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ORCIDAlexandros Stamatakis
Person information
- affiliation: Heidelberg Institute for Theoretical Studies, Exelixis Lab, Germany
- affiliation: Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Germany
- affiliation: Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- affiliation: Foundation for Research & Technology Hellas (FORTH), Heraklion, Greece
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Books and Theses
- 2004
[b1]Alexandros Stamatakis:
Distributed and parallel algorithms and systems for inference of huge phylogenetic trees based on the maximum likelihood method. Technical University Munich, Germany, 2004, pp. 1-132
Journal Articles
- 2023
- [j53]Benoit Morel
, Tom A. Williams, Alexandros Stamatakis:
Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data. Bioinform. 39(1) (2023) - [j52]Ben Bettisworth, Alexander I. Jordan, Alexandros Stamatakis:
Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods. Stat. Comput. 33(4): 80 (2023) - 2022
- [j51]Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis:
RAxML Grove: an empirical phylogenetic tree database. Bioinform. 38(6): 1741-1742 (2022) - [j50]Sarah Lutteropp, Céline Scornavacca, Alexey M. Kozlov, Benoit Morel, Alexandros Stamatakis:
NetRAX: accurate and fast maximum likelihood phylogenetic network inference. Bioinform. 38(15): 3725-3733 (2022) - [j49]Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera:
Metagenomic Analysis Using Phylogenetic Placement - A Review of the First Decade. Frontiers Bioinform. 2 (2022) - 2021
- [j48]Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis:
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG. Bioinform. 37(22): 4056-4063 (2021) - [j47]Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes:
Swarm v3: towards tera-scale amplicon clustering. Bioinform. 38(1): 267-269 (2021) - [j46]Ben Bettisworth, Alexandros Stamatakis:
Root Digger: a root placement program for phylogenetic trees. BMC Bioinform. 22(1): 225 (2021) - 2020
- [j45]Sarah Lutteropp, Alexey M. Kozlov, Alexandros Stamatakis:
A fast and memory-efficient implementation of the transfer bootstrap. Bioinform. 36(7): 2280-2281 (2020) - [j44]Lucas Czech, Pierre Barbera, Alexandros Stamatakis:
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data. Bioinform. 36(10): 3263-3265 (2020) - [j43]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:
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Bioinform. 36(18): 4822-4824 (2020) - 2019
- [j42]Lucas Czech, Pierre Barbera, Alexandros Stamatakis:
Methods for automatic reference trees and multilevel phylogenetic placement. Bioinform. 35(7): 1151-1158 (2019) - [j41]Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis:
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes. Bioinform. 35(10): 1771-1773 (2019) - [j40]Alexey M. Kozlov, Diego Darriba, Tomás Flouri, Benoit Morel, Alexandros Stamatakis:
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinform. 35(21): 4453-4455 (2019) - 2018
- [j39]Rudolf Biczok, Peter Bozsoky, Peter Eisenmann, Johannes Ernst, Tobias Ribizel, Fedor Scholz, Axel Trefzer, Florian Weber, Michael Hamann, Alexandros Stamatakis:
Two C++ libraries for counting trees on a phylogenetic terrace. Bioinform. 34(19): 3399-3401 (2018) - 2017
- [j38]Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlidis, Alexandros Stamatakis, Tomás Flouri:
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinform. 33(11): 1630-1638 (2017) - 2016
- [j37]Diego Darriba, Michael Weiß, Alexandros Stamatakis:
Prediction of missing sequences and branch lengths in phylogenomic data. Bioinform. 32(9): 1331-1337 (2016) - [j36]Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba, Alexandros Stamatakis:
Does the choice of nucleotide substitution models matter topologically? BMC Bioinform. 17: 143 (2016) - 2015
- [j35]Alexey M. Kozlov, Andre J. Aberer, Alexandros Stamatakis:
ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinform. 31(15): 2577-2579 (2015) - 2014
