesis Consensus Algorithms for Trees and Strings for the final version.]


  7. J. Jansson and T. Tokuyama. Semi-Balanced Colorings of Graphs: Generalized 2-Colorings Based on a Relaxed Discrepancy Condition. Graphs and Combinatorics, Vol. 20, Number 2, pp. 205-222, Springer-Verlag Tokyo, 2004.


  8. C. Choy, J. Jansson, K. Sadakane, and W.-K. Sung. Computing the Maximum Agreement of Phylogenetic Networks. Theoretical Computer Science (TCS), Vol. 335, Number 1, pp. 93-107, Elsevier B.V., 2005 (special issue on "Pattern Discovery in the Post Genome"). A preliminary version appeared in Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS2004), Electronic Notes in Theoretical Computer Science Vol. 91, pp. 134-147, Elsevier B.V., 2004.


  9. J. Jansson, J. H.-K. Ng, K. Sadakane, and W.-K. Sung. Rooted Maximum Agreement Supertrees. Algorithmica, Vol. 43, Number 4, pp. 293-307, Springer Science+Business Media, 2005. A preliminary version appeared in Proceedings of the Sixth Latin American Symposium on Theoretical Informatics (LATIN 2004), LNCS, Vol. 2976, pp. 499-508, Springer-Verlag Berlin Heidelberg, 2004.


  10. A. Dessmark, J. Jansson, A. Lingas, and E.-M. Lundell. Polynomial-Time Algorithms for the Ordered Maximum Agreement Subtree Problem. Algorithmica, Vol. 48, Number 3, pp. 233-248, Springer Science+Business Media, 2007. A preliminary version appeared in Proceedings of the Fifteenth Annual Symposium on Combinatorial Pattern Matching (CPM 2004), LNCS, Vol. 3109, pp. 220-229, Springer-Verlag Berlin Heidelberg, 2004.


  11. J. Jansson and W.-K. Sung. Inferring a Level-1 Phylogenetic Network from a Dense Set of Rooted Triplets. Theoretical Computer Science (TCS), Vol. 363, Number 1, pp. 60-68, Elsevier B.V., 2006 (special issue containing selected papers from COCOON 2004). A preliminary version appeared in Proceedings of the Tenth Annual International Computing and Combinatorics Conference (COCOON 2004), LNCS, Vol. 3106, pp. 462-471, Springer-Verlag Berlin Heidelberg, 2004.


  12. J. Jansson, S.-K. Ng, W.-K. Sung, and H. Willy. A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment. Algorithmica, Vol. 46, Number 2, pp. 223-245, Springer Science+Business Media, 2006. A preliminary version appeared in Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics (WABI 2004), LNBI, Vol. 3240, pp. 302-313, Springer-Verlag Berlin Heidelberg, 2004.


  13. J. Jansson, T. H. Ngo, and W.-K. Sung. Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs. Journal of Computational Biology (JCB), Vol. 13, Number 3, pp. 702-718, Mary Ann Liebert, Inc. publishers, 2006. A preliminary version appeared in Proceedings of the Fifteenth Annual International Symposium on Algorithms and Computation (ISAAC 2004), LNCS, Vol. 3341, pp. 569-580, Springer-Verlag Berlin Heidelberg, 2004.


  14. J. Jansson and W.-K. Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. Proceedings of the Fifteenth Annual International Symposium on Algorithms and Computation (ISAAC 2004), LNCS, Vol. 3341, pp. 581-593, Springer-Verlag Berlin Heidelberg, 2004.
    [See the book chapter above for the final version.]


  15. Y.-J. He, T. N. D. Huynh, J. Jansson, and W.-K. Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. Journal of Bioinformatics and Computational Biology (JBCB), Vol. 4, Number 1, pp. 59-74, Imperial College Press, 2006 (special issue containing selected papers from APBC2005). A preliminary version appeared in Proceedings of the Third Asia-Pacific Bioinformatics Conference (APBC2005), Series on Advances in Bioinformatics and Computational Biology Vol. 1, pp. 339-348, Imperial College Press, 2005.


