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ORCIDBibTeX records: Alexandros Stamatakis
@inproceedings{DBLP:conf/sigtype/HauserJLRS24,
author = {Luise H{\"{a}}user and
Gerhard J{\"{a}}ger and
Johann{-}Mattis List and
Taraka Rama and
Alexandros Stamatakis},
editor = {Michael Hahn and
Alexey Sorokin and
Ritesh Kumar and
Andreas Scherbakov and
Yulia Otmakhova and
Jinrui Yang and
Oleg Serikov and
Priya Rani and
Edoardo M. Ponti and
Saliha Muradoglu and
Rena Gao and
Ryan Cotterell and
Ekaterina Vylomova},
title = {Are Sounds Sound for Phylogenetic Reconstruction?},
booktitle = {Proceedings of the 6th Workshop on Research in Computational Linguistic
Typology and Multilingual NLP, {SIGTYPE} 2024, St. Julian's, Malta,
March 22, 2024},
pages = {78--87},
publisher = {Association for Computational Linguistics},
year = {2024},
url = {https://aclanthology.org/2024.sigtyp-1.11},
timestamp = {Thu, 22 Aug 2024 15:23:07 +0200},
biburl = {https://dblp.org/rec/conf/sigtype/HauserJLRS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/HubnerS24,
author = {Lukas H{\"{u}}bner and
Alexandros Stamatakis},
editor = {Solon P. Pissis and
Wing{-}Kin Sung},
title = {Memoization on Shared Subtrees Accelerates Computations on Genealogical
Forests},
booktitle = {24th International Workshop on Algorithms in Bioinformatics, {WABI}
2024, September 2-4, 2024, Royal Holloway, London, United Kingdom},
series = {LIPIcs},
volume = {312},
pages = {5:1--5:22},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2024},
url = {https://doi.org/10.4230/LIPIcs.WABI.2024.5},
doi = {10.4230/LIPICS.WABI.2024.5},
timestamp = {Mon, 26 Aug 2024 16:40:52 +0200},
biburl = {https://dblp.org/rec/conf/wabi/HubnerS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-02807,
author = {Luise H{\"{a}}user and
Gerhard J{\"{a}}ger and
Taraka Rama and
Johann{-}Mattis List and
Alexandros Stamatakis},
title = {Are Sounds Sound for Phylogenetic Reconstruction?},
journal = {CoRR},
volume = {abs/2402.02807},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.02807},
doi = {10.48550/ARXIV.2402.02807},
eprinttype = {arXiv},
eprint = {2402.02807},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-02807.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-19328,
author = {Luise H{\"{a}}user and
Gerhard J{\"{a}}ger and
Alexandros Stamatakis},
title = {Computational Approaches for Integrating out Subjectivity in Cognate
Synonym Selection},
journal = {CoRR},
volume = {abs/2404.19328},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2404.19328},
doi = {10.48550/ARXIV.2404.19328},
eprinttype = {arXiv},
eprint = {2404.19328},
timestamp = {Mon, 27 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2404-19328.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorelWS23,
author = {Benoit Morel and
Tom A. Williams and
Alexandros Stamatakis},
title = {Asteroid: a new algorithm to infer species trees from gene trees under
high proportions of missing data},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac832},
doi = {10.1093/BIOINFORMATICS/BTAC832},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorelWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sac/BettisworthJS23,
author = {Ben Bettisworth and
Alexander I. Jordan and
Alexandros Stamatakis},
title = {Phylourny: efficiently calculating elimination tournament win probabilities
via phylogenetic methods},
journal = {Stat. Comput.},
volume = {33},
number = {4},
pages = {80},
year = {2023},
url = {https://doi.org/10.1007/s11222-023-10246-y},
doi = {10.1007/S11222-023-10246-Y},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sac/BettisworthJS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/TogkousidisCS23,
author = {Anastasis Togkousidis and
Olga Chernomor and
Alexandros Stamatakis},
title = {Parallel Inference of Phylogenetic Stands with Gentrius},
booktitle = {{IEEE} International Parallel and Distributed Processing Symposium,
{IPDPS} 2023 - Workshops, St. Petersburg, FL, USA, May 15-19, 2023},
pages = {139--148},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/IPDPSW59300.2023.00035},
doi = {10.1109/IPDPSW59300.2023.00035},
timestamp = {Wed, 09 Aug 2023 16:25:12 +0200},
biburl = {https://dblp.org/rec/conf/ipps/TogkousidisCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HohlerPISS22,
author = {Dimitri H{\"{o}}hler and
Wayne Pfeiffer and
Vassilios Ioannidis and
Heinz Stockinger and
Alexandros Stamatakis},
title = {RAxML Grove: an empirical phylogenetic tree database},
journal = {Bioinform.},
volume = {38},
number = {6},
pages = {1741--1742},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btab863},
doi = {10.1093/BIOINFORMATICS/BTAB863},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HohlerPISS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LutteroppSKMS22,
author = {Sarah Lutteropp and
C{\'{e}}line Scornavacca and
Alexey M. Kozlov and
Benoit Morel and
Alexandros Stamatakis},
title = {NetRAX: accurate and fast maximum likelihood phylogenetic network
inference},
journal = {Bioinform.},
volume = {38},
number = {15},
pages = {3725--3733},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac396},
doi = {10.1093/BIOINFORMATICS/BTAC396},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LutteroppSKMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/CzechSDB22,
author = {Lucas Czech and
Alexandros Stamatakis and
Micah Dunthorn and
Pierre Barbera},
title = {Metagenomic Analysis Using Phylogenetic Placement - {A} Review of
the First Decade},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.871393},
doi = {10.3389/FBINF.2022.871393},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/CzechSDB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ftxs/HubnerHSS22,
author = {Lukas H{\"{u}}bner and
Demian Hespe and
Peter Sanders and
Alexandros Stamatakis},
title = {ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant
Algorithms},
booktitle = {12th {IEEE/ACM} Workshop on Fault Tolerance for {HPC} at eXtreme Scale,
FTXS@SC 2022, Dallas, TX, USA, November 13-18, 2022},
pages = {24--35},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/FTXS56515.2022.00008},
doi = {10.1109/FTXS56515.2022.00008},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ftxs/HubnerHSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-01107,
author = {Demian Hespe and
Lukas H{\"{u}}bner and
Peter Sanders and
Alexandros Stamatakis},
title = {ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant
Algorithms},
journal = {CoRR},
volume = {abs/2203.01107},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.01107},
doi = {10.48550/ARXIV.2203.01107},
eprinttype = {arXiv},
eprint = {2203.01107},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-01107.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HubnerKHSS21,
author = {Lukas H{\"{u}}bner and
Alexey M. Kozlov and
Demian Hespe and
Peter Sanders and
Alexandros Stamatakis},
title = {Exploring parallel {MPI} fault tolerance mechanisms for phylogenetic
inference with RAxML-NG},
journal = {Bioinform.},
volume = {37},
number = {22},
pages = {4056--4063},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab399},
doi = {10.1093/BIOINFORMATICS/BTAB399},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HubnerKHSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MaheCSQVDR21,
author = {Fr{\'{e}}d{\'{e}}ric Mah{\'{e}} and
Lucas Czech and
Alexandros Stamatakis and
Christopher Quince and
Colomban de Vargas and
Micah Dunthorn and
Torbj{\o}rn Rognes},
title = {Swarm v3: towards tera-scale amplicon clustering},
journal = {Bioinform.},
volume = {38},
number = {1},
pages = {267--269},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab493},
doi = {10.1093/BIOINFORMATICS/BTAB493},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MaheCSQVDR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BettisworthS21,
author = {Ben Bettisworth and
Alexandros Stamatakis},
title = {Root Digger: a root placement program for phylogenetic trees},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {225},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-03956-5},
doi = {10.1186/S12859-021-03956-5},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BettisworthS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/BarberaS21,
author = {Pierre Barbera and
Alexandros Stamatakis},
title = {Efficient Memory Management in Likelihood-based Phylogenetic Placement},
booktitle = {{IEEE} International Parallel and Distributed Processing Symposium
Workshops, {IPDPS} Workshops 2021, Portland, OR, USA, June 17-21,
2021},
pages = {218--227},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/IPDPSW52791.2021.00041},
doi = {10.1109/IPDPSW52791.2021.00041},
timestamp = {Mon, 28 Jun 2021 11:45:26 +0200},
biburl = {https://dblp.org/rec/conf/ipps/BarberaS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LutteroppKS20,
