Alexandros Stamatakis

127 papers A 9B 9C 8Misc 3Journal 61Unranked 34

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Bit-reproducible parallel phylogenetic tree inference. Bioinform. Christoph Stelz, Lukas Hübner, Alexandros Stamatakis
2025	J	`jnl`	The Cognate Data Bottleneck in Language Phylogenetics. CoRR Luise Häuser, Alexandros Stamatakis
2024	J	`jnl`	AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss. Bioinform. Benoit Morel, Tom A. Williams, Alexandros Stamatakis, Gergely J. Szöllosi
2024	—	`conf`	Are Sounds Sound for Phylogenetic Reconstruction? SIGTYPE Luise Häuser, Gerhard Jäger, Johann-Mattis List, Taraka Rama, Alexandros Stamatakis
2024	J	`jnl`	Are Sounds Sound for Phylogenetic Reconstruction? CoRR Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis
2024	J	`jnl`	Computational Approaches for Integrating out Subjectivity in Cognate Synonym Selection. CoRR Luise Häuser, Gerhard Jäger, Alexandros Stamatakis
2024	C	`conf`	EcoFreq: Compute with Cheaper, Cleaner Energy via Carbon-Aware Power Scaling. ISC Oleksiy M. Kozlov, Alexandros Stamatakis
2024	C	`conf`	Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. WABI Lukas Hübner, Alexandros Stamatakis
2023	J	`jnl`	Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data. Bioinform. Benoit Morel, Tom A. Williams, Alexandros Stamatakis
2023	—	`conf`	Parallel Inference of Phylogenetic Stands with Gentrius. IPDPS Workshops Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis
2023	J	`jnl`	Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods. Stat. Comput. Ben Bettisworth, Alexander I. Jordan, Alexandros Stamatakis
2022	J	`jnl`	A LASSO-based approach to sample sites for phylogenetic tree search. Bioinform. Noa Ecker, Dana Azouri, Ben Bettisworth, Alexandros Stamatakis, Yishay Mansour, Itay Mayrose, Tal Pupko
2022	J	`jnl`	Metagenomic Analysis Using Phylogenetic Placement - A Review of the First Decade. Frontiers Bioinform. Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera
2022	J	`jnl`	NetRAX: accurate and fast maximum likelihood phylogenetic network inference. Bioinform. Sarah Lutteropp, Céline Scornavacca, Alexey M. Kozlov, Benoit Morel, Alexandros Stamatakis
2022	J	`jnl`	RAxML Grove: an empirical phylogenetic tree database. Bioinform. Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis
2022	—	`conf`	ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms. FTXS@SC Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis
2022	J	`jnl`	ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms. CoRR Demian Hespe, Lukas Hübner, Peter Sanders, Alexandros Stamatakis
2021	—	`conf`	Efficient Memory Management in Likelihood-based Phylogenetic Placement. IPDPS Workshops Pierre Barbera, Alexandros Stamatakis
2021	J	`jnl`	Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG. Bioinform. Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis
2021	J	`jnl`	Root Digger: a root placement program for phylogenetic trees. BMC Bioinform. Ben Bettisworth, Alexandros Stamatakis
2021	J	`jnl`	Swarm v3: towards tera-scale amplicon clustering. Bioinform. Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes
2020	J	`jnl`	A fast and memory-efficient implementation of the transfer bootstrap. Bioinform. Sarah Lutteropp, Alexey M. Kozlov, Alexandros Stamatakis
2020	J	`jnl`	Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data. Bioinform. Lucas Czech, Pierre Barbera, Alexandros Stamatakis
2020	J	`jnl`	Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Bioinform. Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Céline Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier, David P. Parsons
2019	J	`jnl`	12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
2019	—	`conf`	Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning. IPDPS Workshops Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel
2019	J	`jnl`	Methods for automatic reference trees and multilevel phylogenetic placement. Bioinform. Lucas Czech, Pierre Barbera, Alexandros Stamatakis
2019	J	`jnl`	ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes. Bioinform. Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis
2019	J	`jnl`	RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinform. Alexey M. Kozlov, Diego Darriba, Tomás Flouri, Benoit Morel, Alexandros Stamatakis
2018	J	`jnl`	Two C++ libraries for counting trees on a phylogenetic terrace. Bioinform. Rudolf Biczok, Peter Bozsoky, Peter Eisenmann, Johannes Ernst, Tobias Ribizel, Fedor Scholz, Axel Trefzer, Florian Weber, Michael Hamann, Alexandros Stamatakis
2017	—	`conf`	A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats. HPCC/SmartCity/DSS Benoit Morel, Tomás Flouri, Alexandros Stamatakis
