Conference and Workshop Publications:

Extended Abstracts:

  1. Hales, J., Manuch, J., Ponty, Y., Stacho, L., Combinatorial RNA design: Designability and structure-approximating algorithm Combinatorial Pattern Matching (CPM, 2015) LNCS 9133, 231-246 2015 SLIDES
  2. Chen H-L., Doty, D., Manuch, J., Rafiey, A., Stacho, L., Pattern overlap implies runaway growth in hierarchical tile systems Annual Symposium on Computational Geometry (SOCG, 2015) LIPIcs 34, 360-373 2015 SLIDES
  3. Safaei, J., Manuch, J., Stacho, L., Learning polytrees with constant number of roots from data Australasian Joint Conference on Artificial Intelligence (AI, 2013) LNCS 8272, 447-452 2013 SLIDES
  4. Manuch, J., Patterson, M., Wittler, R., Chauve, C., Tannier, E., Linearization of ancestral multichromosomal genomes Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG, 2012) BMC Bioinformatics 13(Suppl 19), S11 2012 SLIDES by M. Patterson
  5. Condon, A., Kirkpatrick, B., Manuch, J., Reachability bounds for chemical reaction networks and strand displacement systems International Meeting on DNA Computing and Molecular Programming (DNA, 2012) Lecture Notes in Computer Science 7433, 43-57 2012 SLIDES by B. Kirkpatrick
  6. Behsaz, B., Manuch, J., Stacho, L., Turing universality of step-wise and stage assembly at temperature 1 International Meeting on DNA Computing and Molecular Programming (DNA, 2012) Lecture Notes in Computer Science 7433, 1-11 2012 SLIDES by B. Behsaz
  7. Condon, A., Manuch, J., Thachuk, C., The complexity of string partitioning Combinatorial Pattern Matching (CPM, 2012) Lecture Notes in Computer Science 7354, 159-172 2012 SLIDES
  8. Safaei, J., Manuch, J., Gupta, A., Stacho, L., Pelech, S., Evolutionary conservation of human phosphorylation sites IEEE International Conference of Bioinformatics and Biomedicine (BIBM, 2011) IEEE Computer Society 222-227 2011 SLIDES by J. Safaei
  9. Condon, A., Hu, A., Manuch, J., Thachuk, C., Less haste, less waste: On recycling and its limits in strand displacement systems International Meeting on DNA Computing and Molecular Programming (DNA17, 2011) Lecture Notes in Computer Science 6937, 84-99 2011 SLIDES by C. Thachuk
  10. Chauve, C., Manuch, J., Patterson, M., Wittler, R., Tractability results for the consecutive-ones property with multiplicity Combinatorial Pattern Matching (CPM, 2011) Lecture Notes in Computer Science 6661, 90-103 2011 SLIDES by M. Patterson
  11. Manuch, J., Patterson, M., A. Gupta, Towards a characterisation of the generalised character compatibility problem for non-branching character trees International Symposium on Bioinformatics Research and Applications (ISBRA, 2011) Lecture Notes in Bioinformatics 6674, 440-451 2011 SLIDES
  12. Safaei, J., Manuch, J., Gupta, A., Stacho, L., Pelech, S., Prediction of human protein kinase substrate specificities IEEE International Conference of Bioinformatics and Biomedicine (BIBM, 2010) IEEE Computer Society 259-264 2010 SLIDES by J. Safaei
  13. Manuch, J., Patterson, M., The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG, 2010) Lecture Notes in Bioinformatics 6398, 278-289 2010 SLIDES
  14. Manuch, J., Patterson, M., Poon S.-H., Thachuk, C., Complexity of finding non-planar rectilinear drawings of graphs International Symposium on Graph Drawing (GD, 2010) Lecture Notes in Computer Science 6502, 305-316 2011 SLIDES by M. Patterson
  15. Thachuk, C., Manuch, J., Rafiey, A., Mathieson, L-A., Stacho, L., Condon, A., An algorithm for the energy barrier problem without pseudoknots and temporary arcs Pacific Symposium on Biocomputing (PSB, 2010) World Scientific Publishing 108-119 2010 SLIDES by C. Thachuk
  16. Manuch, J., Stacho, L., Stoll, C., Step-assembly with a constant number of tile types International Symposium on Algorithms and Computation (ISAAC, 2009) Lecture Notes in Computer Science 5878, 954-963 2009 SLIDES
  17. Chauve, C., Manuch, J., Patterson, M., On the gapped consecutive-one property European Conference on Combinatorics, Graph Theory and Applications (EUROCOMB, 2009) Electronic Notes in Discrete Mathematics 34, 121-125 2009 SLIDES by M. Patterson
  18. Manuch, J., Thachuk, C., Stacho, L., Condon, A., NP-completeness of the direct energy barrier problem without pseudoknots International Meeting on DNA computing and Molecular Programming (DNA15, 2009) Lecture Notes in Computer Science 5877, 106-115 2009 SLIDES by A. Condon
  19. Manuch, J., Patterson, M., Gupta, A., On the generalized character compatibility problem for non-branching character trees Annual International Computing and Combinatorics Conference (COCOON, 2009) Lecture Notes in Computer Science 5609, 268-276 2009 SLIDES by M. Patterson