author = {Sarah Lutteropp and
Alexey M. Kozlov and
Alexandros Stamatakis},
title = {A fast and memory-efficient implementation of the transfer bootstrap},
journal = {Bioinform.},
volume = {36},
number = {7},
pages = {2280--2281},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz874},
doi = {10.1093/BIOINFORMATICS/BTZ874},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LutteroppKS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CzechBS20,
author = {Lucas Czech and
Pierre Barbera and
Alexandros Stamatakis},
title = {Genesis and Gappa: processing, analyzing and visualizing phylogenetic
(placement) data},
journal = {Bioinform.},
volume = {36},
number = {10},
pages = {3263--3265},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa070},
doi = {10.1093/BIOINFORMATICS/BTAA070},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CzechBS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ComteMHGBDPSGST20,
author = {Nicolas Comte and
Benoit Morel and
Damir Hasic and
Laurent Gu{\'{e}}guen and
Bastien Boussau and
Vincent Daubin and
Simon Penel and
C{\'{e}}line Scornavacca and
Manolo Gouy and
Alexandros Stamatakis and
Eric Tannier and
David P. Parsons},
title = {Treerecs: an integrated phylogenetic tool, from sequences to reconciliations},
journal = {Bioinform.},
volume = {36},
number = {18},
pages = {4822--4824},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa615},
doi = {10.1093/BIOINFORMATICS/BTAA615},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ComteMHGBDPSGST20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CzechBS19,
author = {Lucas Czech and
Pierre Barbera and
Alexandros Stamatakis},
title = {Methods for automatic reference trees and multilevel phylogenetic
placement},
journal = {Bioinform.},
volume = {35},
number = {7},
pages = {1151--1158},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty767},
doi = {10.1093/BIOINFORMATICS/BTY767},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CzechBS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorelKS19,
author = {Benoit Morel and
Alexey M. Kozlov and
Alexandros Stamatakis},
title = {ParGenes: a tool for massively parallel model selection and phylogenetic
tree inference on thousands of genes},
journal = {Bioinform.},
volume = {35},
number = {10},
pages = {1771--1773},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty839},
doi = {10.1093/BIOINFORMATICS/BTY839},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorelKS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KozlovDFMS19,
author = {Alexey M. Kozlov and
Diego Darriba and
Tom{\'{a}}s Flouri and
Benoit Morel and
Alexandros Stamatakis},
title = {RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood
phylogenetic inference},
journal = {Bioinform.},
volume = {35},
number = {21},
pages = {4453--4455},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz305},
doi = {10.1093/BIOINFORMATICS/BTZ305},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KozlovDFMS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/BaarHOZSSM19,
author = {Ivo Baar and
Lukas H{\"{u}}bner and
Peter Oettig and
Adrian Zapletal and
Sebastian Schlag and
Alexandros Stamatakis and
Benoit Morel},
title = {Data Distribution for Phylogenetic Inference with Site Repeats via
Judicious Hypergraph Partitioning},
booktitle = {{IEEE} International Parallel and Distributed Processing Symposium
Workshops, {IPDPSW} 2019, Rio de Janeiro, Brazil, May 20-24, 2019},
pages = {175--184},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/IPDPSW.2019.00038},
doi = {10.1109/IPDPSW.2019.00038},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/BaarHOZSSM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/peerjpre/LaehnemannKSMHR19,
author = {David Laehnemann and
Johannes K{\"{o}}ster and
Ewa Szczurek and
Davis J. McCarthy and
Stephanie C. Hicks and
Mark D. Robinson and
Catalina A. Vallejos and
Niko Beerenwinkel and
Kieran R. Campbell and
Ahmed Mahfouz and
Luca Pinello and
Pavel Skums and
Alexandros Stamatakis and
Camille Stephan{-}Otto Attolini and
Samuel Aparicio and
Jasmijn A. Baaijens and
Marleen Balvert and
Buys de Barbanson and
Antonio Cappuccio and
Giacomo Corleone and
Bas E. Dutilh and
Maria Florescu and
Victor Guryev and
Rens Holmer and
Katharina Jahn and
Thamar Jessurun Lobo and
Emma M. Keizer and
Indu Khatri and
Szymon M. Kielbasa and
Jan O. Korbel and
Alexey M. Kozlov and
Tzu{-}Hao Kuo and
Boudewijn P. F. Lelieveldt and
Ion I. Mandoiu and
John C. Marioni and
Tobias Marschall and
Felix M{\"{o}}lder and
Amir Niknejad and
Lukasz Raczkowski and
Marcel J. T. Reinders and
Jeroen de Ridder and
Antoine{-}Emmanuel Saliba and
Antonios Somarakis and
Oliver Stegle and
Fabian J. Theis and
Huan Yang and
Alex Zelikovsky and
Alice C. McHardy and
Benjamin J. Raphael and
Sohrab P. Shah and
Alexander Sch{\"{o}}nhuth},
title = {12 Grand Challenges in Single-Cell Data Science},
journal = {PeerJ Prepr.},
volume = {7},
pages = {e27885},
year = {2019},
url = {https://doi.org/10.7287/peerj.preprints.27885v3},
doi = {10.7287/PEERJ.PREPRINTS.27885V3},
timestamp = {Thu, 09 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/peerjpre/LaehnemannKSMHR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BiczokBEERSTWHS18,
author = {Rudolf Biczok and
Peter Bozsoky and
Peter Eisenmann and
Johannes Ernst and
Tobias Ribizel and
Fedor Scholz and
Axel Trefzer and
Florian Weber and
Michael Hamann and
Alexandros Stamatakis},
title = {Two {C++} libraries for counting trees on a phylogenetic terrace},
journal = {Bioinform.},
volume = {34},
number = {19},
pages = {3399--3401},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty384},
doi = {10.1093/BIOINFORMATICS/BTY384},
timestamp = {Mon, 20 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BiczokBEERSTWHS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KapliLZKPSF17,
author = {Paschalia Kapli and
Sarah Lutteropp and
Jiajie Zhang and
Kassian Kobert and
Pavlos Pavlidis and
Alexandros Stamatakis and
Tom{\'{a}}s Flouri},
title = {Multi-rate Poisson tree processes for single-locus species delimitation
under maximum likelihood and Markov chain Monte Carlo},
journal = {Bioinform.},
volume = {33},
number = {11},
pages = {1630--1638},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx025},
doi = {10.1093/BIOINFORMATICS/BTX025},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KapliLZKPSF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpcc/MorelFS17,
author = {Benoit Morel and
Tom{\'{a}}s Flouri and
Alexandros Stamatakis},
title = {A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic
Inference Using Site Repeats},
booktitle = {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,
HPCC/SmartCity/DSS 2017, Bangkok, Thailand, December 18-20, 2017},
pages = {81--88},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/HPCC-SmartCity-DSS.2017.11},
doi = {10.1109/HPCC-SMARTCITY-DSS.2017.11},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hpcc/MorelFS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/17/FlouriZCKS17,
author = {Tom{\'{a}}s Flouri and
Jiajie Zhang and
Lucas Czech and
Kassian Kobert and
Alexandros Stamatakis},
editor = {Mourad Elloumi},
title = {An Efficient Approach to Merging Paired-End Reads and Incorporation
of Uncertainties},
booktitle = {Algorithms for Next-Generation Sequencing Data, Techniques, Approaches,
and Applications},
pages = {299--325},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-59826-0\_13},
doi = {10.1007/978-3-319-59826-0\_13},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/sp/17/FlouriZCKS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DarribaWS16,
author = {Diego Darriba and
Michael Wei{\ss} and
Alexandros Stamatakis},
title = {Prediction of missing sequences and branch lengths in phylogenomic
data},
journal = {Bioinform.},
volume = {32},
number = {9},
pages = {1331--1337},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv768},
doi = {10.1093/BIOINFORMATICS/BTV768},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DarribaWS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HoffORDS16,
author = {Michael Hoff and
Stefan Orf and
Benedikt Riehm and
Diego Darriba and
Alexandros Stamatakis},
title = {Does the choice of nucleotide substitution models matter topologically?},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {143},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-0985-x},
doi = {10.1186/S12859-016-0985-X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HoffORDS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/SchollKFS16,
author = {Constantin Scholl and
Kassian Kobert and
Tom{\'{a}}s Flouri and
Alexandros Stamatakis},
title = {The Divisible Load Balance Problem with Shared Cost and Its Application
to Phylogenetic Inference},
booktitle = {2016 {IEEE} International Parallel and Distributed Processing Symposium