  16. J. Jansson, N. B. Nguyen, and W.-K. Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. SIAM Journal on Computing, Vol. 35, Number 5, pp. 1098-1121, Society for Industrial and Applied Mathematics (SIAM), 2006. An extended abstract of this article appeared in Proceedings of the Sixteenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2005), pp. 349-358, Society for Industrial and Applied Mathematics (SIAM), 2005.


  17. T. N. D. Huynh, J. Jansson, N. B. Nguyen, and W.-K. Sung. Constructing a Smallest Refining Galled Phylogenetic Network. Proceedings of the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), LNBI, Vol. 3500, pp. 265-280, Springer-Verlag Berlin Heidelberg, 2005.


  18. S. Dobrev, J. Jansson, K. Sadakane, and W.-K. Sung. Finding Short Right-Hand-on-the-Wall Walks in Graphs. Proceedings of the Twelfth International Colloquium on Structural Information and Communication Complexity (SIROCCO 2005), LNCS, Vol. 3499, pp. 127-139, Springer-Verlag Berlin Heidelberg, 2005.


  19. H.-L. Chan, J. Jansson, T.-W. Lam, and S.-M. Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. Journal of Bioinformatics and Computational Biology (JBCB), Vol. 4, Number 4, pp. 807-832, Imperial College Press, 2006. A preliminary version appeared in Proceedings of the Thirtieth International Symposium on Mathematical Foundations of Computer Science (MFCS 2005), LNCS, Vol. 3618, pp. 224-235, Springer-Verlag Berlin Heidelberg, 2005.


  20. J. Jansson and Z. Peng. Online and Dynamic Recognition of Squarefree Strings. International Journal of Foundations of Computer Science (IJFCS), Vol. 18, Number 2, pp. 401-414, World Scientific Publishing Co., 2007. A preliminary version appeared in Proceedings of the Thirtieth International Symposium on Mathematical Foundations of Computer Science (MFCS 2005), LNCS, Vol. 3618, pp. 520-531, Springer-Verlag Berlin Heidelberg, 2005.


  21. A. Dessmark, J. Jansson, A. Lingas, E.-M. Lundell, and M. Persson. On the Approximability of Maximum and Minimum Edge Clique Partition Problems. International Journal of Foundations of Computer Science (IJFCS), Vol. 18, Number 2, pp. 217-226, World Scientific Publishing Co., 2007 (special issue containing selected papers from CATS2006). [Note: The author order given in the paper is incorrect. The correct order should be the alphabetical one, as specified here and here.] A preliminary version appeared in Proceedings of Computing: the Twelfth Australasian Theory Symposium (CATS2006), Conferences in Research and Practice in Information Technology (CRPIT) Series, Vol. 51, pp. 101-105, Australian Computer Society Inc., 2006.


  22. J. Jansson and Z. Peng. Algorithms for Finding a Most Similar Subforest. Theory of Computing Systems (TOCS), Vol. 48, Number 4, pp. 865-887, Springer-Verlag New York, 2011. A preliminary version appeared in Proceedings of the Seventeenth Annual Symposium on Combinatorial Pattern Matching (CPM 2006), LNCS, Vol. 4009, pp. 377-388, Springer-Verlag Berlin Heidelberg, 2006.


  23. J. Jansson, K. Sadakane, and W.-K. Sung. Ultra-Succinct Representation of Ordered Trees with Applications. Journal of Computer and System Sciences (JCSS), Vol. 78, Number 2, pp. 619-631, Elsevier, 2012. A preliminary version appeared in Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), pp. 575-584, Society for Industrial and Applied Mathematics (SIAM), 2007.


  24. Y. Asahiro, J. Jansson, E. Miyano, H. Ono, and K. Zenmyo. Approximation Algorithms for the Graph Orientation Minimizing the Maximum Weighted Outdegree. Journal of Combinatorial Optimization (JOCO), Vol. 22, Number 1, pp. 78-96, Springer Science+Business Media, LLC., 2011. A preliminary version appeared in Proceedings of the Third International Conference on Algorithmic Aspects in Information and Management (AAIM 2007), LNCS, Vol. 4508, pp. 167-177, Springer-Verlag Berlin Heidelberg, 2007.