  20. Manuch, J., Stacho, L., Stoll, C., Two lower bounds for self-assemblies at temperature 1 International Conference on Bioinformatics and Biomedical Engineering (iCBBE, 2009) 10.1109/ICBBE:2009.5163719 1-4 2009 SLIDES
  21. Khodabakhshi, A.H., Manuch, J., Rafiey, A., Gupta, A., Inverse protein folding in 3D hexagonal prism lattice under HP model International Conference on Bioinformatics & Computational Biology (BIOCOMP, 2008) CSREA Press 619-625 2008
  22. Khodabakhshi, A.H., Manuch, J., Rafiey, A., Gupta, A., A robust class of stable proteins in the 2D HPC model International Conference on Bioinformatics Research and Development (BIRD, 2008) Communications in Computer and Information Science 13, 180-192 2008 SLIDES by A.H. Khodabakhshi
  23. Gupta, A., Manuch, J., Stacho, L., Zhao, X., Haplotype inferring via galled-tree networks is NP-complete Annual International Computing and Combinatorics Conference (COCOON, 2008) Lecture Notes in Computer Science 5902, 287-298 2008 SLIDES
  24. Condon, A., Manuch, J., Thachuk, C., Complexity of a collision-aware string partition problem and its relation to oligo design for gene synthesis Annual International Computing and Combinatorics Conference (COCOON, 2008) Lecture Notes in Computer Science 5902, 265-275 2008 SLIDES by C. Thachuk
  25. Khodabakhshi, A.H., Manuch, J., Rafiey, A., Gupta, A., Structure-approximating design of stable proteins in 2D HP model fortified by cysteine monomers Asia Pacific Bioinformatics Conference (APBC, 2008) Advances in Bioinformatics and Computational Biology 6, 49-58 2008 SLIDES
  26. Gupta, A., Karimi, M., Khodabakhshi, A.H., Manuch, J., Rafiey, A., Design of artificial protein structures in 3D hexagonal prism lattice under HP model International Conference on Bioinformatics & Computational Biology (BIOCOMP, 2007) CSREA Press 362-369 2007 SLIDES
  27. Gupta, A., Manuch, J., Stacho, L., Zhao, X., Algorithm for haplotype inferring via galled-tree networks with simple galls (extended abstract) International Symposium on Bioinformatics Research and Applications (ISBRA, 2007) Lecture Notes in Bioinformatics 4463, 121-132 2007 SLIDES
  28. Manuch, J., Gaur, D.R., Fitting protein chains to cubic lattice is NP-complete Asia Pacific Bioinformatics Conference (APBC, 2007) Advances in Bioinformatics and Computational Biology 5, 153-164 2007 SLIDES
  29. Kavanagh, J., Mitchell, D., Ternovska, E., Manuch, J., Zhao, X., Gupta, A., Constructing Camin-Sokal phylogenies via answer set programming Logic for Programming, Artificial Intelligence, and Reasoning (LPAR, 2006) Lecture Notes in Computer Science 4246, 452-466 2006
  30. Gaur, D.R., Krishnamurti, R., Manuch, J., Improved approximation algorithm for scheduling tasks with a choice of start times Algorithms and Complexity in Durham (ACiD, 2006) Texts in Algorithmics 7, 85-94 2006 SLIDES
  31. Gupta, A., Manuch, J., Stacho, L., Zhao, X., Characterization of the existence of galled-tree networks (extended abstract) Asia Pacific Bioinformatics Conference (APBC, 2006) Imperial College Press 297-306 2006 SLIDES
  32. Brown, T., Manuch, J., A simple proof of Lerch's formula International Conference on Fibonacci Numbers and Their Applications (2004) Kluwer Academic Publishers Applications of Fibonacci Numbers 10, to appear
  33. Gupta, A., Manuch, J., Stacho, L., Inverse protein folding in 2D HP model (extended abstract) Computation System Bioinformatics (CSB, 2004) IEEE Computer Society 311-318 2004 POSTER
  34. Gupta, A., Manuch, J., Stacho, L., Zhu, C., Small phylogeny problem: Character evolution trees Combinatorial Pattern Matching (CPM, 2004) Lecture Notes in Computer Science 3109, 230-243 2004 SLIDES
  35. Gupta, A., Manuch, J., Stacho, L., Fault tolerant forwarding and optical indexes: A design theory approach Colloquium on Struct. Information and Comm. Complexity (SIROCCO, 2004) Lecture Notes in Computer Science 3104, 197-208 2004
  36. Duris, P., Manuch, J., On the computational complexity of infinite words Math. Foundations of Comp. Sci. (MFCS, 2001) Lecture Notes in Computer Science 2136, 328-337 2001
  37. Manuch, J., Characterization of a word by its subwords Developments in language theory: Foundations, applications, and perspectives (DLT, 2000) World Scientific 210-219 2000
  38. Manuch, J., Stacho, L., Fault-tolerant wavelength allocations in faulty all-optical hypercubes Colloquium on Struct. Information and Comm. Complexity (SIROCCO, 1999) Carleton Scientific 219-222 1999
  39. Manuch, J., Multiparty communication complexity: Very hard functions Math. Foundations of Comp. Sci. (MFCS, 1999) Lecture Notes in Computer Science 1672, 160-169 1999
  40. Karhumaki, J., Manuch, J., Plandowski, W., On defect effect of bi-infinite words Math. Foundations of Comp. Sci. (MFCS, 1998) Lecture Notes in Computer Science 1450, 674-682 1998