Workshops, {IPDPS} Workshops 2016, Chicago, IL, USA, May 23-27, 2016},
pages = {408--417},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/IPDPSW.2016.38},
doi = {10.1109/IPDPSW.2016.38},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/SchollKFS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kse/HoangVFSHM16,
author = {Diep Thi Hoang and
Le Sy Vinh and
Tom{\'{a}}s Flouri and
Alexandros Stamatakis and
Arndt von Haeseler and
Bui Quang Minh},
editor = {Minh Le Nguyen and
Le Sy Vinh and
Lam Thu Bui and
Van{-}Giang Nguyen and
Yew{-}Soon Ong and
Keiji Hirata},
title = {A new phylogenetic tree sampling method for maximum parsimony bootstrapping
and proof-of-concept implementation},
booktitle = {2016 Eighth International Conference on Knowledge and Systems Engineering,
{KSE} 2016, Hanoi, Vietnam, October 6-8, 2016},
pages = {1--6},
publisher = {{IEEE}},
year = {2016},
url = {https://doi.org/10.1109/KSE.2016.7758020},
doi = {10.1109/KSE.2016.7758020},
timestamp = {Fri, 17 Nov 2023 08:06:20 +0100},
biburl = {https://dblp.org/rec/conf/kse/HoangVFSHM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KozlovAS15,
author = {Alexey M. Kozlov and
Andre J. Aberer and
Alexandros Stamatakis},
title = {ExaML version 3: a tool for phylogenomic analyses on supercomputers},
journal = {Bioinform.},
volume = {31},
number = {15},
pages = {2577--2579},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv184},
doi = {10.1093/BIOINFORMATICS/BTV184},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KozlovAS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangKFS14,
author = {Jiajie Zhang and
Kassian Kobert and
Tom{\'{a}}s Flouri and
Alexandros Stamatakis},
title = {{PEAR:} a fast and accurate Illumina Paired-End reAd mergeR},
journal = {Bioinform.},
volume = {30},
number = {5},
pages = {614--620},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt593},
doi = {10.1093/BIOINFORMATICS/BTT593},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangKFS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ValleSPSSRS14,
author = {Mario Valle and
Hannes Schabauer and
Christoph Pacher and
Heinz Stockinger and
Alexandros Stamatakis and
Marc Robinson{-}Rechavi and
Nicolas Salamin},
title = {Optimization strategies for fast detection of positive selection on
phylogenetic trees},
journal = {Bioinform.},
volume = {30},
number = {8},
pages = {1129--1137},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt760},
doi = {10.1093/BIOINFORMATICS/BTT760},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ValleSPSSRS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Stamatakis14,
author = {Alexandros Stamatakis},
title = {RAxML version 8: a tool for phylogenetic analysis and post-analysis
of large phylogenies},
journal = {Bioinform.},
volume = {30},
number = {9},
pages = {1312--1313},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu033},
doi = {10.1093/BIOINFORMATICS/BTU033},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Stamatakis14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Izquierdo-CarrascoCSS14,
author = {Fernando Izquierdo{-}Carrasco and
John Cazes and
Stephen A. Smith and
Alexandros Stamatakis},
title = {PUmPER: phylogenies updated perpetually},
journal = {Bioinform.},
volume = {30},
number = {10},
pages = {1476--1477},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu053},
doi = {10.1093/BIOINFORMATICS/BTU053},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Izquierdo-CarrascoCSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/KobertHS14,
author = {Kassian Kobert and
J{\"{o}}rg Hauser and
Alexandros Stamatakis},
title = {Is the Protein Model Assignment problem under linked branch lengths
NP-hard?},
journal = {Theor. Comput. Sci.},
volume = {524},
pages = {48--58},
year = {2014},
url = {https://doi.org/10.1016/j.tcs.2013.12.022},
doi = {10.1016/J.TCS.2013.12.022},
timestamp = {Tue, 04 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/KobertHS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/KozlovGS14,
author = {Alexey M. Kozlov and
Christian Goll and
Alexandros Stamatakis},
title = {Efficient Computation of the Phylogenetic Likelihood Function on the
Intel {MIC} Architecture},
booktitle = {2014 {IEEE} International Parallel {\&} Distributed Processing
Symposium Workshops, Phoenix, AZ, USA, May 19-23, 2014},
pages = {518--527},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/IPDPSW.2014.198},
doi = {10.1109/IPDPSW.2014.198},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/KozlovGS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/KobertFAS14,
author = {Kassian Kobert and
Tom{\'{a}}s Flouri and
Andre J. Aberer and
Alexandros Stamatakis},
editor = {Daniel G. Brown and
Burkhard Morgenstern},
title = {The Divisible Load Balance Problem and Its Application to Phylogenetic
Inference},
booktitle = {Algorithms in Bioinformatics - 14th International Workshop, {WABI}
2014, Wroclaw, Poland, September 8-10, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8701},
pages = {204--216},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-662-44753-6\_16},
doi = {10.1007/978-3-662-44753-6\_16},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/KobertFAS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangKPS13,
author = {Jiajie Zhang and
Paschalia Kapli and
Pavlos Pavlidis and
Alexandros Stamatakis},
title = {A general species delimitation method with applications to phylogenetic
placements},
journal = {Bioinform.},
volume = {29},
number = {22},
pages = {2869--2876},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt499},
doi = {10.1093/BIOINFORMATICS/BTT499},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangKPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AbererS13,
author = {Andre J. Aberer and
Alexandros Stamatakis},
title = {Rapid forward-in-time simulation at the chromosome and genome level},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {216},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-216},
doi = {10.1186/1471-2105-14-216},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AbererS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlachiotisBFPS13,
author = {Nikolaos Alachiotis and
Simon A. Berger and
Tom{\'{a}}s Flouri and
Solon P. Pissis and
Alexandros Stamatakis},
title = {libgapmis: extending short-read alignments},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-11}},
pages = {S4},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S11-S4},
doi = {10.1186/1471-2105-14-S11-S4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlachiotisBFPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/PissisSP13,
author = {Solon P. Pissis and
Alexandros Stamatakis and
Pavlos Pavlidis},
editor = {Jing Gao},
title = {MoTeX: {A} word-based {HPC} tool for MoTif eXtraction},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {13},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2506587},
doi = {10.1145/2506583.2506587},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/PissisSP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/Izquierdo-CarrascoABFPS13,
author = {Fernando Izquierdo{-}Carrasco and
Nikolaos Alachiotis and
Simon A. Berger and
Tom{\'{a}}s Flouri and
Solon P. Pissis and
Alexandros Stamatakis},
title = {A Generic Vectorization Scheme and a {GPU} Kernel for the Phylogenetic
Likelihood Library},
booktitle = {2013 {IEEE} International Symposium on Parallel {\&} Distributed
Processing, Workshops and Phd Forum, Cambridge, MA, USA, May 20-24,
2013},
pages = {530--538},
publisher = {{IEEE}},
year = {2013},
url = {https://doi.org/10.1109/IPDPSW.2013.103},
doi = {10.1109/IPDPSW.2013.103},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/Izquierdo-CarrascoABFPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/DarribaAFHIS13,
author = {Diego Darriba and
Andre J. Aberer and
Tom{\'{a}}s Flouri and
Tracy A. Heath and
Fernando Izquierdo{-}Carrasco and
Alexandros Stamatakis},
title = {Boosting the Performance of Bayesian Divergence Time Estimation with
the Phylogenetic Likelihood Library},
booktitle = {2013 {IEEE} International Symposium on Parallel {\&} Distributed
Processing, Workshops and Phd Forum, Cambridge, MA, USA, May 20-24,
2013},
pages = {539--548},
publisher = {{IEEE}},
year = {2013},
url = {https://doi.org/10.1109/IPDPSW.2013.267},
doi = {10.1109/IPDPSW.2013.267},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/DarribaAFHIS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/StamatakisA13,
author = {Alexandros Stamatakis and
Andre J. Aberer},
title = {Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic
Inference},
booktitle = {27th {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2013, Cambridge, MA, USA, May 20-24, 2013},
pages = {1195--1204},
publisher = {{IEEE} Computer Society},
year = {2013},
url = {https://doi.org/10.1109/IPDPS.2013.70},
