| 2007 | RECOMB | Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. | Jol R. Pradines, Vlado Danck, Alan Ruttenberg, Victor Farutin |
| 2000 | RECOMB | Mutation-tolerant protein identification by mass-spectrometry. | Pavel A. Pevzner, Vlado Danck, Chris L. Tang |
| 1999 | RECOMB | De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach. | Vlado Danck, Theresa A. Addona, Karl R. Clauser, James E. Vath |
| 1998 | RECOMB | Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo. | Jae Kyu Lee, Vlado Danck, Michael S. Waterman |
| 1997 | RECOMB | Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. | Richa Agarwala, Serafim Batzoglou, Vlado Danck, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, Steven Skiena |
| 1997 | SODA | Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model. | Richa Agarwala, Serafim Batzoglou, Vlado Danck, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena |
| 1995 | CPM | Common Subsequences and Supersequences and Their expected Length. | Vlado Danck |
| 1994 | MFCS | Longest Common Subsequences. | Mike Paterson, Vlado Danck |
| 1994 | STACS | Upper Bounds for the Expected Length of a Longest Common Subsequence of Two Binary Sequences. | Vlado Danck, Mike Paterson |