  25. J. Jansson, K. Sadakane, and W.-K. Sung. Linked Dynamic Tries with Applications to LZ-Compression in Sublinear Time and Space. Algorithmica, Vol. 71, Number 4, pp. 969-988, Springer Science+Business Media New York, 2015. A preliminary version appeared in Proceedings of the Twenty-Seventh Annual International Conference on the Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2007), LNCS, Vol. 4855, pp. 424-435, Springer-Verlag Berlin Heidelberg, 2007.


  26. J. Byrka, S. Guillemot, and J. Jansson. New Results on Optimizing Rooted Triplets Consistency. Discrete Applied Mathematics (DAM), Vol. 158, Number 11, pp. 1136-1147, Elsevier B.V., 2010. A preliminary version appeared in Proceedings of the Nineteenth Annual International Symposium on Algorithms and Computation (ISAAC 2008), LNCS, Vol. 5369, pp. 484-495, Springer-Verlag Berlin Heidelberg, 2008.


  27. Y. Asahiro, J. Jansson, E. Miyano, and H. Ono. Graph Orientation to Maximize the Minimum Weighted Outdegree. International Journal of Foundations of Computer Science (IJFCS), Vol. 22, Number 3, pp. 583-601, World Scientific Publishing Co., 2011 (special issue containing selected papers from APDCM 2009). A preliminary version appeared in Proceedings of the Eleventh Workshop on Advances in Parallel and Distributed Computational Models (APDCM 2009), part of the Twenty-Third IEEE International Parallel and Distributed Processing Symposium (IPDPS 2009), Institute of Electrical and Electronics Engineers (IEEE) CS Press, 2009.


  28. A. Czumaj, J. Czyzowicz, L. Gąsieniec, J. Jansson, A. Lingas, and P. Zylinski. Approximation Algorithms for Buy-at-Bulk Geometric Network Design. International Journal of Foundations of Computer Science (IJFCS), Vol. 22, Number 8, pp. 1949-1969, World Scientific Publishing Co., 2011. A preliminary version appeared in Proceedings of the Eleventh International Symposium on Algorithms and Data Structures (WADS 2009), LNCS, Vol. 5664, pp. 168-180, Springer-Verlag Berlin Heidelberg, 2009.


  29. T. Shibuya, J. Jansson, and K. Sadakane. Linear-Time Protein 3-D Structure Searching with Insertions and Deletions. Algorithms for Molecular Biology (AMB), Vol. 5, Article 7, BioMed Central Ltd., 2010 (special issue containing selected papers from WABI 2009). A preliminary version appeared in Proceedings of the Ninth International Workshop on Algorithms in Bioinformatics (WABI 2009), LNBI, Vol. 5724, pp. 310-320, Springer-Verlag Berlin Heidelberg, 2009.


  30. J. Czyzowicz, S. Dobrev, L. Gąsieniec, D. Ilcinkas, J. Jansson, R. Klasing, I. Lignos, R. Martin, K. Sadakane, and W.-K. Sung. More Efficient Periodic Traversal in Anonymous Undirected Graphs. Theoretical Computer Science (TCS), Vol. 444, pp. 60-76, Elsevier B.V., 2012 (special issue containing selected papers from SIROCCO 2009). A preliminary version appeared in Proceedings of the Sixteenth International Colloquium on Structural Information and Communication Complexity (SIROCCO 2009), LNCS, Vol. 5869, pp. 167-181, Springer-Verlag Berlin Heidelberg, 2009.


  31. S. Guillemot, J. Jansson, and W.-K. Sung. Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Vol. 8, Number 4, pp. 1141-1147, Institute of Electrical and Electronics Engineers (IEEE), 2011. A preliminary version appeared in Proceedings of the Twentieth Annual International Symposium on Algorithms and Computation (ISAAC 2009), LNCS, Vol. 5878, pp. 1205-1214, Springer-Verlag Berlin Heidelberg, 2009.


  32. J. C. Clemente, J. Jansson, and G. Valiente. Accurate Taxonomic Assignment of Short Pyrosequencing Reads. Proceedings of the Fifteenth Pacific Symposium on Biocomputing (PSB 2010), PSB Online Proceedings, pp. 3-9, 2010.


  33. T. Asano, J. Jansson, K. Sadakane, R. Uehara, and G. Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. Information Sciences, Vol. 197, pp. 77-90, Elsevier B.V., 2012. A preliminary version appeared in Proceedings of the Twenty-First Annual Symposium on Combinatorial Pattern Matching (CPM 2010), LNCS, Vol. 6129, pp. 190-201, Springer-Verlag Berlin Heidelberg, 2010.


  34. J. Jansson, R. S. Lemence, and A. Lingas. The Complexity of Inferring a Minimally Resolved Phylogenetic Supertree. SIAM Journal on Computing, Vol. 41, Number 1, pp. 272-291, Society for Industrial and Applied Mathematics (SIAM), 2012. A preliminary version appeared in Proceedings of the Tenth International Workshop on Algorithms in Bioinformatics (WABI 2010), LNBI, Vol. 6293, pp. 262-273, Springer-Verlag Berlin Heidelberg, 2010.


  35. J. C. Clemente, J. Jansson, and G. Valiente. Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics, Vol. 12, Article 8, BioMed Central Ltd., 2011.


  36. D. Alonso-Alemany, J. C. Clemente, J. Jansson, and G. Valiente. Taxonomic Assignment in Metagenomics with TANGO. EMBnet.journal, Vol. 17, Number 2, pp. 16-20, EMBnet, 2011.


  37. J. Jansson and W.-K. Sung. Constructing the R* Consensus Tree of Two Trees in Subcubic Time. Algorithmica, Vol. 66, Number 2, pp. 329-345, Springer Science+Business Media, 2013. A preliminary version appeared in Proceedings of the Eighteenth Annual European Symposium on Algorithms (ESA 2010), LNCS, Vol. 6346, pp. 573-584, Springer-Verlag Berlin Heidelberg, 2010.


  38. Y. Cui, J. Jansson, and W.-K. Sung. Polynomial-Time Algorithms for Building a Consensus MUL-Tree. Journal of Computational Biology (JCB), Vol. 19, Number 9, pp. 1073-1088, Mary Ann Liebert, Inc. publishers, 2012. A preliminary version appeared in Proceedings of the Twenty-Second International Symposium on Algorithms and Computation (ISAAC 2011), LNCS, Vol. 7074, pp. 744-753, Springer-Verlag Berlin Heidelberg, 2011.


  39. T. Akutsu, D. Fukagawa, J. Jansson, and K. Sadakane. Inferring a Graph from Path Frequency. Discrete Applied Mathematics (DAM), Vol. 160, Number 10-11, pp. 1416-1428, Elsevier B.V., 2012.


  40. Y. Asahiro, J. Jansson, E. Miyano, and H. Ono. Upper and Lower Degree-Constrained Graph Orientation with Minimum Penalty. Theoretical Computer Science (TCS), Vol. 900, pp. 53-78, Elsevier B.V., 2022. A preliminary version appeared in Proceedings of Computing: the Eighteenth Australasian Theory Symposium (CATS2012), Conferences in Research and Practice in Information Technology (CRPIT) Series, Vol. 128, pp. 139-146, Australian Computer Society Inc., 2012. Also listed as Australian Computer Science Communications, Vol. 34, Number 8.


  41. H. H. Do, J. Jansson, K. Sadakane, and W.-K. Sung. Fast Relative Lempel-Ziv Self-Index for Similar Sequences. Theoretical Computer Science (TCS), Vol. 532, pp. 14-30, Elsevier B.V., 2014 (special issue containing selected papers from FAW-AAIM 2012). A preliminary version appeared in Proceedings of the Second Joint International Conference on Frontiers in Algorithmics and Algorithmic Aspects in Information and Management (FAW-AAIM 2012), LNCS, Vol. 7285, pp. 291-302, Springer-Verlag Berlin Heidelberg, 2012.


  42. K.-M. Chao, A.-C. Chu, J. Jansson, R. S. Lemence, and A. Mancheron. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. Proceedings of the Ninth Annual Conference on Theory and Applications of Models of Computation (TAMC 2012), LNCS, Vol. 7287, pp. 177-188, Springer-Verlag Berlin Heidelberg, 2012.


