Journal Publications:

  1. Condon, A., Hu, A., Manuch, J., Thachuk, C., Less haste, less waste: on recycling and its limits in strand displacement systems Interface Focus to appear
  2. Manuch, J., Stacho, L., Stoll, C., Step-wise tile assembly with a constant number of tile types Natural Computing to appear
  3. Gupta, A., Manuch, J., Stacho, L., Zhao, X., Algorithm for haplotype inference via galled-tree networks with simple galls Journal of Computational Biology to appear
  4. Manuch, J., Patterson, M., The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree Journal of Computational Biology 18 9 1243-1253 2011
  5. Wittler, R., Manuch, J., Patterson, M., Stoye, J., Consistency of sequence-based gene clusters Journal of Computational Biology 18 9 1023-1039 2011
  6. Safaei, J., Manuch, J., Gupta, A., Stacho, L., Pelech, S., Prediction of 492 human protein kinase substrate specificities Proteome Science 9(Suppl 1) S6 2011
  7. Manuch, J., Thachuk, C., Stacho, L., Condon, A., NP-completeness of the energy barrier problem without pseudoknots and temporary arcs Natural Computing 10 1 391-405 2011
  8. Gupta, A., Karimi, M., Manuch, J., Stacho, L., Zhao, X., Haplotype inference via galled-tree networks is NP-complete Journal of Computational Biology 17 10 1435-1449 2010
  9. Manuch, J., Stacho, L., Stoll, C., Two lower bounds for self-assemblies at temperature 1 Journal of Computational Biology 17 6 841-852 2010
  10. Adams, P., Ardal, H., Manuch, J., Hoa, V.D., Rosenfeld, M., Stacho, L., Spanning cubic graph designs Discrete Mathematics 309 18 5781-5788 2009
  11. Khodabakhshi, A.H., Manuch, J., Rafiey, A., Gupta, A., Inverse protein folding in 3D hexagonal prism lattice under HPC model Journal of Computational Biology 16 6 769-802 2009
  12. Ardal, H., Manuch, J., Rosenfeld, M., Shelah, S., Stacho, L., The odd-distance plane graph Discrete & Computational Geometry 42 2 132-141 2009
  13. Gupta, A., Manuch, J., Stacho, L., Zhao, X., Haplotype inferring via galled-tree networks using a hypergraph covering problem for special genotype matrices Discrete Applied Mathematics 157 10 2310-2324 2009
  14. Khodabakhshi, A., Manuch, J., Rafiey, A., Gupta, A., Stable structure-approximating inverse protein folding in 2D Hydrophobic-Polar-Cysteine (HPC) model Journal of Computational Biology 16 1 19-30 2009
  15. Gupta, A., Heuvel, J., Manuch, J., Stacho, L., Zhao, X., On the complexity of ordered colorings SIAM Journal on Discrete Mathematics 22 2 832-847 2008
  16. Manuch, J., Gaur, D.R., Fitting protein chains to cubic lattice is NP-complete Journal of Bioinformatics and Computational Biology 6 1 93-106 2008
  17. Gupta, A., Manuch, J., Stacho, L., Zhao, X., Characterization of the existence of galled-tree networks Journal of Bioinformatics and Computational Biology 4 6 1309-1328 2006
  18. Gupta, A., Manuch, J., Stacho, L., Fault tolerant forwarding and optical indexes: A design theory approach Journal of Combinatorial Designs 14 1 25-40 2006
  19. Gupta, A., Manuch, J., Stacho, L., Structure-approximating inverse protein folding problem in 2D HP model Journal of Computational Biology 12 10 1328-1345 2005
  20. Berenbrink, P., Friedetzky, T., Manuch, J., Stacho, L., (Quasi) spanners for mobile ad hoc networks Journal of Interconnection Networks 6 2 63-84 2005
  21. Manuch, J., Stacho, L., On f-wise arc forwarding index and wavelength allocations in faulty all-optical hypercubes Theoretical Informatics and Applications 37 3 255-270 2003
  22. Duris, P., Manuch, J., On the computational complexity of infinite words Theoretical Computer Science 295 1-3 141-151 2003
  23. Karhumaki, J., Manuch, J., Plandowski, W., A defect theorem for bi-infinite words Theoretical Computer Science 292 1 237-243 2003
  24. Karhumaki, J., Manuch, J., Multiple factorizations of words and defect effect Theoretical Computer Science 273 1-2 81-97 2002
  25. Cassaigne, J., Karhumaki, J., Manuch, J., On conjugacy of languages Theoretical Informatics and Applications 35 6 535-550 2001
  26. Manuch, J., Defect effect of bi-infinite words in the two-element case Discrete Mathematics and Theoretical Computer Science 4 2 273-290 2001
  27. Manuch, J., Construction of very hard functions for multiparty communication complexity Theoretical Informatics and Applications 34 1 61-75 2000
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