| 2019 | WABI | Empirical Performance of Tree-Based Inference of Phylogenetic Networks. | Zhen Cao, Jiafan Zhu, Luay Nakhleh |
| 2019 | WABI | A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. | Mohammad Amin Edrisi, Hamim Zafar, Luay Nakhleh |
| 2018 | RECOMB | Detecting Large Indels Using Optical Map Data. | Xian Fan, Jie Xu, Luay Nakhleh |
| 2018 | WABI | DGEN: A Test Statistic for Detection of General Introgression Scenarios. | Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh |
| 2017 | RECOMB | Inferring Local Genealogies on Closely Related Genomes. | Ryan A. Leo Elworth, Luay Nakhleh |
| 2013 | PSB | Session introduction. | Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow |
| 2012 | CIBCB | On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks. | Natalie Berestovsky, Riya Fukui, Luay Nakhleh |
| 2012 | WABI | Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. | Yun Zhu, Luay Nakhleh |
| 2011 | RECOMB | Algorithms for MDC-Based Multi-locus Phylogeny Inference. | Yun Yu, Tandy J. Warnow, Luay Nakhleh |
| 2008 | APBC | SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. | Cuong Than, Luay Nakhleh |
| 2008 | ISMB | Efficient inference of bacterial strain trees from genome-scale multilocus data. | Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh |
| 2008 | RECOMB | Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. | Cuong Than, Guohua Jin, Luay Nakhleh |
| 2006 | APBC | RECOMP: A Parsimony-Based Method for Detecting Recombination. | Derek A. Ruths, Luay Nakhleh |
| 2006 | APBC | Techniques for Assessing Phylogenetic Branch Support: A Performance Study. | Derek A. Ruths, Luay Nakhleh |
| 2006 | COCOON | Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. | Iyad A. Kanj, Luay Nakhleh, Ge Xia |
| 2006 | RECOMB | De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. | Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram |
| 2006 | RECOMB | Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. | Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh |
| 2005 | COCOON | RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. | Luay Nakhleh, Derek A. Ruths, Li-San Wang |
| 2005 | HPCC | Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. | Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh |
| 2005 | ICCS | Phylogenetic Networks, Trees, and Clusters. | Luay Nakhleh, Li-San Wang |
| 2005 | ICPADS | PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction. | Cristian Coarfa, Yuri Dotsenko, John M. Mellor-Crummey, Luay Nakhleh, Usman Roshan |
| 2004 | RECOMB | Reconstructing reticulate evolution in species: theory and practice. | Luay Nakhleh, Tandy J. Warnow, C. Randal Linder |
| 2003 | BIBE | Requirements of Phylogenetic Databases. | Luay Nakhleh, Daniel P. Miranker, Franois Barbanon, William H. Piel, Michael J. Donoghue |
| 2003 | PADL | Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. | Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe |
| 2003 | PSB | Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. | Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse |
| 2002 | PSB | The Accuracy of Fast Phylogenetic Methods for Large Datasets. | Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |
| 2002 | WABI | Estimating the Deviation from a Molecular Clock. | Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow |
| 2001 | ISMB | Designing fast converging phylogenetic methods. | Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |
| 2001 | WABI | The Performance of Phylogenetic Methods on Trees of Bounded Diameter. | Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |