Alexandros Stamatakis

According to our database1, Alexandros Stamatakis
  • authored at least 95 papers between 2001 and 2017.
  • has a "Dijkstra number"2 of four.

Timeline

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Bibliography

2017
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.
Bioinformatics, 2017

2016
Does the choice of nucleotide substitution models matter topologically?
BMC Bioinformatics, 2016

Prediction of missing sequences and branch lengths in phylogenomic data.
Bioinformatics, 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
ExaML version 3: a tool for phylogenomic analyses on supercomputers.
Bioinformatics, 2015

2014
Is the Protein Model Assignment problem under linked branch lengths NP-hard?
Theor. Comput. Sci., 2014

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.
Bioinformatics, 2014

Optimization strategies for fast detection of positive selection on phylogenetic trees.
Bioinformatics, 2014

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Bioinformatics, 2014

PUmPER: phylogenies updated perpetually.
Bioinformatics, 2014

The Divisible Load Balance Problem and Its Application to Phylogenetic Inference.
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
libgapmis: extending short-read alignments.
BMC Bioinformatics, 2013

Rapid forward-in-time simulation at the chromosome and genome level.
BMC Bioinformatics, 2013

A general species delimitation method with applications to phylogenetic placements.
Bioinformatics, 2013

Accelerating String Matching on MIC Architecture for Motif Extraction.
Proceedings of the Parallel Processing and Applied Mathematics, 2013

An Optimal Algorithm for Computing All Subtree Repeats in Trees.
Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

Heuristic Algorithms for the Protein Model Assignment Problem.
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

MoTeX: A word-based HPC tool for MoTif eXtraction.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Fine-grain parallelism using multi-core, Cell/BE, and GPU Systems.
Parallel Computing, 2012

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
BMC Bioinformatics, 2012

RAxML-Light: a tool for computing terabyte phylogenies.
Bioinformatics, 2012

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.
Bioinformatics, 2012

A versatile UDP/IP based PC ↔ FPGA communication platform.
Proceedings of the 2012 International Conference on Reconfigurable Computing and FPGAs, 2012

The Multi-Processor Scheduling Problem in Phylogenetics.
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model.
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

Inference of Huge Trees under Maximum Likelihood.
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

Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection.
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

Libgapmis: An ultrafast library for short-read single-gap alignment.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011
Phylogenetics.
Proceedings of the Encyclopedia of Parallel Computing, 2011

Uncovering Hidden Phylogenetic Consensus in Large Data Sets.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm.
Int. J. Reconfig. Comp., 2011

PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination.
BMC Bioinformatics, 2011

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees.
BMC Bioinformatics, 2011

Aligning short reads to reference alignments and trees.
Bioinformatics, 2011

Result verification, code verification and computation of support values in phylogenetics.
Briefings in Bioinformatics, 2011

Parallel Structural Graph Clustering.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2011

Computing the Phylogenetic Likelihood Function Out-of-Core.
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011

FPGA Acceleration of the Phylogenetic Parsimony Kernel?
Proceedings of the International Conference on Field Programmable Logic and Applications, 2011

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs.
Proceedings of the IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011

A Simple and Accurate Method for Rogue Taxon Identification.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

FPGA Optimizations for a Pipelined Floating-Point Exponential Unit.
Proceedings of the Reconfigurable Computing: Architectures, Tools and Applications, 2011

2010
Parallel computation of phylogenetic consensus trees.
Proceedings of the International Conference on Computational Science, 2010

Parallelized phylogenetic post-analysis on multi-core architectures.
J. Comput. Science, 2010

How Many Bootstrap Replicates Are Necessary?
Journal of Computational Biology, 2010

Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.
Bioinformatics [ISMB], 2010

Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010

Efficient floating-point logarithm unit for FPGAs.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010

Evolutionary placement of short sequence reads on multi-core architectures.
Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010

Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood.
Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010

Efficient PC-FPGA Communication over Gigabit Ethernet.
Proceedings of the 10th IEEE International Conference on Computer and Information Technology, 2010

2009
Large-Scale Co-Phylogenetic Analysis on the Grid.
IJGHPC, 2009

How Many Bootstrap Replicates Are Necessary?
Proceedings of the Research in Computational Molecular Biology, 2009

Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction.
Proceedings of the Parallel Processing and Applied Mathematics, 2009

Exploring FPGAs for accelerating the phylogenetic likelihood function.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

Load Balance in the Phylogenetic Likelihood Kernel.
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

A reconfigurable architecture for the Phylogenetic Likelihood Function.
Proceedings of the 19th International Conference on Field Programmable Logic and Applications, 2009

2008
Large-scale phylogenetic analysis on current HPC architectures.
Scientific Programming, 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.
VLSI Signal Processing, 2007

Runtime scheduling of dynamic parallelism on accelerator-based multi-core systems.
Parallel Computing, 2007

AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.
BMC Bioinformatics, 2007

Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L.
Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007

Dynamic multigrain parallelization on the cell broadband engine.
Proceedings of the 12th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 2007

RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine.
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.
Bioinformatics, 2006

Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions.
Advances in Computers, 2006

Phylogenetic models of rate heterogeneity: a high performance computing perspective.
Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

2005
DRAxML at home: a distributed program for computation of large phylogenetic trees.
Future Generation Comp. Syst., 2005

RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees.
Concurrency and Computation: Practice and Experience, 2005

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
Bioinformatics, 2005

Initial Experiences Porting a Bioinformatics Application to a Graphics Processor.
Proceedings of the Advances in Informatics, 2005

RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs.
Proceedings of the Parallel Computing Technologies, 2005

Using Treemaps to Visualize Phylogenetic Trees.
Proceedings of the Biological and Medical Data Analysis, 6th International Symposium, 2005

An Efficient Program for Phylogenetic Inference Using Simulated Annealing.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood.
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

The AxML program family for maximum likelihood-based phylogenetic tree inference.
Concurrency - Practice and Experience, 2004

A fast program for maximum likelihood-based inference of large phylogenetic trees.
Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004

New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood.
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

Phylogenetic Tree Inference on PC Architectures with AxML/PAxML.
Proceedings of the 17th International Parallel and Distributed Processing Symposium (IPDPS 2003), 2003

2002
Efficiently building on-line tools for distributed heterogeneous environments.
Scientific Programming, 2002

Tool environments in CORBA-based medical high-performance computing.
Future Generation Comp. 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

2001
Tool Environments in CORBA-Based Medical High Performance Computing.
Proceedings of the Parallel Computing Technologies, 2001


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