2017	—	`ch.`	An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties. Algorithms for Next-Generation Sequencing Data Tomás Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis
2017	J	`jnl`	Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinform. Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlidis, Alexandros Stamatakis, Tomás Flouri
2016	—	`conf`	A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. KSE Diep Thi Hoang, Le Sy Vinh, Tomás Flouri, Alexandros Stamatakis, Arndt von Haeseler, Bui Quang Minh
2016	J	`jnl`	Does the choice of nucleotide substitution models matter topologically? BMC Bioinform. Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba, Alexandros Stamatakis
2016	J	`jnl`	Prediction of missing sequences and branch lengths in phylogenomic data. Bioinform. Diego Darriba, Michael Weiß, Alexandros Stamatakis
2016	—	`conf`	The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference. IPDPS Workshops Constantin Scholl, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis
2015	J	`jnl`	ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinform. Alexey M. Kozlov, Andre J. Aberer, Alexandros Stamatakis
2014	—	`conf`	Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture. IPDPS Workshops Alexey M. Kozlov, Christian Goll, Alexandros Stamatakis
2014	J	`jnl`	Is the Protein Model Assignment problem under linked branch lengths NP-hard? Theor. Comput. Sci. Kassian Kobert, Jörg Hauser, Alexandros Stamatakis
2014	J	`jnl`	Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinform. Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin
2014	J	`jnl`	PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinform. Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis
2014	J	`jnl`	PUmPER: phylogenies updated perpetually. Bioinform. Fernando Izquierdo-Carrasco, John Cazes, Stephen A. Smith, Alexandros Stamatakis
2014	J	`jnl`	RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinform. Alexandros Stamatakis
2014	C	`conf`	The Divisible Load Balance Problem and Its Application to Phylogenetic Inference. WABI Kassian Kobert, Tomás Flouri, Andre J. Aberer, Alexandros Stamatakis
2013	—	`conf`	A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. IPDPS Workshops Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis
2013	J	`jnl`	A general species delimitation method with applications to phylogenetic placements. Bioinform. Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis, Alexandros Stamatakis
2013	—	`conf`	Accelerating String Matching on MIC Architecture for Motif Extraction. PPAM (2) Solon P. Pissis, Christian Goll, Pavlos Pavlidis, Alexandros Stamatakis
2013	C	`conf`	An Optimal Algorithm for Computing All Subtree Repeats in Trees. IWOCA Tomás Flouri, Kassian Kobert, Solon P. Pissis, Alexandros Stamatakis
2013	—	`conf`	Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library. IPDPS Workshops Diego Darriba, Andre J. Aberer, Tomás Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis
2013	—	`conf`	Heuristic Algorithms for the Protein Model Assignment Problem. ISBRA Jörg Hauser, Kassian Kobert, Fernando Izquierdo-Carrasco, Karen Meusemann, Bernhard Misof, Michael Gertz, Alexandros Stamatakis
2013	—	`conf`	MoTeX: A word-based HPC tool for MoTif eXtraction. BCB Solon P. Pissis, Alexandros Stamatakis, Pavlos Pavlidis
2013	A	`conf`	Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference. IPDPS Alexandros Stamatakis, Andre J. Aberer
2013	J	`jnl`	Rapid forward-in-time simulation at the chromosome and genome level. BMC Bioinform. Andre J. Aberer, Alexandros Stamatakis
2013	J	`jnl`	libgapmis: extending short-read alignments. BMC Bioinform. Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis
2012	—	`conf`	A versatile UDP/IP based PC ↔ FPGA communication platform. ReConFig Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2012	—	`conf`	An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data. IPDPS Workshops Simon A. Berger, Nikolaos Alachiotis, Alexandros Stamatakis
2012	J	`jnl`	Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. BMC Bioinform. Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2012	—	`conf`	Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection. ICA3PP (1) Nikolaos Alachiotis, Pavlos Pavlidis, Alexandros Stamatakis
2012	J	`jnl`	Fine-grain parallelism using multi-core, Cell/BE, and GPU Systems. Parallel Comput. Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr V. Kindratenko
2012	—	`conf`	Inference of Huge Trees under Maximum Likelihood. IPDPS Workshops Fernando Izquierdo-Carrasco, Alexandros Stamatakis
2012	—	`conf`	Libgapmis: An ultrafast library for short-read single-gap alignment. BIBM Workshops Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis
2012	J	`jnl`	OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinform. Nikolaos Alachiotis, Alexandros Stamatakis, Pavlos Pavlidis