  43. J. Jansson, K. Sadakane, and W.-K. Sung. CRAM: Compressed Random Access Memory. Proceedings of the Thirty-Ninth International Colloquium on Automata, Languages, and Programming (ICALP 2012) - Track A, LNCS, Vol. 7391, pp. 510-521, Springer-Verlag Berlin Heidelberg, 2012.


  44. J. Jansson and A. Lingas. Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles. Journal of Discrete Algorithms (JDA), Vol. 25, pp. 66-78, Elsevier B.V., 2014 (special issue containing selected papers from CPM 2012). A preliminary version appeared in Proceedings of the Twenty-Third Annual Symposium on Combinatorial Pattern Matching (CPM 2012), LNCS, Vol. 7354, pp. 385-398, Springer-Verlag Berlin Heidelberg, 2012.


  45. Y. Asahiro, J. Jansson, E. Miyano, and H. Ono. Graph Orientations Optimizing the Number of Light or Heavy Vertices. Journal of Graph Algorithms and Applications (JGAA), Vol. 19, Number 1, pp. 441-465, 2015. A preliminary version appeared in Proceedings of the Second International Symposium on Combinatorial Optimization (ISCO 2012), LNCS, Vol. 7422, pp. 332-343, Springer-Verlag Berlin Heidelberg, 2012.


  46. J. Jansson, C. Shen, and W.-K. Sung. Improved Algorithms for Constructing Consensus Trees. Journal of the ACM (JACM), Vol. 63, Number 3, Article 28, Association for Computing Machinery (ACM), 2016. The results in this article appeared in preliminary form in Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2013), pp. 1800-1813, Society for Industrial and Applied Mathematics (SIAM), 2013, and in Proceedings of the Seventeenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013), LNBI, Vol. 7821, pp. 88-99, Springer-Verlag Berlin Heidelberg, 2013.


  47. J. Jansson, R. Rajaby, C. Shen, and W.-K. Sung. Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Vol. 15, Number 1, pp. 15-26, Institute of Electrical and Electronics Engineers (IEEE), 2018. A preliminary version appeared in Proceedings of the Thirteenth Workshop on Algorithms in Bioinformatics (WABI 2013), LNBI, Vol. 8126, pp. 141-155, Springer-Verlag Berlin Heidelberg, 2013.


  48. Y. Asahiro, J. Jansson, E. Miyano, and H. Ono. Degree-Constrained Graph Orientation: Maximum Satisfaction and Minimum Violation. Theory of Computing Systems (TOCS), Vol. 58, Number 1, pp. 60-93, Springer Science+Business Media, LLC., 2016 (special issue containing selected papers from WAOA 2013). A preliminary version appeared in Proceedings of the Eleventh International Workshop on Approximation and Online Algorithms (WAOA 2013), LNCS, Vol. 8447, pp. 24-36, Springer International Publishing Switzerland, 2013.


  49. J. Jansson, W.-K. Sung, H. Vu, and S.-M. Yiu. Faster Algorithms for Computing the R* Consensus Tree. Algorithmica, Vol. 76, Number 4, pp. 1224-1244, Springer Science+Business Media New York, 2016 (special issue containing selected papers from ISAAC 2014). A preliminary version appeared in Proceedings of the Twenty-Fifth International Symposium on Algorithms and Computation (ISAAC 2014), LNCS, Vol. 8889, pp. 414-425, Springer International Publishing Switzerland, 2014.


  50. P. Floderus, J. Jansson, C. Levcopoulos, A. Lingas, and D. Sledneu. 3D Rectangulations and Geometric Matrix Multiplication. Algorithmica, Vol. 80, Number 1, pp. 136-154, Springer Science+Business Media New York, 2018. A preliminary version appeared in Proceedings of the Twenty-Fifth International Symposium on Algorithms and Computation (ISAAC 2014), LNCS, Vol. 8889, pp. 65-78, Springer International Publishing Switzerland, 2014.