doi = {10.1109/IPDPS.2013.70},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/StamatakisA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/HauserKIMMGS13,
author = {J{\"{o}}rg Hauser and
Kassian Kobert and
Fernando Izquierdo{-}Carrasco and
Karen Meusemann and
Bernhard Misof and
Michael Gertz and
Alexandros Stamatakis},
editor = {Zhipeng Cai and
Oliver Eulenstein and
Daniel Janies and
Daniel Schwartz},
title = {Heuristic Algorithms for the Protein Model Assignment Problem},
booktitle = {Bioinformatics Research and Applications, 9th International Symposium,
{ISBRA} 2013, Charlotte, NC, USA, May 20-22, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7875},
pages = {137--148},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-38036-5\_16},
doi = {10.1007/978-3-642-38036-5\_16},
timestamp = {Mon, 07 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/isbra/HauserKIMMGS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/FlouriKPS13,
author = {Tom{\'{a}}s Flouri and
Kassian Kobert and
Solon P. Pissis and
Alexandros Stamatakis},
editor = {Thierry Lecroq and
Laurent Mouchard},
title = {An Optimal Algorithm for Computing All Subtree Repeats in Trees},
booktitle = {Combinatorial Algorithms - 24th International Workshop, {IWOCA} 2013,
Rouen, France, July 10-12, 2013, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {8288},
pages = {269--282},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-45278-9\_23},
doi = {10.1007/978-3-642-45278-9\_23},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/FlouriKPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppam/PissisGPS13,
author = {Solon P. Pissis and
Christian Goll and
Pavlos Pavlidis and
Alexandros Stamatakis},
editor = {Roman Wyrzykowski and
Jack J. Dongarra and
Konrad Karczewski and
Jerzy Wasniewski},
title = {Accelerating String Matching on {MIC} Architecture for Motif Extraction},
booktitle = {Parallel Processing and Applied Mathematics - 10th International Conference,
{PPAM} 2013, Warsaw, Poland, September 8-11, 2013, Revised Selected
Papers, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {8385},
pages = {258--267},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-55195-6\_24},
doi = {10.1007/978-3-642-55195-6\_24},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/ppam/PissisGPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StamatakisAGSBI12,
author = {Alexandros Stamatakis and
Andre J. Aberer and
Christian Goll and
Stephen A. Smith and
Simon A. Berger and
Fernando Izquierdo{-}Carrasco},
title = {RAxML-Light: a tool for computing terabyte phylogenies},
journal = {Bioinform.},
volume = {28},
number = {15},
pages = {2064--2066},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts309},
doi = {10.1093/BIOINFORMATICS/BTS309},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StamatakisAGSBI12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AlachiotisSP12,
author = {Nikolaos Alachiotis and
Alexandros Stamatakis and
Pavlos Pavlidis},
title = {OmegaPlus: a scalable tool for rapid detection of selective sweeps
in whole-genome datasets},
journal = {Bioinform.},
volume = {28},
number = {17},
pages = {2274--2275},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts419},
doi = {10.1093/BIOINFORMATICS/BTS419},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AlachiotisSP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlachiotisBS12,
author = {Nikolaos Alachiotis and
Simon A. Berger and
Alexandros Stamatakis},
title = {Coupling {SIMD} and {SIMT} architectures to boost performance of a
phylogeny-aware alignment kernel},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {196},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-196},
doi = {10.1186/1471-2105-13-196},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlachiotisBS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/PratasTSSSK12,
author = {Frederico Pratas and
Pedro Trancoso and
Leonel Sousa and
Alexandros Stamatakis and
Guochun Shi and
Volodymyr V. Kindratenko},
title = {Fine-grain parallelism using multi-core, Cell/BE, and {GPU} Systems},
journal = {Parallel Comput.},
volume = {38},
number = {8},
pages = {365--390},
year = {2012},
url = {https://doi.org/10.1016/j.parco.2011.08.002},
doi = {10.1016/J.PARCO.2011.08.002},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/pc/PratasTSSSK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/AlachiotisBFPS12,
author = {Nikolaos Alachiotis and
Simon A. Berger and
Tom{\'{a}}s Flouri and
Solon P. Pissis and
Alexandros Stamatakis},
title = {Libgapmis: An ultrafast library for short-read single-gap alignment},
booktitle = {2012 {IEEE} International Conference on Bioinformatics and Biomedicine
Workshops, {BIBMW} 2012, Philadelphia, USA, October 4-7, 2012},
pages = {688--695},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/BIBMW.2012.6470221},
doi = {10.1109/BIBMW.2012.6470221},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/AlachiotisBFPS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/Izquierdo-CarrascoGS12,
author = {Fernando Izquierdo{-}Carrasco and
Julien Gagneur and
Alexandros Stamatakis},
editor = {Jan Schier and
Carlos Manuel B. A. Correia and
Ana L. N. Fred and
Hugo Gamboa},
title = {Trading Running Time for Memory in Phylogenetic Likelihood Computations},
booktitle = {{BIOINFORMATICS} 2012 - Proceedings of the International Conference
on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve,
Portugal, 1 - 4 February, 2012},
pages = {86--95},
publisher = {SciTePress},
year = {2012},
timestamp = {Tue, 29 May 2012 10:31:06 +0200},
biburl = {https://dblp.org/rec/conf/biostec/Izquierdo-CarrascoGS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ica3pp/AlachiotisPS12,
author = {Nikolaos Alachiotis and
Pavlos Pavlidis and
Alexandros Stamatakis},
editor = {Yang Xiang and
Ivan Stojmenovic and
Bernady O. Apduhan and
Guojun Wang and
Koji Nakano and
Albert Y. Zomaya},
title = {Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection},
booktitle = {Algorithms and Architectures for Parallel Processing - 12th International
Conference, {ICA3PP} 2012, Fukuoka, Japan, September 4-7, 2012, Proceedings,
Part {I}},
series = {Lecture Notes in Computer Science},
volume = {7439},
pages = {56--68},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33078-0\_5},
doi = {10.1007/978-3-642-33078-0\_5},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ica3pp/AlachiotisPS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/BergerAS12,
author = {Simon A. Berger and
Nikolaos Alachiotis and
Alexandros Stamatakis},
title = {An Optimized Reconfigurable System for Computing the Phylogenetic
Likelihood Function on {DNA} Data},
booktitle = {26th {IEEE} International Parallel and Distributed Processing Symposium
Workshops {\&} PhD Forum, {IPDPS} 2012, Shanghai, China, May 21-25,
2012},
pages = {352--359},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/IPDPSW.2012.43},
doi = {10.1109/IPDPSW.2012.43},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/BergerAS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/ZhangS12,
author = {Jiajie Zhang and
Alexandros Stamatakis},
title = {The Multi-Processor Scheduling Problem in Phylogenetics},
booktitle = {26th {IEEE} International Parallel and Distributed Processing Symposium
Workshops {\&} PhD Forum, {IPDPS} 2012, Shanghai, China, May 21-25,
2012},
pages = {691--698},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/IPDPSW.2012.86},
doi = {10.1109/IPDPSW.2012.86},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/ZhangS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/SchabauerVPSSRYS12,
author = {Hannes Schabauer and
Mario Valle and
Christoph Pacher and
Heinz Stockinger and
Alexandros Stamatakis and
Marc Robinson{-}Rechavi and
Ziheng Yang and
Nicolas Salamin},
title = {SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model},
booktitle = {26th {IEEE} International Parallel and Distributed Processing Symposium
Workshops {\&} PhD Forum, {IPDPS} 2012, Shanghai, China, May 21-25,
2012},
pages = {706--714},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/IPDPSW.2012.88},
doi = {10.1109/IPDPSW.2012.88},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/SchabauerVPSSRYS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/Izquierdo-CarrascoS12,
author = {Fernando Izquierdo{-}Carrasco and
Alexandros Stamatakis},
title = {Inference of Huge Trees under Maximum Likelihood},
booktitle = {26th {IEEE} International Parallel and Distributed Processing Symposium
Workshops {\&} PhD Forum, {IPDPS} 2012, Shanghai, China, May 21-25,
2012},
pages = {2490--2493},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/IPDPSW.2012.309},
doi = {10.1109/IPDPSW.2012.309},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/Izquierdo-CarrascoS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/reconfig/AlachiotisBS12,