2012	J	`jnl`	RAxML-Light: a tool for computing terabyte phylogenies. Bioinform. Alexandros Stamatakis, Andre J. Aberer, Christian Goll, Stephen A. Smith, Simon A. Berger, Fernando Izquierdo-Carrasco
2012	—	`conf`	SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. IPDPS Workshops Hannes Schabauer, Mario Valle, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Ziheng Yang, Nicolas Salamin
2012	—	`conf`	The Multi-Processor Scheduling Problem in Phylogenetics. IPDPS Workshops Jiajie Zhang, Alexandros Stamatakis
2012	—	`conf`	Trading Running Time for Memory in Phylogenetic Likelihood Computations. BIOINFORMATICS Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis
2011	—	`conf`	A Simple and Accurate Method for Rogue Taxon Identification. BIBM Andre J. Aberer, Alexandros Stamatakis
2011	J	`jnl`	A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm. Int. J. Reconfigurable Comput. Nikolaos Alachiotis, Alexandros Stamatakis
2011	Misc	`conf`	Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. FCCM Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2011	J	`jnl`	Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinform. Fernando Izquierdo-Carrasco, Stephen A. Smith, Alexandros Stamatakis
2011	J	`jnl`	Aligning short reads to reference alignments and trees. Bioinform. Simon A. Berger, Alexandros Stamatakis
2011	—	`conf`	Computing the Phylogenetic Likelihood Function Out-of-Core. IPDPS Workshops Fernando Izquierdo-Carrasco, Alexandros Stamatakis
2011	B	`conf`	FPGA Acceleration of the Phylogenetic Parsimony Kernel? FPL Nikolaos Alachiotis, Alexandros Stamatakis
2011	—	`conf`	FPGA Optimizations for a Pipelined Floating-Point Exponential Unit. ARC Nikolaos Alachiotis, Alexandros Stamatakis
2011	J	`jnl`	PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination. BMC Bioinform. Robert K. Luecking, Brendan P. Hodkinson, Alexandros Stamatakis, Reed A. Cartwright
2011	—	`conf`	Parallel Structural Graph Clustering. ECML/PKDD (3) Madeleine Seeland, Simon A. Berger, Alexandros Stamatakis, Stefan Kramer
2011	—	`ch.`	Phylogenetics. Encyclopedia of Parallel Computing Alexandros Stamatakis
2011	J	`jnl`	Result verification, code verification and computation of support values in phylogenetics. Briefings Bioinform. Alexandros Stamatakis, Fernando Izquierdo-Carrasco
2011	J	`jnl`	Uncovering Hidden Phylogenetic Consensus in Large Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret
2010	C	`conf`	Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood. AICCSA Simon A. Berger, Alexandros Stamatakis
2010	C	`conf`	Efficient PC-FPGA Communication over Gigabit Ethernet. CIT Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2010	—	`conf`	Efficient floating-point logarithm unit for FPGAs. IPDPS Workshops Nikolaos Alachiotis, Alexandros Stamatakis
2010	C	`conf`	Evolutionary placement of short sequence reads on multi-core architectures. AICCSA Alexandros Stamatakis, Zsolt Komornik, Simon A. Berger
2010	J	`jnl`	How Many Bootstrap Replicates Are Necessary? J. Comput. Biol. Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis
2010	—	`conf`	Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. IPDPS Workshops Wayne Pfeiffer, Alexandros Stamatakis
2010	Misc	`conf`	Parallel computation of phylogenetic consensus trees. ICCS Andre J. Aberer, Nicholas D. Pattengale, Alexandros Stamatakis
2010	J	`jnl`	Parallelized phylogenetic post-analysis on multi-core architectures. J. Comput. Sci. Andre J. Aberer, Nicholas D. Pattengale, Alexandros Stamatakis
2010	J	`jnl`	Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinform. Alexandros Stamatakis, Nikolaos Alachiotis
2009	B	`conf`	A reconfigurable architecture for the Phylogenetic Likelihood Function. FPL Nikolaos Alachiotis, Alexandros Stamatakis, Euripides Sotiriades, Apostolos Dollas
2009	—	`conf`	Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction. PPAM (2) Simon A. Berger, Alexandros Stamatakis
2009	A	`conf`	Exploring FPGAs for accelerating the phylogenetic likelihood function. IPDPS Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, Alexandros Stamatakis
2009	B	`conf`	Fine-grain Parallelism Using Multi-core, Cell/BE, and GPU Systems: Accelerating the Phylogenetic Likelihood Function. ICPP Frederico Pratas, Pedro Trancoso, Alexandros Stamatakis, Leonel Sousa
2009	B	`conf`	How Many Bootstrap Replicates Are Necessary? RECOMB Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis
2009	J	`jnl`	Large-Scale Co-Phylogenetic Analysis on the Grid. Int. J. Grid High Perform. Comput. Heinz Stockinger, Alexander F. Auch, Markus Göker, Jan P. Meier-Kolthoff, Alexandros Stamatakis
2009	B	`conf`	Load Balance in the Phylogenetic Likelihood Kernel. ICPP Alexandros Stamatakis, Michael Ott