  51. T. Akutsu, J. Jansson, A. Takasu, and T. Tamura. On the Parameterized Complexity of Associative and Commutative Unification. Theoretical Computer Science (TCS), Vol. 660, pp. 57-74, Elsevier B.V., 2017. A preliminary version appeared in Proceedings of the Ninth International Symposium on Parameterized and Exact Computation (IPEC 2014), LNCS, Vol. 8894, pp. 15-27, Springer International Publishing Switzerland, 2014.


  52. J. Jansson, Z. Li, and W.-K. Sung. On Finding the Adams Consensus Tree. Information and Computation, Vol. 256, pp. 334-347, Elsevier Inc., 2017. A preliminary version appeared in Proceedings of the Thirty-Second International Symposium on Theoretical Aspects of Computer Science (STACS 2015), LIPIcs, Vol. 30, pp. 487-499, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2015.


  53. J. Jansson and R. Rajaby. A More Practical Algorithm for the Rooted Triplet Distance. Journal of Computational Biology (JCB), Vol. 24, Number 2, pp. 106-126, Mary Ann Liebert, Inc. publishers, 2017 (special issue containing selected papers from AlCoB 2015). A preliminary version appeared in Proceedings of the Second International Conference on Algorithms for Computational Biology (AlCoB 2015), LNBI, Vol. 9199, pp. 109-125, Springer International Publishing Switzerland, 2015.


  54. K. Dannenberg, J. Jansson, A. Lingas, and E.-M. Lundell. The Approximability of Maximum Rooted Triplets Consistency with Fan Triplets and Forbidden Triplets. Discrete Applied Mathematics (DAM), Vol. 257, pp. 101-114, Elsevier B.V., 2019. A preliminary version appeared in Proceedings of the Twenty-Sixth Annual Symposium on Combinatorial Pattern Matching (CPM 2015), LNCS, Vol. 9133, pp. 272-283, Springer International Publishing Switzerland, 2015.


  55. T. Mori, A. Takasu, J. Jansson, J. Hwang, T. Tamura, and T. Akutsu. Similar Subtree Search Using Extended Tree Inclusion. IEEE Transactions on Knowledge and Data Engineering (TKDE), Vol. 27, Number 12, pp. 3360-3373, Institute of Electrical and Electronics Engineers (IEEE), 2015. An extended abstract appeared in Proceedings of the Thirty-Second IEEE International Conference on Data Engineering (ICDE 2016), pp. 1558-1559, Institute of Electrical and Electronics Engineers (IEEE), 2016.


  56. J. Jansson, R. Rajaby, and W.-K. Sung. Minimal Phylogenetic Supertrees and Local Consensus Trees. AIMS Medical Science, Vol. 5, Number 2, pp. 181-203, AIMS Press, 2018 (special issue on "The Future of Informatics in Biomedicine"). A preliminary version appeared in Proceedings of the Forty-First International Symposium on Mathematical Foundations of Computer Science (MFCS 2016), LIPIcs, Vol. 58, Article No. 53, pp. 53:1-53:14, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2016.


  57. J. Jansson, A. Lingas, R. Rajaby, and W.-K. Sung. Determining the Consistency of Resolved Triplets and Fan Triplets. Journal of Computational Biology (JCB), Vol. 25, Number 7, pp. 740-754, Mary Ann Liebert, Inc. publishers, 2018 (special issue containing selected papers from RECOMB 2017). A preliminary version appeared in Proceedings of the Twenty-First Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017), LNBI, Vol. 10229, pp. 82-98, Springer International Publishing AG, 2017. See also the summary in Algorithmic Advances and Applications from RECOMB 2017, Cell Systems, Vol. 5, Number 3, p. 181, 2017.


  58. J. Jansson, R. Rajaby, and W.-K. Sung. An Efficient Algorithm for the Rooted Triplet Distance between Galled Trees. Journal of Computational Biology (JCB), Vol. 26, Number 9, pp. 893-907, Mary Ann Liebert, Inc. publishers, 2019 (special issue containing selected papers from AlCoB 2017). A preliminary version appeared in Proceedings of the Fourth International Conference on Algorithms for Computational Biology (AlCoB 2017), LNBI, Vol. 10252, pp. 115-126, Springer International Publishing AG, 2017.


  59. Y. Asahiro, J. Jansson, E. Miyano, H. Nikpey, and H. Ono. Graph Orientation with Splits. Theoretical Computer Science (TCS), Vol. 844, pp. 16-25, Elsevier B.V., 2020. A preliminary version appeared in Proceedings of the Fifth International Symposium on Combinatorial Optimization (ISCO 2018), LNCS, Vol. 10856, pp. 52-63, Springer International Publishing AG, 2018.


  60. N. Nakajima, M. Hayashida, J. Jansson, O. Maruyama, and T. Akutsu. Determining the Minimum Number of Protein-Protein Interactions Required to Support Known Protein Complexes. PLOS ONE, Vol. 13, Number 4, Article e0195545, Public Library of Science (PLOS), 2018. Supplement.


  61. T. Akutsu, J. Jansson, R. Li, A. Takasu, and T. Tamura. New and Improved Algorithms for Unordered Tree Inclusion. Theoretical Computer Science (TCS), Vol. 883, pp. 83-98, Elsevier B.V., 2021. A preliminary version appeared in Proceedings of the Twenty-Ninth International Symposium on Algorithms and Computation (ISAAC 2018), LIPIcs, Vol. 123, Article No. 27, pp. 27:1-27:12, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2018.


  62. Y. Asahiro, J. Jansson, E. Miyano, H. Ono, and S. Thekkumpadan Puthiyaveedu. Graph Orientation with Edge Modifications. International Journal of Foundations of Computer Science (IJFCS), Vol. 32, Number 2, pp. 209-233, World Scientific Publishing Co., 2021. A preliminary version appeared in Proceedings of the Thirteenth International Workshop on Frontiers in Algorithmics (FAW 2019), LNCS, Vol. 11458, pp. 38-50, Springer Nature Switzerland AG, 2019.


  63. L. Gąsieniec, J. Jansson, C. Levcopoulos, A. Lingas, and M. Persson. Pushing the Online Boolean Matrix-Vector Conjecture Off-Line and Identifying Its Easy Cases. Journal of Computer and System Sciences (JCSS), Vol. 118, pp. 108-118, Elsevier Inc., 2021. A preliminary version appeared in Proceedings of the Thirteenth International Workshop on Frontiers in Algorithmics (FAW 2019), LNCS, Vol. 11458, pp. 156-169, Springer Nature Switzerland AG, 2019.


  64. J. Jansson, K. Mampentzidis, R. Rajaby, and W.-K. Sung. Computing the Rooted Triplet Distance between Phylogenetic Networks. Algorithmica, Vol. 83, Number 6, pp. 1786-1828, Springer Nature Switzerland AG, 2021. A preliminary version appeared in Proceedings of the Thirtieth International Workshop on Combinatorial Algorithms (IWOCA 2019), LNCS, Vol. 11638, pp. 290-303, Springer Nature Switzerland AG, 2019.


  65. Y. Asahiro, J. Jansson, G. Lin, E. Miyano, H. Ono, and T. Utashima. Exact Algorithms for the Bounded Repetition Longest Common Subsequence Problem, Theoretical Computer Science (TCS), Vol. 838, pp. 238-249, Elsevier B.V., 2020 (special issue containing selected papers from COCOA 2019). A preliminary version appeared in Proceedings of the Thirteenth International Conference on Combinatorial Optimization and Applications (COCOA 2019), LNCS, Vol. 11949, pp. 1-12, Springer Nature Switzerland AG, 2019.


  66. J. Jansson, K. Mampentzidis, and S. Thekkumpadan Puthiyaveedu. Building a Small and Informative Phylogenetic Supertree. Information and Computation, Vol. 294, Article 105082, Elsevier Inc., 2023. A preliminary version appeared in Proceedings of the Nineteenth International Workshop on Algorithms in Bioinformatics (WABI 2019), LIPIcs, Vol. 143, Article No. 1, pp. 1:1-1:14, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2019.