author = {Nikolaos Alachiotis and
Simon A. Berger and
Alexandros Stamatakis},
title = {A versatile {UDP/IP} based {PC} {\(\leftrightarrow\)} {FPGA} communication
platform},
booktitle = {2012 International Conference on Reconfigurable Computing and FPGAs,
ReConFig 2012, Cancun, Mexico, December 5-7, 2012},
pages = {1--6},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/ReConFig.2012.6416725},
doi = {10.1109/RECONFIG.2012.6416725},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/reconfig/AlachiotisBS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/StamatakisI11,
author = {Alexandros Stamatakis and
Fernando Izquierdo{-}Carrasco},
title = {Result verification, code verification and computation of support
values in phylogenetics},
journal = {Briefings Bioinform.},
volume = {12},
number = {3},
pages = {270--279},
year = {2011},
url = {https://doi.org/10.1093/bib/bbq079},
doi = {10.1093/BIB/BBQ079},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/StamatakisI11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergerS11,
author = {Simon A. Berger and
Alexandros Stamatakis},
title = {Aligning short reads to reference alignments and trees},
journal = {Bioinform.},
volume = {27},
number = {15},
pages = {2068--2075},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr320},
doi = {10.1093/BIOINFORMATICS/BTR320},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BergerS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LueckingHSC11,
author = {Robert K. Luecking and
Brendan P. Hodkinson and
Alexandros Stamatakis and
Reed A. Cartwright},
title = {PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity
and Cost Scores Ordination},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {10},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-10},
doi = {10.1186/1471-2105-12-10},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LueckingHSC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Izquierdo-CarrascoSS11,
author = {Fernando Izquierdo{-}Carrasco and
Stephen A. Smith and
Alexandros Stamatakis},
title = {Algorithms, data structures, and numerics for likelihood-based phylogenetic
inference of huge trees},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {470},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-470},
doi = {10.1186/1471-2105-12-470},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Izquierdo-CarrascoSS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijrc/AlachiotisS11,
author = {Nikolaos Alachiotis and
Alexandros Stamatakis},
title = {A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm},
journal = {Int. J. Reconfigurable Comput.},
volume = {2011},
pages = {341510:1--341510:12},
year = {2011},
url = {https://doi.org/10.1155/2011/341510},
doi = {10.1155/2011/341510},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijrc/AlachiotisS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/PattengaleASSM11,
author = {Nicholas D. Pattengale and
Andre J. Aberer and
Krister M. Swenson and
Alexandros Stamatakis and
Bernard M. E. Moret},
title = {Uncovering Hidden Phylogenetic Consensus in Large Data Sets},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {4},
pages = {902--911},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2011.28},
doi = {10.1109/TCBB.2011.28},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/PattengaleASSM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/arc/AlachiotisS11,
author = {Nikolaos Alachiotis and
Alexandros Stamatakis},
editor = {Andreas Koch and
Ram Krishnamurthy and
John McAllister and
Roger F. Woods and
Tarek A. El{-}Ghazawi},
title = {{FPGA} Optimizations for a Pipelined Floating-Point Exponential Unit},
booktitle = {Reconfigurable Computing: Architectures, Tools and Applications -
7th International Symposium, {ARC} 2011, Belfast, UK, March 23-25,
2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6578},
pages = {316--327},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-19475-7\_34},
doi = {10.1007/978-3-642-19475-7\_34},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/arc/AlachiotisS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/AbererS11,
author = {Andre J. Aberer and
Alexandros Stamatakis},
editor = {Fang{-}Xiang Wu and
Mohammed Javeed Zaki and
Shinichi Morishita and
Yi Pan and
Stephen Wong and
Anastasia Christianson and
Xiaohua Hu},
title = {A Simple and Accurate Method for Rogue Taxon Identification},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2011, Atlanta, GA, USA, November 12-15, , 2011},
pages = {118--122},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/BIBM.2011.70},
doi = {10.1109/BIBM.2011.70},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/AbererS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fccm/AlachiotisBS11,
author = {Nikolaos Alachiotis and
Simon A. Berger and
Alexandros Stamatakis},
editor = {Paul Chow and
Michael J. Wirthlin},
title = {Accelerating Phylogeny-Aware Short {DNA} Read Alignment with FPGAs},
booktitle = {{IEEE} 19th Annual International Symposium on Field-Programmable Custom
Computing Machines, {FCCM} 2011, Salt Lake City, Utah, USA, 1-3 May
2011},
pages = {226--233},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/FCCM.2011.13},
doi = {10.1109/FCCM.2011.13},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/fccm/AlachiotisBS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpl/AlachiotisS11,
author = {Nikolaos Alachiotis and
Alexandros Stamatakis},
title = {{FPGA} Acceleration of the Phylogenetic Parsimony Kernel?},
booktitle = {International Conference on Field Programmable Logic and Applications,
{FPL} 2011, September 5-7, Chania, Crete, Greece},
pages = {417--422},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/FPL.2011.83},
doi = {10.1109/FPL.2011.83},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/fpl/AlachiotisS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/Izquierdo-CarrascoS11,
author = {Fernando Izquierdo{-}Carrasco and
Alexandros Stamatakis},
title = {Computing the Phylogenetic Likelihood Function Out-of-Core},
booktitle = {25th {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2011, Anchorage, Alaska, USA, 16-20 May 2011 - Workshop Proceedings},
pages = {444--451},
publisher = {{IEEE}},
year = {2011},
url = {https://doi.org/10.1109/IPDPS.2011.185},
doi = {10.1109/IPDPS.2011.185},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/Izquierdo-CarrascoS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pkdd/SeelandBSK11,
author = {Madeleine Seeland and
Simon A. Berger and
Alexandros Stamatakis and
Stefan Kramer},
editor = {Dimitrios Gunopulos and
Thomas Hofmann and
Donato Malerba and
Michalis Vazirgiannis},
title = {Parallel Structural Graph Clustering},
booktitle = {Machine Learning and Knowledge Discovery in Databases - European Conference,
{ECML} {PKDD} 2011, Athens, Greece, September 5-9, 2011, Proceedings,
Part {III}},
series = {Lecture Notes in Computer Science},
volume = {6913},
pages = {256--272},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-23808-6\_17},
doi = {10.1007/978-3-642-23808-6\_17},
timestamp = {Tue, 14 May 2019 10:00:47 +0200},
biburl = {https://dblp.org/rec/conf/pkdd/SeelandBSK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/parallel/Stamatakis11,
author = {Alexandros Stamatakis},
editor = {David A. Padua},
title = {Phylogenetics},
booktitle = {Encyclopedia of Parallel Computing},
pages = {1545--1554},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-0-387-09766-4\_443},
doi = {10.1007/978-0-387-09766-4\_443},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/parallel/Stamatakis11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StamatakisA10,
author = {Alexandros Stamatakis and
Nikolaos Alachiotis},
title = {Time and memory efficient likelihood-based tree searches on phylogenomic
alignments with missing data},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {132--139},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq205},
doi = {10.1093/BIOINFORMATICS/BTQ205},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StamatakisA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/PattengaleABMS10,
author = {Nicholas D. Pattengale and
Masoud Alipour and
Olaf R. P. Bininda{-}Emonds and
Bernard M. E. Moret and
Alexandros Stamatakis},
title = {How Many Bootstrap Replicates Are Necessary?},
journal = {J. Comput. Biol.},
volume = {17},
number = {3},
pages = {337--354},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0179},
doi = {10.1089/CMB.2009.0179},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/PattengaleABMS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jocs/AbererPS10,
author = {Andre J. Aberer and
Nicholas D. Pattengale and
Alexandros Stamatakis},
title = {Parallelized phylogenetic post-analysis on multi-core architectures},
