| 2024 | WABI | Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. | Lukas Hbner, Alexandros Stamatakis |
| 2017 | HPCC | A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats. | Benoit Morel, Toms Flouri, Alexandros Stamatakis |
| 2014 | WABI | The Divisible Load Balance Problem and Its Application to Phylogenetic Inference. | Kassian Kobert, Toms Flouri, Andre J. Aberer, Alexandros Stamatakis |
| 2013 | IWOCA | An Optimal Algorithm for Computing All Subtree Repeats in Trees. | Toms Flouri, Kassian Kobert, Solon P. Pissis, Alexandros Stamatakis |
| 2013 | PPAM | Accelerating String Matching on MIC Architecture for Motif Extraction. | Solon P. Pissis, Christian Goll, Pavlos Pavlidis, Alexandros Stamatakis |
| 2012 | ICA3PP | Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection. | Nikolaos Alachiotis, Pavlos Pavlidis, Alexandros Stamatakis |
| 2011 | FCCM | Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. | Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis |
| 2011 | FPL | FPGA Acceleration of the Phylogenetic Parsimony Kernel? | Nikolaos Alachiotis, Alexandros Stamatakis |
| 2010 | AICCSA | Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood. | Simon A. Berger, Alexandros Stamatakis |
| 2010 | AICCSA | Evolutionary placement of short sequence reads on multi-core architectures. | Alexandros Stamatakis, Zsolt Komornik, Simon A. Berger |
| 2009 | FPL | A reconfigurable architecture for the Phylogenetic Likelihood Function. | Nikolaos Alachiotis, Alexandros Stamatakis, Euripides Sotiriades, Apostolos Dollas |
| 2009 | ICPP | Fine-grain Parallelism Using Multi-core, Cell/BE, and GPU Systems: Accelerating the Phylogenetic Likelihood Function. | Frederico Pratas, Pedro Trancoso, Alexandros Stamatakis, Leonel Sousa |
| 2009 | ICPP | Load Balance in the Phylogenetic Likelihood Kernel. | Alexandros Stamatakis, Michael Ott |
| 2009 | PPAM | Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction. | Simon A. Berger, Alexandros Stamatakis |
| 2009 | RECOMB | How Many Bootstrap Replicates Are Necessary? | Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis |
| 2007 | PPoPP | Dynamic multigrain parallelization on the cell broadband engine. | Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos |
| 2007 | SC | Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. | Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru |
| 2005 | HPCC | Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. | Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh |
| 2005 | PACT | RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs. | Alexandros Stamatakis, Michael Ott, Thomas Ludwig |
| 2004 | EuroPar | Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood. | Alexandros Stamatakis, Thomas Ludwig, Harald Meier |
| 2004 | SAC | A fast program for maximum likelihood-based inference of large phylogenetic trees. | Alexandros Stamatakis, Thomas Ludwig, Harald Meier |
| 2003 | PACT | DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA. | Alexandros Stamatakis, Markus Lindermeier, Michael Ott, Thomas Ludwig, Harald Meier |
| 2002 | SC | Accelerating parallel maximum likelihood-based phylogenetic tree calculations using subtree equality vectors. | Alexandros Stamatakis, Thomas Ludwig, Harald Meier, Marty J. Wolf |
| 2001 | PACT | Tool Environments in CORBA-Based Medical High Performance Computing. | Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, Gnther Rackl |