2008	—	`conf`	Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study. PRIB Alexandros Stamatakis, Michael Ott
2008	J	`jnl`	Large-scale phylogenetic analysis on current HPC architectures. Sci. Program. Michael Ott, Jaroslaw Zola, Srinivas Aluru, Andrew D. Johnson, Daniel Janies, Alexandros Stamatakis
2007	J	`jnl`	AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinform. Alexandros Stamatakis, Alexander F. Auch, Jan P. Meier-Kolthoff, Markus Göker
2007	B	`conf`	Dynamic multigrain parallelization on the cell broadband engine. PPoPP Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos
2007	J	`jnl`	Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell. J. VLSI Signal Process. Alexandros Stamatakis, Filip Blagojevic, Dimitrios S. Nikolopoulos, Christos D. Antonopoulos
2007	A	`conf`	Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. SC Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru
2007	A	`conf`	RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine. IPDPS Filip Blagojevic, Alexandros Stamatakis, Christos D. Antonopoulos, Dimitrios S. Nikolopoulos
2007	J	`jnl`	Runtime scheduling of dynamic parallelism on accelerator-based multi-core systems. Parallel Comput. Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos, Matthew Curtis-Maury
2006	J	`jnl`	Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions. Adv. Comput. David A. Bader, Usman Roshan, Alexandros Stamatakis
2006	A	`conf`	Phylogenetic models of rate heterogeneity: a high performance computing perspective. IPDPS Alexandros Stamatakis
2006	J	`jnl`	RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinform. Alexandros Stamatakis
2005	A	`conf`	An Efficient Program for Phylogenetic Inference Using Simulated Annealing. IPDPS Alexandros Stamatakis
2005	J	`jnl`	DRAxML at home: a distributed program for computation of large phylogenetic trees. Future Gener. Comput. Syst. Alexandros Stamatakis, Markus Lindermeier, Michael Ott, Thomas Ludwig, Harald Meier
2005	—	`conf`	Initial Experiences Porting a Bioinformatics Application to a Graphics Processor. Panhellenic Conference on Informatics Maria Charalambous, Pedro Trancoso, Alexandros Stamatakis
2005	C	`conf`	Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh
2005	J	`jnl`	RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees. Concurr. Comput. Pract. Exp. Alexandros Stamatakis, Thomas Ludwig, Harald Meier
2005	J	`jnl`	RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinform. Alexandros Stamatakis, Thomas Ludwig, Harald Meier
2005	B	`conf`	RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs. PaCT Alexandros Stamatakis, Michael Ott, Thomas Ludwig
2005	—	`conf`	Using Treemaps to Visualize Phylogenetic Trees. ISBMDA Adam Arvelakis, Martin Reczko, Alexandros Stamatakis, Alkiviadis Symeonidis, Ioannis G. Tollis
2004	Misc	`conf`	A fast program for maximum likelihood-based inference of large phylogenetic trees. SAC Alexandros Stamatakis, Thomas Ludwig, Harald Meier
2004	—	`—`	Distributed and parallel algorithms and systems for inference of huge phylogenetic trees based on the maximum likelihood method. Alexandros Stamatakis
2004	A	`conf`	New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees. IPDPS Alexandros Stamatakis, Harald Meier, Thomas Ludwig
2004	—	`conf`	Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood. Euro-Par Alexandros Stamatakis, Thomas Ludwig, Harald Meier
2004	J	`jnl`	The AxML program family for maximum likelihood-based phylogenetic tree inference. Concurr. Pract. Exp. Alexandros Stamatakis, Thomas Ludwig, Harald Meier
2003	B	`conf`	DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA. PaCT Alexandros Stamatakis, Markus Lindermeier, Michael Ott, Thomas Ludwig, Harald Meier
2003	A	`conf`	Phylogenetic Tree Inference on PC Architectures with AxML/PAxML. IPDPS Alexandros Stamatakis, Thomas Ludwig
2002	A	`conf`	Accelerating parallel maximum likelihood-based phylogenetic tree calculations using subtree equality vectors. SC Alexandros Stamatakis, Thomas Ludwig, Harald Meier, Marty J. Wolf
2002	—	`conf`	AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method. CSB Alexandros Stamatakis, Thomas Ludwig, Harald Meier, Marty J. Wolf
2002	J	`jnl`	Efficiently building on-line tools for distributed heterogeneous environments. Sci. Program. Günther Rackl, Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis
2002	J	`jnl`	Tool environments in CORBA-based medical high-performance computing. Future Gener. Comput. Syst. Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, Günther Rackl
2001	B	`conf`	Tool Environments in CORBA-Based Medical High Performance Computing. PaCT Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, Günther Rackl