journal = {J. Comput. Sci.},
volume = {1},
number = {2},
pages = {107--114},
year = {2010},
url = {https://doi.org/10.1016/j.jocs.2010.03.006},
doi = {10.1016/J.JOCS.2010.03.006},
timestamp = {Tue, 25 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jocs/AbererPS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/IEEEcit/AlachiotisBS10,
author = {Nikolaos Alachiotis and
Simon A. Berger and
Alexandros Stamatakis},
title = {Efficient {PC-FPGA} Communication over Gigabit Ethernet},
booktitle = {10th {IEEE} International Conference on Computer and Information Technology,
{CIT} 2010, Bradford, West Yorkshire, UK, June 29-July 1, 2010},
pages = {1727--1734},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/CIT.2010.302},
doi = {10.1109/CIT.2010.302},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/IEEEcit/AlachiotisBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aiccsa/BergerS10,
author = {Simon A. Berger and
Alexandros Stamatakis},
title = {Accuracy of morphology-based phylogenetic fossil placement under Maximum
Likelihood},
booktitle = {The 8th {ACS/IEEE} International Conference on Computer Systems and
Applications, {AICCSA} 2010, Hammamet, Tunisia, May 16-19, 2010},
pages = {1--9},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/AICCSA.2010.5586939},
doi = {10.1109/AICCSA.2010.5586939},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/aiccsa/BergerS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aiccsa/StamatakisKB10,
author = {Alexandros Stamatakis and
Zsolt Komornik and
Simon A. Berger},
title = {Evolutionary placement of short sequence reads on multi-core architectures},
booktitle = {The 8th {ACS/IEEE} International Conference on Computer Systems and
Applications, {AICCSA} 2010, Hammamet, Tunisia, May 16-19, 2010},
pages = {1--8},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/AICCSA.2010.5586973},
doi = {10.1109/AICCSA.2010.5586973},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/aiccsa/StamatakisKB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/AlachiotisS10,
author = {Nikolaos Alachiotis and
Alexandros Stamatakis},
title = {Efficient floating-point logarithm unit for FPGAs},
booktitle = {24th {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2010, Atlanta, Georgia, USA, 19-23 April 2010 - Workshop Proceedings},
pages = {1--8},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/IPDPSW.2010.5470752},
doi = {10.1109/IPDPSW.2010.5470752},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/AlachiotisS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/PfeifferS10,
author = {Wayne Pfeiffer and
Alexandros Stamatakis},
title = {Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code},
booktitle = {24th {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2010, Atlanta, Georgia, USA, 19-23 April 2010 - Workshop Proceedings},
pages = {1--8},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/IPDPSW.2010.5470900},
doi = {10.1109/IPDPSW.2010.5470900},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/PfeifferS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/AbererPS10,
author = {Andre J. Aberer and
Nicholas D. Pattengale and
Alexandros Stamatakis},
editor = {Peter M. A. Sloot and
G. Dick van Albada and
Jack J. Dongarra},
title = {Parallel computation of phylogenetic consensus trees},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2010, University of Amsterdam, The Netherlands, May 31 - June
2, 2010},
series = {Procedia Computer Science},
volume = {1},
number = {1},
pages = {1065--1073},
publisher = {Elsevier},
year = {2010},
url = {https://doi.org/10.1016/j.procs.2010.04.118},
doi = {10.1016/J.PROCS.2010.04.118},
timestamp = {Thu, 08 Jul 2021 14:29:22 +0200},
biburl = {https://dblp.org/rec/journals/procedia/AbererPS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijghpc/StockingerAGMS09,
author = {Heinz Stockinger and
Alexander F. Auch and
Markus G{\"{o}}ker and
Jan P. Meier{-}Kolthoff and
Alexandros Stamatakis},
title = {Large-Scale Co-Phylogenetic Analysis on the Grid},
journal = {Int. J. Grid High Perform. Comput.},
volume = {1},
number = {1},
pages = {39--54},
year = {2009},
url = {https://doi.org/10.4018/jghpc.2009010104},
doi = {10.4018/JGHPC.2009010104},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijghpc/StockingerAGMS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpl/AlachiotisSSD09,
author = {Nikolaos Alachiotis and
Alexandros Stamatakis and
Euripides Sotiriades and
Apostolos Dollas},
editor = {Martin Danek and
Jiri Kadlec and
Brent E. Nelson},
title = {A reconfigurable architecture for the Phylogenetic Likelihood Function},
booktitle = {19th International Conference on Field Programmable Logic and Applications,
{FPL} 2009, August 31 - September 2, 2009, Prague, Czech Republic},
pages = {674--678},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/FPL.2009.5272341},
doi = {10.1109/FPL.2009.5272341},
timestamp = {Mon, 09 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fpl/AlachiotisSSD09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/PratasTSS09,
author = {Frederico Pratas and
Pedro Trancoso and
Alexandros Stamatakis and
Leonel Sousa},
title = {Fine-grain Parallelism Using Multi-core, Cell/BE, and {GPU} Systems:
Accelerating the Phylogenetic Likelihood Function},
booktitle = {{ICPP} 2009, International Conference on Parallel Processing, Vienna,
Austria, 22-25 September 2009},
pages = {9--17},
publisher = {{IEEE} Computer Society},
year = {2009},
url = {https://doi.org/10.1109/ICPP.2009.30},
doi = {10.1109/ICPP.2009.30},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icpp/PratasTSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/StamatakisO09,
author = {Alexandros Stamatakis and
Michael Ott},
title = {Load Balance in the Phylogenetic Likelihood Kernel},
booktitle = {{ICPP} 2009, International Conference on Parallel Processing, Vienna,
Austria, 22-25 September 2009},
pages = {348--355},
publisher = {{IEEE} Computer Society},
year = {2009},
url = {https://doi.org/10.1109/ICPP.2009.29},
doi = {10.1109/ICPP.2009.29},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icpp/StamatakisO09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/AlachiotisSDS09,
author = {Nikolaos Alachiotis and
Euripides Sotiriades and
Apostolos Dollas and
Alexandros Stamatakis},
title = {Exploring FPGAs for accelerating the phylogenetic likelihood function},
booktitle = {23rd {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2009, Rome, Italy, May 23-29, 2009},
pages = {1--8},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/IPDPS.2009.5160929},
doi = {10.1109/IPDPS.2009.5160929},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/AlachiotisSDS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppam/BergerS09,
author = {Simon A. Berger and
Alexandros Stamatakis},
editor = {Roman Wyrzykowski and
Jack J. Dongarra and
Konrad Karczewski and
Jerzy Wasniewski},
title = {Accuracy and Performance of Single versus Double Precision Arithmetics
for Maximum Likelihood Phylogeny Reconstruction},
booktitle = {Parallel Processing and Applied Mathematics, 8th International Conference,
{PPAM} 2009, Wroclaw, Poland, September 13-16, 2009, Revised Selected
Papers, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {6068},
pages = {270--279},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-14403-5\_29},
doi = {10.1007/978-3-642-14403-5\_29},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/ppam/BergerS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PattengaleABMS09,
author = {Nicholas D. Pattengale and
Masoud Alipour and
Olaf R. P. Bininda{-}Emonds and
Bernard M. E. Moret and
Alexandros Stamatakis},
editor = {Serafim Batzoglou},
title = {How Many Bootstrap Replicates Are Necessary?},
booktitle = {Research in Computational Molecular Biology, 13th Annual International
Conference, {RECOMB} 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5541},
pages = {184--200},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_13},
doi = {10.1007/978-3-642-02008-7\_13},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PattengaleABMS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sp/OttZAJJS08,
author = {Michael Ott and
Jaroslaw Zola and
Srinivas Aluru and
Andrew D. Johnson and
Daniel Janies and
Alexandros Stamatakis},
title = {Large-scale phylogenetic analysis on current {HPC} architectures},
journal = {Sci. Program.},
volume = {16},
number = {2-3},
pages = {255--270},
year = {2008},
url = {https://doi.org/10.3233/SPR-2008-0247},
doi = {10.3233/SPR-2008-0247},
timestamp = {Wed, 06 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sp/OttZAJJS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/StamatakisO08,
author = {Alexandros Stamatakis and
Michael Ott},
editor = {Madhu Chetty and
Alioune Ngom and
Shandar Ahmad},