- [j34]Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis:
PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinform. 30(5): 614-620 (2014) - [j33]Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin:
Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinform. 30(8): 1129-1137 (2014) - [j32]Alexandros Stamatakis:
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinform. 30(9): 1312-1313 (2014) - [j31]Fernando Izquierdo-Carrasco, John Cazes, Stephen A. Smith, Alexandros Stamatakis:
PUmPER: phylogenies updated perpetually. Bioinform. 30(10): 1476-1477 (2014) - [j30]Kassian Kobert, Jörg Hauser, Alexandros Stamatakis:
Is the Protein Model Assignment problem under linked branch lengths NP-hard? Theor. Comput. Sci. 524: 48-58 (2014) - 2013
- [j29]Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis, Alexandros Stamatakis:
A general species delimitation method with applications to phylogenetic placements. Bioinform. 29(22): 2869-2876 (2013) - [j28]Andre J. Aberer, Alexandros Stamatakis:
Rapid forward-in-time simulation at the chromosome and genome level. BMC Bioinform. 14: 216 (2013) - [j27]Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis:
libgapmis: extending short-read alignments. BMC Bioinform. 14(S-11): S4 (2013) - 2012
- [j26]Alexandros Stamatakis, Andre J. Aberer, Christian Goll, Stephen A. Smith, Simon A. Berger, Fernando Izquierdo-Carrasco:
RAxML-Light: a tool for computing terabyte phylogenies. Bioinform. 28(15): 2064-2066 (2012) - [j25]Nikolaos Alachiotis, Alexandros Stamatakis, Pavlos Pavlidis:
OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinform. 28(17): 2274-2275 (2012) - [j24]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. BMC Bioinform. 13: 196 (2012) - [j23]Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr V. Kindratenko:
Fine-grain parallelism using multi-core, Cell/BE, and GPU Systems. Parallel Comput. 38(8): 365-390 (2012) - 2011
- [j22]Alexandros Stamatakis, Fernando Izquierdo-Carrasco:
Result verification, code verification and computation of support values in phylogenetics. Briefings Bioinform. 12(3): 270-279 (2011) - [j21]Simon A. Berger, Alexandros Stamatakis:
Aligning short reads to reference alignments and trees. Bioinform. 27(15): 2068-2075 (2011) - [j20]Robert K. Luecking, Brendan P. Hodkinson, Alexandros Stamatakis, Reed A. Cartwright:
PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination. BMC Bioinform. 12: 10 (2011) - [j19]Fernando Izquierdo-Carrasco, Stephen A. Smith, Alexandros Stamatakis:
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinform. 12: 470 (2011) - [j18]Nikolaos Alachiotis, Alexandros Stamatakis:
A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm. Int. J. Reconfigurable Comput. 2011: 341510:1-341510:12 (2011) - [j17]Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret:
Uncovering Hidden Phylogenetic Consensus in Large Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 902-911 (2011) - 2010
- [j16]Alexandros Stamatakis, Nikolaos Alachiotis:
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinform. 26(12): 132-139 (2010) - [j15]Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis:
How Many Bootstrap Replicates Are Necessary? J. Comput. Biol. 17(3): 337-354 (2010) - [j14]Andre J. Aberer, Nicholas D. Pattengale, Alexandros Stamatakis:
Parallelized phylogenetic post-analysis on multi-core architectures. J. Comput. Sci. 1(2): 107-114 (2010) - 2009
- [j13]Heinz Stockinger, Alexander F. Auch, Markus Göker, Jan P. Meier-Kolthoff, Alexandros Stamatakis:
Large-Scale Co-Phylogenetic Analysis on the Grid. Int. J. Grid High Perform. Comput. 1(1): 39-54 (2009) - 2008
- [j12]Michael Ott, Jaroslaw Zola, Srinivas Aluru, Andrew D. Johnson, Daniel Janies, Alexandros Stamatakis:
Large-scale phylogenetic analysis on current HPC architectures. Sci. Program. 16(2-3): 255-270 (2008) - 2007
- [j11]Alexandros Stamatakis, Alexander F. Auch, Jan P. Meier-Kolthoff, Markus Göker:
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinform. 8 (2007) - [j10]Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos, Matthew Curtis-Maury:
Runtime scheduling of dynamic parallelism on accelerator-based multi-core systems. Parallel Comput. 33(10-11): 700-719 (2007) - [j9]Alexandros Stamatakis, Filip Blagojevic, Dimitrios S. Nikolopoulos, Christos D. Antonopoulos:
Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell. J. VLSI Signal Process. 48(3): 271-286 (2007) - 2006
- [j8]David A. Bader, Usman Roshan, Alexandros Stamatakis:
Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions. Adv. Comput. 68: 128-179 (2006) - [j7]Alexandros Stamatakis:
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinform. 22(21): 2688-2690 (2006) - 2005
- [j6]Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinform. 21(4): 456-463 (2005) - [j5]Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees. Concurr. Comput. Pract. Exp. 17(14): 1705-1723 (2005) - [j4]Alexandros Stamatakis, Markus Lindermeier, Michael Ott, Thomas Ludwig, Harald Meier:
DRAxML at home: a distributed program for computation of large phylogenetic trees. Future Gener. Comput. Syst. 21(4): 725-730 (2005) - 2004
- [j3]Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
The AxML program family for maximum likelihood-based phylogenetic tree inference. Concurr. Pract. Exp. 16(9): 975-988 (2004) - 2002
- [j2]Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, Günther Rackl:
Tool environments in CORBA-based medical high-performance computing. Future Gener. Comput. Syst. 18(6): 841-847 (2002) - [j1]Günther Rackl, Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis:
Efficiently building on-line tools for distributed heterogeneous environments. Sci. Program. 10(1): 67-74 (2002)
Conference and Workshop Papers
- 2023
- [c60]Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis:
Parallel Inference of Phylogenetic Stands with Gentrius. IPDPS Workshops 2023: 139-148 - 2022
- [c59]Lukas Hübner, Demian Hespe, Peter Sanders, Alexandros Stamatakis:
ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms. FTXS@SC 2022: 24-35 - 2021
- [c58]Pierre Barbera, Alexandros Stamatakis:
Efficient Memory Management in Likelihood-based Phylogenetic Placement. IPDPS Workshops 2021: 218-227 - 2019
- [c57]Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel:
Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning. IPDPS Workshops 2019: 175-184 - 2017
- [c56]Benoit Morel, Tomás Flouri, Alexandros Stamatakis:
A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats. HPCC/SmartCity/DSS 2017: 81-88 - 2016
- [c55]Constantin Scholl, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis:
The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference. IPDPS Workshops 2016: 408-417 - [c54]Diep Thi Hoang, Le Sy Vinh, Tomás Flouri, Alexandros Stamatakis, Arndt von Haeseler, Bui Quang Minh:
A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. KSE 2016: 1-6 - 2014
- [c53]Alexey M. Kozlov, Christian Goll, Alexandros Stamatakis:
Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture. IPDPS Workshops 2014: 518-527 - [c52]Kassian Kobert, Tomás Flouri, Andre J. Aberer, Alexandros Stamatakis:
The Divisible Load Balance Problem and Its Application to Phylogenetic Inference. WABI 2014: 204-216 - 2013
- [c51]Solon P. Pissis, Alexandros Stamatakis, Pavlos Pavlidis:
MoTeX: A word-based HPC tool for MoTif eXtraction. BCB 2013: 13 - [c50]Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis:
A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. IPDPS Workshops 2013: 530-538 - [c49]Diego Darriba, Andre J. Aberer, Tomás Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis:
Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library. IPDPS Workshops 2013: 539-548 - [c48]Alexandros Stamatakis, Andre J. Aberer:
Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference. IPDPS 2013: 1195-1204 - [c47]Jörg Hauser, Kassian Kobert, Fernando Izquierdo-Carrasco, Karen Meusemann, Bernhard Misof, Michael Gertz, Alexandros Stamatakis:
Heuristic Algorithms for the Protein Model Assignment Problem. ISBRA 2013: 137-148 - [c46]Tomás Flouri, Kassian Kobert, Solon P. Pissis, Alexandros Stamatakis:
An Optimal Algorithm for Computing All Subtree Repeats in Trees. IWOCA 2013: 269-282 - [c45]Solon P. Pissis, Christian Goll, Pavlos Pavlidis, Alexandros Stamatakis:
Accelerating String Matching on MIC Architecture for Motif Extraction. PPAM (2) 2013: 258-267 - 2012
- [c44]Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis:
Libgapmis: An ultrafast library for short-read single-gap alignment. BIBM Workshops 2012: 688-695 - [c43]Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis:
Trading Running Time for Memory in Phylogenetic Likelihood Computations. BIOINFORMATICS 2012: 86-95 - [c42]Nikolaos Alachiotis, Pavlos Pavlidis, Alexandros Stamatakis:
Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection. ICA3PP (1) 2012: 56-68 - [c41]Simon A. Berger, Nikolaos Alachiotis, Alexandros Stamatakis:
An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data. IPDPS Workshops 2012: 352-359 - [c40]Jiajie Zhang, Alexandros Stamatakis:
The Multi-Processor Scheduling Problem in Phylogenetics. IPDPS Workshops 2012: 691-698 - [c39]Hannes Schabauer, Mario Valle, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Ziheng Yang, Nicolas Salamin:
SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. IPDPS Workshops 2012: 706-714 - [c38]Fernando Izquierdo-Carrasco, Alexandros Stamatakis:
Inference of Huge Trees under Maximum Likelihood. IPDPS Workshops 2012: 2490-2493 - [c37]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
A versatile UDP/IP based PC ↔ FPGA communication platform. ReConFig 2012: 1-6 - 2011
- [c36]Nikolaos Alachiotis, Alexandros Stamatakis:
FPGA Optimizations for a Pipelined Floating-Point Exponential Unit. ARC 2011: 316-327 - [c35]Andre J. Aberer, Alexandros Stamatakis:
A Simple and Accurate Method for Rogue Taxon Identification. BIBM 2011: 118-122 - [c34]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. FCCM 2011: 226-233 - [c33]Nikolaos Alachiotis, Alexandros Stamatakis:
FPGA Acceleration of the Phylogenetic Parsimony Kernel? FPL 2011: 417-422 - [c32]Fernando Izquierdo-Carrasco, Alexandros Stamatakis:
Computing the Phylogenetic Likelihood Function Out-of-Core. IPDPS Workshops 2011: 444-451 - [c31]Madeleine Seeland, Simon A. Berger, Alexandros Stamatakis, Stefan Kramer:
Parallel Structural Graph Clustering. ECML/PKDD (3) 2011: 256-272 - 2010
- [c30]Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
Efficient PC-FPGA Communication over Gigabit Ethernet. CIT 2010: 1727-1734 - [c29]Simon A. Berger, Alexandros Stamatakis:
Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood. AICCSA 2010: 1-9 - [c28]Alexandros Stamatakis, Zsolt Komornik, Simon A. Berger:
Evolutionary placement of short sequence reads on multi-core architectures. AICCSA 2010: 1-8 - [c27]Nikolaos Alachiotis, Alexandros Stamatakis:
Efficient floating-point logarithm unit for FPGAs. IPDPS Workshops 2010: 1-8 - [c26]Wayne Pfeiffer, Alexandros Stamatakis:
Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. IPDPS Workshops 2010: 1-8 - [c25]Andre J. Aberer, Nicholas D. Pattengale, Alexandros Stamatakis:
Parallel computation of phylogenetic consensus trees. ICCS 2010: 1065-1073 - 2009
- [c24]Nikolaos Alachiotis, Alexandros Stamatakis, Euripides Sotiriades, Apostolos Dollas:
A reconfigurable architecture for the Phylogenetic Likelihood Function. FPL 2009: 674-678 - [c23]Frederico Pratas, Pedro Trancoso, Alexandros Stamatakis, Leonel Sousa:
Fine-grain Parallelism Using Multi-core, Cell/BE, and GPU Systems: Accelerating the Phylogenetic Likelihood Function. ICPP 2009: 9-17 - [c22]Alexandros Stamatakis, Michael Ott:
Load Balance in the Phylogenetic Likelihood Kernel. ICPP 2009: 348-355 - [c21]Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, Alexandros Stamatakis:
Exploring FPGAs for accelerating the phylogenetic likelihood function. IPDPS 2009: 1-8 - [c20]Simon A. Berger, Alexandros Stamatakis:
Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction. PPAM (2) 2009: 270-279 - [c19]Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis:
