| 2016 | CPM | Fast Compatibility Testing for Rooted Phylogenetic Trees. | Yun Deng, David Fernndez-Baca |
| 2016 | WABI | Fast Compatibility Testing for Phylogenies with Nested Taxa. | Yun Deng, David Fernndez-Baca |
| 2013 | WABI | Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. | Sudheer Vakati, David Fernndez-Baca |
| 2012 | CPM | Fixed-Parameter Algorithms for Finding Agreement Supertrees. | David Fernndez-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati |
| 2012 | WABI | Extracting Conflict-Free Information from Multi-labeled Trees. | Akshay Deepak, David Fernndez-Baca, Michelle M. McMahon |
| 2012 | WABI | Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. | Brad Shutters, Sudheer Vakati, David Fernndez-Baca |
| 2011 | WABI | Constructing Large Conservative Supertrees. | Jianrong Dong, David Fernndez-Baca |
| 2009 | WABI | Constructing Majority-Rule Supertrees. | Jianrong Dong, David Fernndez-Baca, Fred R. McMorris |
| 2008 | LATIN | Comparing and Aggregating Partially Resolved Trees. | Mukul S. Bansal, Jianrong Dong, David Fernndez-Baca |
| 2005 | CPM | Parametric Analysis for Ungapped Markov Models of Evolution. | David Fernndez-Baca, Balaji Venkatachalam |
| 2002 | COCOON | Supertrees by Flipping. | Duhong Chen, Oliver Eulenstein, David Fernndez-Baca, Michael J. Sanderson |
| 2002 | COCOON | Inverse Parametric Sequence Alignment. | Fangting Sun, David Fernndez-Baca, Wei Yu |
| 2000 | CPM | Parametric Multiple Sequence Alignment and Phylogeny Construction. | David Fernndez-Baca, Timo Sepplinen, Giora Slutzki |
| 2000 | LATIN | Multi-parameter Minimum Spanning Trees. | David Fernndez-Baca |
| 1999 | SPIRE | Bounds for Parametric Sequence Comparison. | David Fernndez-Baca, Timo Sepplinen, Giora Slutzki |
| 1998 | LATIN | Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry. | David Fernndez-Baca |
| 1996 | ICALP | A Polynomial-Time Algorithm for Near-Perfect Phylogeny. | David Fernndez-Baca, Jens Lagergren |
| 1996 | ISAAC | On the Approximability of the Steiner Tree Problem in Phylogeny. | David Fernndez-Baca, Jens Lagergren |
| 1995 | LATIN | Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. | David Fernndez-Baca, Giora Slutzki |
| 1993 | FOCS | A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed | Richa Agarwala, David Fernndez-Baca |
| 1989 | WADS | Augmentation Problems on Hierarchically Defined Graphs (Preliminary Version). | David Fernndez-Baca, Mark A. Williams |
| 1988 | STACS | Solving Parametric Problems on Trees. | David Fernndez-Baca, Giora Slutzki |