title = {Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood
Function with MPI, Pthreads, and OpenMP: {A} Performance Study},
booktitle = {Pattern Recognition in Bioinformatics, Third {IAPR} International
Conference, {PRIB} 2008, Melbourne, Australia, October 15-17, 2008.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5265},
pages = {424--435},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-88436-1\_36},
doi = {10.1007/978-3-540-88436-1\_36},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/StamatakisO08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/StamatakisAMG07,
author = {Alexandros Stamatakis and
Alexander F. Auch and
Jan P. Meier{-}Kolthoff and
Markus G{\"{o}}ker},
title = {AxPcoords {\&} parallel AxParafit: statistical co-phylogenetic
analyses on thousands of taxa},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-405},
doi = {10.1186/1471-2105-8-405},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/StamatakisAMG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/BlagojevicNSAC07,
author = {Filip Blagojevic and
Dimitrios S. Nikolopoulos and
Alexandros Stamatakis and
Christos D. Antonopoulos and
Matthew Curtis{-}Maury},
title = {Runtime scheduling of dynamic parallelism on accelerator-based multi-core
systems},
journal = {Parallel Comput.},
volume = {33},
number = {10-11},
pages = {700--719},
year = {2007},
url = {https://doi.org/10.1016/j.parco.2007.09.004},
doi = {10.1016/J.PARCO.2007.09.004},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/pc/BlagojevicNSAC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/vlsisp/StamatakisBNA07,
author = {Alexandros Stamatakis and
Filip Blagojevic and
Dimitrios S. Nikolopoulos and
Christos D. Antonopoulos},
title = {Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML
Meets the {IBM} Cell},
journal = {J. {VLSI} Signal Process.},
volume = {48},
number = {3},
pages = {271--286},
year = {2007},
url = {https://doi.org/10.1007/s11265-007-0067-4},
doi = {10.1007/S11265-007-0067-4},
timestamp = {Wed, 20 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/vlsisp/StamatakisBNA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/BlagojevicSAN07,
author = {Filip Blagojevic and
Alexandros Stamatakis and
Christos D. Antonopoulos and
Dimitrios S. Nikolopoulos},
title = {RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband
Engine},
booktitle = {21th International Parallel and Distributed Processing Symposium {(IPDPS}
2007), Proceedings, 26-30 March 2007, Long Beach, California, {USA}},
pages = {1--10},
publisher = {{IEEE}},
year = {2007},
url = {https://doi.org/10.1109/IPDPS.2007.370267},
doi = {10.1109/IPDPS.2007.370267},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/BlagojevicSAN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppopp/BlagojevicNSA07,
author = {Filip Blagojevic and
Dimitrios S. Nikolopoulos and
Alexandros Stamatakis and
Christos D. Antonopoulos},
editor = {Katherine A. Yelick and
John M. Mellor{-}Crummey},
title = {Dynamic multigrain parallelization on the cell broadband engine},
booktitle = {Proceedings of the 12th {ACM} {SIGPLAN} Symposium on Principles and
Practice of Parallel Programming, {PPOPP} 2007, San Jose, California,
USA, March 14-17, 2007},
pages = {90--100},
publisher = {{ACM}},
year = {2007},
url = {https://doi.org/10.1145/1229428.1229445},
doi = {10.1145/1229428.1229445},
timestamp = {Sun, 12 Jun 2022 19:46:08 +0200},
biburl = {https://dblp.org/rec/conf/ppopp/BlagojevicNSA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/OttZSA07,
author = {Michael Ott and
Jaroslaw Zola and
Alexandros Stamatakis and
Srinivas Aluru},
editor = {Becky Verastegui},
title = {Large-scale maximum likelihood-based phylogenetic analysis on the
{IBM} BlueGene/L},
booktitle = {Proceedings of the {ACM/IEEE} Conference on High Performance Networking
and Computing, {SC} 2007, November 10-16, 2007, Reno, Nevada, {USA}},
pages = {4},
publisher = {{ACM} Press},
year = {2007},
url = {https://doi.org/10.1145/1362622.1362628},
doi = {10.1145/1362622.1362628},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sc/OttZSA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ac/BaderRS06,
author = {David A. Bader and
Usman Roshan and
Alexandros Stamatakis},
title = {Computational Grand Challenges in Assembling the Tree of Life: Problems
and Solutions},
journal = {Adv. Comput.},
volume = {68},
pages = {128--179},
year = {2006},
url = {https://doi.org/10.1016/S0065-2458(06)68004-2},
doi = {10.1016/S0065-2458(06)68004-2},
timestamp = {Wed, 20 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ac/BaderRS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Stamatakis06,
author = {Alexandros Stamatakis},
title = {RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
thousands of taxa and mixed models},
journal = {Bioinform.},
volume = {22},
number = {21},
pages = {2688--2690},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl446},
doi = {10.1093/BIOINFORMATICS/BTL446},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Stamatakis06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/Stamatakis06,
author = {Alexandros Stamatakis},
title = {Phylogenetic models of rate heterogeneity: a high performance computing
perspective},
booktitle = {20th International Parallel and Distributed Processing Symposium {(IPDPS}
2006), Proceedings, 25-29 April 2006, Rhodes Island, Greece},
publisher = {{IEEE}},
year = {2006},
url = {https://doi.org/10.1109/IPDPS.2006.1639535},
doi = {10.1109/IPDPS.2006.1639535},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/Stamatakis06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StamatakisLM05,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier},
title = {RAxML-III: a fast program for maximum likelihood-based inference of
large phylogenetic trees},
journal = {Bioinform.},
volume = {21},
number = {4},
pages = {456--463},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti191},
doi = {10.1093/BIOINFORMATICS/BTI191},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/StamatakisLM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/StamatakisLM05,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier},
title = {RAxML-II: a program for sequential, parallel and distributed inference
of large phylogenetic trees},
journal = {Concurr. Comput. Pract. Exp.},
volume = {17},
number = {14},
pages = {1705--1723},
year = {2005},
url = {https://doi.org/10.1002/cpe.954},
doi = {10.1002/CPE.954},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/concurrency/StamatakisLM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fgcs/StamatakisLOLM05,
author = {Alexandros Stamatakis and
Markus Lindermeier and
Michael Ott and
Thomas Ludwig and
Harald Meier},
title = {DRAxML at home: a distributed program for computation of large phylogenetic
trees},
journal = {Future Gener. Comput. Syst.},
volume = {21},
number = {4},
pages = {725--730},
year = {2005},
url = {https://doi.org/10.1016/j.future.2004.05.013},
doi = {10.1016/J.FUTURE.2004.05.013},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fgcs/StamatakisLOLM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpcc/DuSLRN05,
author = {Z. Du and
Alexandros Stamatakis and
F. Lin and
Usman Roshan and
Luay Nakhleh},
editor = {Laurence Tianruo Yang and
Omer F. Rana and
Beniamino Di Martino and
Jack J. Dongarra},
title = {Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood},
booktitle = {High Performance Computing and Communications, First International
Conference, {HPCC} 2005, Sorrento, Italy, September 21-23, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3726},
pages = {776--785},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557654\_88},
doi = {10.1007/11557654\_88},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/hpcc/DuSLRN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/Stamatakis05,
author = {Alexandros Stamatakis},
title = {An Efficient Program for Phylogenetic Inference Using Simulated Annealing},
booktitle = {19th International Parallel and Distributed Processing Symposium {(IPDPS}
2005), {CD-ROM} / Abstracts Proceedings, 4-8 April 2005, Denver, CO,
{USA}},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/IPDPS.2005.90},
doi = {10.1109/IPDPS.2005.90},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/Stamatakis05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismda/ArvelakisRSST05,
author = {Adam Arvelakis and
Martin Reczko and
Alexandros Stamatakis and
Alkiviadis Symeonidis and
Ioannis G. Tollis},
editor = {Jos{\'{e}} Lu{\'{\i}}s Oliveira and
Victor Maojo and
Fernando Mart{\'{\i}}n{-}S{\'{a}}nchez and
Ant{\'{o}}nio Sousa Pereira},
title = {Using Treemaps to Visualize Phylogenetic Trees},
booktitle = {Biological and Medical Data Analysis, 6th International Symposium,
{ISBMDA} 2005, Aveiro, Portugal, November 10-11, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3745},