How Many Bootstrap Replicates Are Necessary? RECOMB 2009: 184-200 - 2008
- [c18]Alexandros Stamatakis, Michael Ott:
Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study. PRIB 2008: 424-435 - 2007
- [c17]Filip Blagojevic, Alexandros Stamatakis, Christos D. Antonopoulos, Dimitrios S. Nikolopoulos:
RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine. IPDPS 2007: 1-10 - [c16]Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos:
Dynamic multigrain parallelization on the cell broadband engine. PPoPP 2007: 90-100 - [c15]Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru:
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. SC 2007: 4 - 2006
- [c14]Alexandros Stamatakis:
Phylogenetic models of rate heterogeneity: a high performance computing perspective. IPDPS 2006 - 2005
- [c13]Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh:
Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC 2005: 776-785 - [c12]Alexandros Stamatakis:
An Efficient Program for Phylogenetic Inference Using Simulated Annealing. IPDPS 2005 - [c11]Adam Arvelakis, Martin Reczko, Alexandros Stamatakis, Alkiviadis Symeonidis, Ioannis G. Tollis:
Using Treemaps to Visualize Phylogenetic Trees. ISBMDA 2005: 283-293 - [c10]Alexandros Stamatakis, Michael Ott, Thomas Ludwig:
RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs. PaCT 2005: 288-302 - [c9]Maria Charalambous, Pedro Trancoso, Alexandros Stamatakis:
Initial Experiences Porting a Bioinformatics Application to a Graphics Processor. Panhellenic Conference on Informatics 2005: 415-425 - 2004
- [c8]Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood. Euro-Par 2004: 997-1004 - [c7]Alexandros Stamatakis, Harald Meier, Thomas Ludwig:
New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees. IPDPS 2004 - [c6]Alexandros Stamatakis, Thomas Ludwig, Harald Meier:
A fast program for maximum likelihood-based inference of large phylogenetic trees. SAC 2004: 197-201 - 2003
- [c5]Alexandros Stamatakis, Thomas Ludwig:
Phylogenetic Tree Inference on PC Architectures with AxML/PAxML. IPDPS 2003: 157 - [c4]Alexandros Stamatakis, Markus Lindermeier, Michael Ott, Thomas Ludwig, Harald Meier:
DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA. PaCT 2003: 538-548 - 2002
- [c3]Alexandros Stamatakis, Thomas Ludwig, Harald Meier, Marty J. Wolf:
AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method. CSB 2002: 21- - [c2]Alexandros Stamatakis, Thomas Ludwig, Harald Meier, Marty J. Wolf:
Accelerating parallel maximum likelihood-based phylogenetic tree calculations using subtree equality vectors. SC 2002: 2:1-2:16 - 2001
- [c1]Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, Günther Rackl:
Tool Environments in CORBA-Based Medical High Performance Computing. PaCT 2001: 447-455
Parts in Books or Collections
- 2017
- [p1]Tomás Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis:
An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties. Algorithms for Next-Generation Sequencing Data 2017: 299-325
Reference Works
- 2011
- [r1]Alexandros Stamatakis:
Phylogenetics. Encyclopedia of Parallel Computing 2011: 1545-1554
Informal and Other Publications
- 2024
- [i3]Luise Häuser, Gerhard Jäger, Taraka Rama, Johann-Mattis List, Alexandros Stamatakis:
Are Sounds Sound for Phylogenetic Reconstruction? CoRR abs/2402.02807 (2024) - 2022
- [i2]Demian Hespe, Lukas Hübner, Peter Sanders, Alexandros Stamatakis:
ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms. CoRR abs/2203.01107 (2022) - 2019
- [i1]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:
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019)
Coauthor Index
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Citation data
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load citations from opencitations.net
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OpenAlex data
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last updated on 2024-03-24 02:43 CET by the dblp team
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