Alexandros Stamatakis
Orcid: 0000-0003-0353-0691Affiliations:
- Heidelberg Institute for Theoretical Studies, Exelixis Lab, Germany
- Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Germany
- Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Foundation for Research & Technology Hellas (FORTH), Heraklion, Greece
According to our database1,
Alexandros Stamatakis
authored at least 117 papers
between 2002 and 2024.
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Bibliography
2024
Computational Approaches for Integrating out Subjectivity in Cognate Synonym Selection.
CoRR, 2024
2023
Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods.
Stat. Comput., August, 2023
Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data.
Bioinform., January, 2023
Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2023
2022
Frontiers Bioinform., 2022
Bioinform., 2022
ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms.
Proceedings of the 12th IEEE/ACM Workshop on Fault Tolerance for HPC at eXtreme Scale, 2022
2021
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG.
Bioinform., November, 2021
Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2021
2020
Bioinform., 2020
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.
Bioinform., 2020
Bioinform., 2020
2019
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.
Bioinform., 2019
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Bioinform., 2019
Bioinform., 2019
Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning.
Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2019
2018
2017
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.
Bioinform., 2017
A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats.
Proceedings of the 19th IEEE International Conference on High Performance Computing and Communications; 15th IEEE International Conference on Smart City; 3rd IEEE International Conference on Data Science and Systems, 2017
An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties.
Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017
2016
BMC Bioinform., 2016
Bioinform., 2016
A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation.
Proceedings of the 2016 Eighth International Conference on Knowledge and Systems Engineering, 2016
The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016
2015
Bioinform., 2015
2014
Theor. Comput. Sci., 2014
Optimization strategies for fast detection of positive selection on phylogenetic trees.
Bioinform., 2014
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Bioinform., 2014
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014
Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture.
Proceedings of the 2014 IEEE International Parallel & Distributed Processing Symposium Workshops, 2014
2013
BMC Bioinform., 2013
Bioinform., 2013
Proceedings of the Parallel Processing and Applied Mathematics, 2013
Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013
Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference.
Proceedings of the 27th IEEE International Symposium on Parallel and Distributed Processing, 2013
A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library.
Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013
Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library.
Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
Parallel Comput., 2012
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
BMC Bioinform., 2012
OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.
Bioinform., 2012
Proceedings of the 2012 International Conference on Reconfigurable Computing and FPGAs, 2012
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012
An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data.
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012
Proceedings of the Algorithms and Architectures for Parallel Processing, 2012
Trading Running Time for Memory in Phylogenetic Likelihood Computations.
Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
2011
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
Int. J. Reconfigurable Comput., 2011
PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination.
BMC Bioinform., 2011
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees.
BMC Bioinform., 2011
Result verification, code verification and computation of support values in phylogenetics.
Briefings Bioinform., 2011
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2011
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011
Proceedings of the International Conference on Field Programmable Logic and Applications, 2011
Proceedings of the IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011
Proceedings of the Reconfigurable Computing: Architectures, Tools and Applications, 2011
2010
Proceedings of the International Conference on Computational Science, 2010
J. Comput. Sci., 2010
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.
Bioinform., 2010
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010
Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010
Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010
Proceedings of the 10th IEEE International Conference on Computer and Information Technology, 2010
2009
Int. J. Grid High Perform. Comput., 2009
Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction.
Proceedings of the Parallel Processing and Applied Mathematics, 2009
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009
Proceedings of the ICPP 2009, 2009
Fine-grain Parallelism Using Multi-core, Cell/BE, and GPU Systems: Accelerating the Phylogenetic Likelihood Function.
Proceedings of the ICPP 2009, 2009
Proceedings of the 19th International Conference on Field Programmable Logic and Applications, 2009
2008
Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study.
Proceedings of the Pattern Recognition in Bioinformatics, 2008
2007
Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell.
J. VLSI Signal Process., 2007
Parallel Comput., 2007
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.
BMC Bioinform., 2007
Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007
Proceedings of the 12th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 2007
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007
2006
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Bioinform., 2006
Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions.
Adv. Comput., 2006
Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006
2005
Future Gener. Comput. Syst., 2005
RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees.
Concurr. Comput. Pract. Exp., 2005
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
Bioinform., 2005
Proceedings of the Advances in Informatics, 2005
Proceedings of the Parallel Computing Technologies, 2005
Proceedings of the Biological and Medical Data Analysis, 6th International Symposium, 2005
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005
Proceedings of the High Performance Computing and Communications, 2005
2004
Distributed and parallel algorithms and systems for inference of huge phylogenetic trees based on the maximum likelihood method.
PhD thesis, 2004
Concurr. Pract. Exp., 2004
Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004
Proceedings of the Euro-Par 2004 Parallel Processing, 2004
2003
DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA.
Proceedings of the Parallel Computing Technologies, 2003
Proceedings of the 17th International Parallel and Distributed Processing Symposium (IPDPS 2003), 2003
2002
Sci. Program., 2002
Future Gener. Comput. Syst., 2002
Accelerating parallel maximum likelihood-based phylogenetic tree calculations using subtree equality vectors.
Proceedings of the 2002 ACM/IEEE conference on Supercomputing, 2002
AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002