Short Abstracts:

  1. Manuch, Stacho, L., Stoll, C., Two lower bounds for self-assemblies at temperature 1 (poster abstract) Annual ACM Symposium on Applied Computing (Bioinformatics Track) (ACM SAC BIO, 2009) ACM 808-809 2009 POSTER by C. Stoll
  2. Gupta, A., Heuvel, J., Manuch, J., Stacho, L., Zhao, X., On the complexity of ordered colorings (short abstract) Algorithms and Complexity in Durham (ACiD, 2006) Texts in Algorithmics 7, 156 2006 SLIDES by J. Heuvel
  3. Mead, C.R., Manuch, J., Huang, X., Bhattacharyya, B., Stacho, L., Gupta, A., Investigating lattice structure for inverse protein folding FEBS Congrese & 9th IUBM Conference: The Protein World (2005) FEBS Journal 272 (s1), 4739_1_380 2005 POSTER by C.R. Mead

Without Proceedings:

  1. Khodabakhshi, A.H., Manuch, J., Rafiey, A., Stacho, L., Gupta, A., Protein designs in HP models Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO) 2008 SLIDES
  2. Thomas, D., Manuch, J., Gaur, D., Experiments on fitting protein chains to lattices (poster) Asia Pacific Bioinformatics Conference (APBC) 2007
  3. Manuch, J., Gaur, D. R., Huang, X., Benkoczi, R., Fitting protein chains to lattices SIAM Conference on Discrete Mathematics 2006 SLIDES
  4. Gupta, A., Manuch, J., Stacho, L., Zhao, X., On intractability of haplotype inferring via galled-tree networks Workshop on Networks in Computational Biology 2006 SLIDES by X. Zhao
  5. Manuch, J., Mead, C.R., Huang, X., Bhattacharyya, B., Stacho, L., Gupta, A., On design of stable proteins in 3D HP Model (poster) Metalloprotein and Protein Design Conference 2005
  6. Cassaigne, J., Karhumaki, J., Manuch, J., Conjugation of languages WORDS 2001
  7. Karhumaki, J., Manuch, J., Multiple factorizations of words and defect effect WORDS 1999
  8. Verdier, A., Manuch, J., Computation on fixed points in a circular machine Particle Accelerator Conference 1997