  67. H. Y. Yuen and J. Jansson. Normalized L3-Based Link Prediction in Protein-Protein Interaction Networks. BMC Bioinformatics, Vol. 24, Article 59, BioMed Central Ltd., 2023. Supplement. A preliminary version appeared in Proceedings of the Twentieth IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2020), pp. 53-60, IEEE Computer Society Conference Publishing Services (CPS), 2020. Winner of a Best Paper Award in Bioinformatics at IEEE BIBE 2020.


  68. J. Jansson, C. Levcopoulos, and A. Lingas. Online and Approximate Network Construction from Bounded Connectivity Constraints. International Journal of Foundations of Computer Science (IJFCS), Vol. 34, Number 5, pp. 453-468, World Scientific Publishing Co., 2023. A preliminary version appeared in Proceedings of the Twelfth International Conference on Algorithms and Complexity (CIAC 2021), LNCS, Vol. 12701, pp. 314-325, Springer Nature Switzerland AG, 2021.


  69. J. Jansson and W. L. Lee. Fast Algorithms for the Rooted Triplet Distance Between Caterpillars. Proceedings of the Twenty-Third International Symposium on Fundamentals of Computation Theory (FCT 2021), LNCS, Vol. 12867, pp. 327-340, Springer Nature Switzerland AG, 2021.


  70. L. Gąsieniec, J. Jansson, C. Levcopoulos, and A. Lingas. Efficient Assignment of Identities in Anonymous Populations. Proceedings of the Twenty-Fifth International Conference on Principles of Distributed Systems (OPODIS 2021), LIPIcs, Vol. 217, Article No. 12, pp. 12:1-12:21, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2021.


  71. Y. Asahiro, J. Jansson, G. Lin, E. Miyano, H. Ono, and T. Utashima. Polynomial-Time Equivalences and Refined Algorithms for Longest Common Subsequence Variants. Proceedings of the Thirty-Third Annual Symposium on Combinatorial Pattern Matching (CPM 2022), LIPIcs, Vol. 223, Article No. 15, pp. 15:1-15:17, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2022.


  72. R. Grossi, C. Iliopoulos, J. Jansson, Z. Lim, W.-K. Sung, and W. Zuba. Finding the Cyclic Covers of a String. Proceedings of the Seventeenth International Conference and Workshops on Algorithms and Computation (WALCOM 2023), LNCS, Vol. 13973, pp. 139-150, Springer Nature Switzerland AG, 2023.


  73. Y. Asahiro, H. Eto, M. Gong, J. Jansson, G. Lin, E. Miyano, H. Ono, and S. Tanaka. Approximation Algorithms for the Longest Run Subsequence Problem. Proceedings of the Thirty-Fourth Annual Symposium on Combinatorial Pattern Matching (CPM 2023), LIPIcs, Vol. 259, Article No. 2, pp. 2:1-2:12, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2023.


  74. C. Hampson, D. Harvey, C. Iliopoulos, J. Jansson, Z. Lim, and W.-K. Sung. MUL-Tree Pruning for Consistency and Compatibility. Proceedings of the Thirty-Fourth Annual Symposium on Combinatorial Pattern Matching (CPM 2023), LIPIcs, Vol. 259, Article No. 14, pp. 14:1-14:18, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2023.


  75. J. Jansson, C. Levcopoulos, and A. Lingas. Convex Hulls and Triangulations of Planar Point Sets on the Congested Clique. Proceedings of the Thirty-Fifth Canadian Conference on Computational Geometry (CCCG 2023), CCCG 2023 Online Proceedings, pp. 183-189, 2023.


  76. Y. Asahiro, J. Jansson, A. Melkman, E. Miyano, H. Ono, Q. Xue, and S. Zakov. Shortest Longest-Path Graph Orientations. Proceedings of the Twenty-Ninth Annual International Computing and Combinatorics Conference (COCOON 2023), LNCS, Vol. 14422, pp. 141-154, Springer Nature Switzerland AG, 2023.


  77. J. Jansson, W.-K. Sung, S. A. Tabatabaee, and Y. Yang. A Faster Algorithm for Constructing the Frequency Difference Consensus Tree. Proceedings of the Forty-First International Symposium on Theoretical Aspects of Computer Science (STACS 2024), LIPIcs, Vol. 289, Article No. 43, pp. 43:1-43:17, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2024.



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