| 2016 | CP | Constraining Redundancy to Improve Protein Docking. | Ludwig Krippahl, Pedro Barahona |
| 2014 | CP | Probabilistic Constraints for Nonlinear Inverse Problems - (Extended Abstract). | Elsa Carvalho, Jorge Cruz, Pedro Barahona |
| 2014 | CPAIOR | Representative Encodings to Translate Finite CSPs into SAT. | Pedro Barahona, Steffen Hlldobler, Van-Hau Nguyen |
| 2014 | ISAIM | Efficient SAT-Encoding of Linear CSP Constraints. | Pedro Barahona, Steffen Hlldobler, Van-Hau Nguyen |
| 2013 | AIME | Constraining Protein Docking with Coevolution Data for Medical Research. | Ludwig Krippahl, Fbio Madeira, Pedro Barahona |
| 2013 | ICTAI | Application of Hierarchical Hybrid Encodings to Efficient Translation of CSPs to SAT. | Van-Hau Nguyen, Miroslav N. Velev, Pedro Barahona |
| 2011 | IWINAC | Classification Tree Generation Constrained with Variable Weights. | Pedro Barahona, Gemma Bel Enguix, Vernica Dahl, Mara Dolores Jimnez-Lpez, Ludwig Krippahl |
| 2010 | ICAART | Biological Concept Formation Grammars - A Flexible, Multiagent Linguistic Tool for Biological Processes. | Vernica Dahl, Pedro Barahona, Gemma Bel Enguix, Ludwig Krippahl |
| 2010 | ICLP | Minimizing enzymes to diferenciate between species. | David Buezas, Joo Almeida, Pedro Barahona |
| 2010 | SAC | Probabilistic constraints for reliability problems. | Elsa Carvalho, Jorge Cruz, Pedro Barahona |
| 2009 | EPIA | Type Parametric Compilation of Algebraic Constraints. | Marco Correia, Pedro Barahona |
| 2009 | EPIA | Constraint-Based Strategy for Pairwise RNA Secondary Structure Prediction. | Olivier Perriquet, Pedro Barahona |
| 2008 | CP | On the Efficiency of Impact Based Heuristics. | Marco Correia, Pedro Barahona |
| 2008 | ICTAI | Probabilistic Continuous Constraint Satisfaction Problems. | Elsa Carvalho, Jorge Cruz, Pedro Barahona |
| 2007 | PADL | A Constraint Programming Approach to Bioinformatics Structural Problems. | Pedro Barahona, Ludwig Krippahl |
| 2005 | CP | Applying Constraint Programming to Rigid Body Protein Docking. | Ludwig Krippahl, Pedro Barahona |
| 2003 | AIME | Constraint Reasoning in Deep Biomedical Models. | Jorge Cruz, Pedro Barahona |
| 2003 | CP | Constraint Satisfaction Differential Problems. | Jorge Cruz, Pedro Barahona |
| 2003 | CP | Propagating N-Ary Rigid-Body Constraints. | Ludwig Krippahl, Pedro Barahona |
| 2002 | CP | On Optimal Correction of Inconsistent Linear Constraints. | Paula Amaral, Pedro Barahona |
| 2001 | CP | Interaction of Constraint Programming and Local Search for Optimisation Problems. | Francisco Azevedo, Pedro Barahona |
| 2001 | EPIA | Global Hull Consistency with Local Search for Continuous Constraint Solving. | Jorge Cruz, Pedro Barahona |
| 2000 | ECAI | Differentiating Diagnosis Theories through Constaints over an Eight-valued Logic. | Francisco Azevedo, Pedro Barahona |
| 1999 | CP | An Interval Constraint Approach to Handle Parametric Ordinary Differential Equations for Decision Support. | Jorge Cruz, Pedro Barahona |
| 1999 | CP | Applying Constraint Programming to Protein Structure Determination. | Ludwig Krippahl, Pedro Barahona |
| 1998 | CP | Generation of Test Patterns for Differential Diagnosis of Digital Circuits. | Francisco Azevedo, Pedro Barahona |
| 1997 | AIME | A Causal-Functional Model Applied to EMG Diagnosis. | Jorge Cruz, Pedro Barahona |
| 1996 | CP | Defeasibility in CLP(Q) through Generalized Slack Variables. | Christian Holzbaur, Francisco Menezes, Pedro Barahona |
| 1995 | AIME | Semi-Qualitative Models and Simulation for Biomedical Applications. | Pedro Barahona |
| 1995 | CP | Defeasible Constraint Solving. | Francisco Menezes, Pedro Barahona |
| 1993 | EPIA | Preliminary Formalization of an Incremental Hierarchical Constraint Solver. | Francisco Menezes, Pedro Barahona |
| 1991 | AIME | A Framework for Causal Reasoning with a Functional Approach. | Pedro Barahona, Mario Veloso |
| 1991 | EPIA | Constraint Solving in Finite Domains under User Control. | Francisco Menezes, Pedro Barahona |
| 1989 | AIME | Some Issues in the Control of Interactive Differential Diagnosis. | Pedro Barahona, Mario Veloso, Ricardo Amador, Francisco Menezes |