| 2017 | WABI | An IP Algorithm for RNA Folding Trajectories. | Amir H. Bayegan, Peter Clote |
| 2013 | RECOMB | Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. | Evan Senter, Saad Sheikh, Ivn Dot, Yann Ponty, Peter Clote |
| 2010 | PSB | RNA Structural Segmentation. | Ivn Dot, W. A. Lorenz, Pascal Van Hentenryck, Peter Clote |
| 2009 | BIBE | Asymptotics of Canonical RNA Secondary Structures. | Peter Clote, Evangelos Kranakis, Danny Krizanc |
| 2008 | AAAI | Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. | Manuel Cebrin, Ivn Dot, Pascal Van Hentenryck, Peter Clote |
| 2008 | CP | Protein Structure Prediction with Large Neighborhood Constraint Programming Search. | Ivn Dot, Manuel Cebrin, Pascal Van Hentenryck, Peter Clote |
| 2003 | BIBE | Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site. | Peter Clote |
| 2002 | PSB | Proteins: Structure, Function and Evolution - Session Introduction. | Peter Clote, Gavin J. P. Naylor, Ziheng Yang |
| 1999 | ICALP | Protein Folding, the Levinthal Paradox and Rapidly Mixing Markov Chains. | Peter Clote |
| 1997 | CSL | Evolution as a Computational Engine. | Rolf Backofen, Peter Clote |
| 1997 | LFCS | A Safe Recursion Scheme for Exponential Time. | Peter Clote |
| 1995 | CSL | A Note on the Relation Between Polynomial Time Functionals and Constable's Class K. | Peter Clote |
| 1993 | FOCS | Parallel computable higher type functionals (Extended Abstract) | Peter Clote, Aleksandar Ignjatovic, Bruce M. Kapron |
| 1992 | LICS | Cutting Planes and constant depth Frege proofs | Peter Clote |
| 1990 | LICS | ALOGTIME and a Conjecture of S. A. Cook (Extended Abstract) | Peter Clote |