| 2017 | CIAC | Weak Coverage of a Rectangular Barrier. | Stefan Dobrev, Evangelos Kranakis, Danny Krizanc, Manuel Lafond, Jn Manuch, Lata Narayanan, Jaroslav Opatrny, Sunil M. Shende, Ladislav Stacho |
| 2017 | DNA | Simplifying Analyses of Chemical Reaction Networks for Approximate Majority. | Anne Condon, Monir Hajiaghayi, David G. Kirkpatrick, Jn Manuch |
| 2015 | CPM | Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. | Jozef Hales, Jn Manuch, Yann Ponty, Ladislav Stacho |
| 2012 | CPM | The Complexity of String Partitioning. | Anne Condon, Jn Manuch, Chris Thachuk |
| 2012 | DNA | Turing Universality of Step-Wise and Stage Assembly at Temperature 1. | Bahar Behsaz, Jn Manuch, Ladislav Stacho |
| 2012 | DNA | Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems. | Anne Condon, Bonnie Kirkpatrick, Jn Manuch |
| 2011 | CPM | Tractability Results for the Consecutive-Ones Property with Multiplicity. | Cdric Chauve, Jn Manuch, Murray Patterson, Roland Wittler |
| 2011 | DNA | Less Haste, Less Waste: On Recycling and Its Limits in Strand Displacement Systems. | Anne Condon, Alan J. Hu, Jn Manuch, Chris Thachuk |
| 2010 | GD | Complexity of Finding Non-Planar Rectilinear Drawings of Graphs. | Jn Manuch, Murray Patterson, Sheung-Hung Poon, Chris Thachuk |
| 2010 | PSB | An Algorithm for the Energy Barrier Problem Without Pseudoknots and Temporary Arcs. | Chris Thachuk, Jn Manuch, Arash Rafiey, Leigh-Anne Mathieson, Ladislav Stacho, Anne Condon |
| 2010 | RECOMB | The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree. | Jn Manuch, Murray Patterson |
| 2009 | COCOON | On the Generalised Character Compatibility Problem for Non-branching Character Trees. | Jn Manuch, Murray Patterson, Arvind Gupta |
| 2009 | DNA | NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. | Jn Manuch, Chris Thachuk, Ladislav Stacho, Anne Condon |
| 2009 | ISAAC | Step-Assembly with a Constant Number of Tile Types. | Jn Manuch, Ladislav Stacho, Christine Stoll |
| 2009 | SAC | Two lower bounds for self-assemblies at temperature 1. | Jn Manuch, Ladislav Stacho, Christine Stoll |
| 2008 | APBC | Structure-Approximating Design of Stable Proteins in 2D HP Model Fortified by Cysteine Monomers. | Alireza Hadj Khodabakhshi, Jn Manuch, Arash Rafiey, Arvind Gupta |
| 2008 | COCOON | Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. | Anne Condon, Jn Manuch, Chris Thachuk |
| 2008 | COCOON | Haplotype Inferring Via Galled-Tree Networks Is NP-Complete. | Arvind Gupta, Jn Manuch, Ladislav Stacho, Xiaohong Zhao |
| 2007 | APBC | Fitting Protein Chains to Cubic Lattice is NP-Complete. | Jn Manuch, Daya Ram Gaur |
| 2006 | APBC | Characterization of the Existence of Galled-Tree Networks. | Jn Manuch, Xiaohong Zhao, Ladislav Stacho, Arvind Gupta |
| 2006 | LPAR | Constructing Camin-Sokal Phylogenies Via Answer Set Programming. | Jonathan Kavanagh, David G. Mitchell, Eugenia Ternovska, Jn Manuch, Xiaohong Zhao, Arvind Gupta |
| 2004 | CPM | Small Phylogeny Problem: Character Evolution Trees. | Arvind Gupta, Jn Manuch, Ladislav Stacho, Chenchen Zhu |
| 2004 | SIROCCO | Fault Tolerant Forwarding and Optical Indexes: A Design Theory Approach. | Arvind Gupta, Jn Manuch, Ladislav Stacho |
| 2001 | MFCS | On the Computational Complexity of Infinite Words. | Pavol Duris, Jn Manuch |
| 1999 | DLT | Characterization of a word by its subwords. | Jn Manuch |
| 1999 | MFCS | Multiparty Communication Complexity: Very Hard Functions. | Jn Manuch |
| 1999 | SIROCCO | Fault-Tolerant Wavelength Allocations in All-optical Hypercubes. | Jn Manuch, Ladislav Stacho |
| 1998 | MFCS | On Defect Effect of Bi-Infinite Words. | Juhani Karhumki, Jn Manuch, Wojciech Plandowski |