pages = {283--293},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11573067\_29},
doi = {10.1007/11573067\_29},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/ismda/ArvelakisRSST05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pact/StamatakisO005,
author = {Alexandros Stamatakis and
Michael Ott and
Thomas Ludwig},
editor = {Victor E. Malyshkin},
title = {RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs},
booktitle = {Parallel Computing Technologies, 8th International Conference, PaCT
2005, Krasnoyarsk, Russia, September 5-9, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3606},
pages = {288--302},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11535294\_25},
doi = {10.1007/11535294\_25},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pact/StamatakisO005.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pci/CharalambousTS05,
author = {Maria Charalambous and
Pedro Trancoso and
Alexandros Stamatakis},
editor = {Panayiotis Bozanis and
Elias N. Houstis},
title = {Initial Experiences Porting a Bioinformatics Application to a Graphics
Processor},
booktitle = {Advances in Informatics, 10th Panhellenic Conference on Informatics,
{PCI} 2005, Volos, Greece, November 11-13, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3746},
pages = {415--425},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11573036\_39},
doi = {10.1007/11573036\_39},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/pci/CharalambousTS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/de/Stamatakis2004,
author = {Alexandros Stamatakis},
title = {Distributed and parallel algorithms and systems for inference of huge
phylogenetic trees based on the maximum likelihood method},
school = {Technical University Munich, Germany},
year = {2004},
url = {http://tumb1.biblio.tu-muenchen.de/publ/diss/in/2004/stamatakis.html},
urn = {urn:nbn:de:bvb:91-diss2004102817457},
timestamp = {Sat, 17 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/de/Stamatakis2004.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/StamatakisLM04,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier},
title = {The AxML program family for maximum likelihood-based phylogenetic
tree inference},
journal = {Concurr. Pract. Exp.},
volume = {16},
number = {9},
pages = {975--988},
year = {2004},
url = {https://doi.org/10.1002/cpe.817},
doi = {10.1002/CPE.817},
timestamp = {Thu, 21 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/StamatakisLM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/StamatakisLM04,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier},
editor = {Marco Danelutto and
Marco Vanneschi and
Domenico Laforenza},
title = {Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood},
booktitle = {Euro-Par 2004 Parallel Processing, 10th International Euro-Par Conference,
Pisa, Italy, August 31-September 3, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3149},
pages = {997--1004},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27866-5\_134},
doi = {10.1007/978-3-540-27866-5\_134},
timestamp = {Tue, 14 May 2019 10:00:46 +0200},
biburl = {https://dblp.org/rec/conf/europar/StamatakisLM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/StamatakisM004,
author = {Alexandros Stamatakis and
Harald Meier and
Thomas Ludwig},
title = {New Fast and Accurate Heuristics for Inference of Large Phylogenetic
Trees},
booktitle = {18th International Parallel and Distributed Processing Symposium {(IPDPS}
2004), {CD-ROM} / Abstracts Proceedings, 26-30 April 2004, Santa Fe,
New Mexico, {USA}},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/IPDPS.2004.1303212},
doi = {10.1109/IPDPS.2004.1303212},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/StamatakisM004.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sac/StamatakisLM04,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier},
editor = {Hisham Haddad and
Andrea Omicini and
Roger L. Wainwright and
Lorie M. Liebrock},
title = {A fast program for maximum likelihood-based inference of large phylogenetic
trees},
booktitle = {Proceedings of the 2004 {ACM} Symposium on Applied Computing (SAC),
Nicosia, Cyprus, March 14-17, 2004},
pages = {197--201},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/967900.967940},
doi = {10.1145/967900.967940},
timestamp = {Tue, 06 Nov 2018 11:06:44 +0100},
biburl = {https://dblp.org/rec/conf/sac/StamatakisLM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/StamatakisL03,
author = {Alexandros Stamatakis and
Thomas Ludwig},
title = {Phylogenetic Tree Inference on {PC} Architectures with AxML/PAxML},
booktitle = {17th International Parallel and Distributed Processing Symposium {(IPDPS}
2003), 22-26 April 2003, Nice, France, CD-ROM/Abstracts Proceedings},
pages = {157},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/IPDPS.2003.1213296},
doi = {10.1109/IPDPS.2003.1213296},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/StamatakisL03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pact/StamatakisLOLM03,
author = {Alexandros Stamatakis and
Markus Lindermeier and
Michael Ott and
Thomas Ludwig and
Harald Meier},
editor = {Victor E. Malyshkin},
title = {DAxML: {A} Program for Distributed Computation of Phylogenetic Trees
Based on Load Managed {CORBA}},
booktitle = {Parallel Computing Technologies, 7th International Conference, PaCT
2003, Novosibirsk, Russia, September 15-19, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2763},
pages = {538--548},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-45145-7\_51},
doi = {10.1007/978-3-540-45145-7\_51},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pact/StamatakisLOLM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fgcs/LudwigLSR02,
author = {Thomas Ludwig and
Markus Lindermeier and
Alexandros Stamatakis and
G{\"{u}}nther Rackl},
title = {Tool environments in CORBA-based medical high-performance computing},
journal = {Future Gener. Comput. Syst.},
volume = {18},
number = {6},
pages = {841--847},
year = {2002},
url = {https://doi.org/10.1016/S0167-739X(02)00056-0},
doi = {10.1016/S0167-739X(02)00056-0},
timestamp = {Wed, 19 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fgcs/LudwigLSR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sp/RacklLLS02,
author = {G{\"{u}}nther Rackl and
Thomas Ludwig and
Markus Lindermeier and
Alexandros Stamatakis},
title = {Efficiently building on-line tools for distributed heterogeneous environments},
journal = {Sci. Program.},
volume = {10},
number = {1},
pages = {67--74},
year = {2002},
url = {https://doi.org/10.1155/2002/250647},
doi = {10.1155/2002/250647},
timestamp = {Thu, 30 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sp/RacklLLS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/StamatakisLMW02,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier and
Marty J. Wolf},
title = {AxML: {A} Fast Program for Sequential and Parallel Phylogenetic Tree
Calculations Based on the Maximum Likelihood Method},
booktitle = {1st {IEEE} Computer Society Bioinformatics Conference, {CSB} 2002,
Stanford, CA, USA, August 14-16, 2002},
pages = {21},
publisher = {{IEEE} Computer Society},
year = {2002},
url = {https://doi.org/10.1109/CSB.2002.1039325},
doi = {10.1109/CSB.2002.1039325},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/StamatakisLMW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/StamatakisLMW02,
author = {Alexandros Stamatakis and
Thomas Ludwig and
Harald Meier and
Marty J. Wolf},
editor = {Roscoe C. Giles and
Daniel A. Reed and
Kathryn Kelley},
title = {Accelerating parallel maximum likelihood-based phylogenetic tree calculations
using subtree equality vectors},
booktitle = {Proceedings of the 2002 {ACM/IEEE} conference on Supercomputing, Baltimore,
Maryland, USA, November 16-22, 2002, {CD-ROM}},
pages = {2:1--2:16},
publisher = {{IEEE} Computer Society},
year = {2002},
url = {https://doi.org/10.1109/SC.2002.10016},
doi = {10.1109/SC.2002.10016},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sc/StamatakisLMW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pact/LudwigLSR01,
author = {Thomas Ludwig and
Markus Lindermeier and
Alexandros Stamatakis and
G{\"{u}}nther Rackl},
editor = {Victor E. Malyshkin},
title = {Tool Environments in CORBA-Based Medical High Performance Computing},
booktitle = {Parallel Computing Technologies, 6th International Conference, PaCT
2001, Novosibirsk, Russia, September 3-7, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2127},
pages = {447--455},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44743-1\_47},
doi = {10.1007/3-540-44743-1\_47},
timestamp = {Tue, 14 May 2019 10:00:36 +0200},
biburl = {https://dblp.org/rec/conf/pact/LudwigLSR01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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