{"id":1352,"date":"2014-10-21T17:36:40","date_gmt":"2014-10-21T15:36:40","guid":{"rendered":"http:\/\/www.h-its.org\/?page_id=1352"},"modified":"2020-04-02T11:49:18","modified_gmt":"2020-04-02T09:49:18","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.h-its.org\/de\/forschung\/cme\/publications\/","title":{"rendered":"Publikationen"},"content":{"rendered":"\n  <div class=\"hits-blocks hits-publications-block\">\n\n      <div class=\"hits-tabs\">\n        <nav>\n          <ul>\n                          <li class=\"is-active\"><a href=\"#\" >Publikationen<\/a><\/li>\n                                      <li class=\"is-active\"><a href=\"#\" >Abschlussarbeiten<\/a><\/li>\n                                  <\/ul>\n        <\/nav>\n        <div class=\"content\">\n                      <div class=\"hits-tabs--tab\">\n            \n              <\/ul><h2 id=\"publication-year-2026\">2026<\/h2><ul class=\"publications-list\"><li>Philippidis A, Mamali A, Pinon V, Vassou D, Nafplioti A, Tabakaki E, Poulakakis N, Stamatakis A, Pavlidis P, Psonis N, Anglos D (2026). <a href=\"https:\/\/doi.org\/10.1016\/j.microc.2026.117446\"><span class=\"publication-title\">In situ microRaman spectroscopy as a screening tool for assessing human DNA preservation in ancient dental remains<\/span><\/a>, Microchemical Journal 224:117446. <span style=\"color:#ddd; font-size:12px\">2239<\/span><\/li><li>H\u00e4user L, Forkel R, List J (2026). <a href=\"https:\/\/doi.org\/10.15475\/calcip.2025.1.4\"><span class=\"publication-title\">PyLexibench \u2014 Generating Data for Lexibench with a Python Package<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">2102<\/span><\/li><li>Psonis N, Tabakaki E, Vassou D, Papadantonakis S, Souleles A, Nafplioti A, Tsampazis GK, Papadopoulou A, Xanthopoulos K, Panailidis P, Georgiadou A, Papakosta D, Koursioti S, Evangelinou M, Papadopoulou V, Evaggeloglou P, Korka E, Christidis I, Ioannou M, Kontogianni T, Arkoumanis A, Stamatakis A, Poulakakis N, Papageorgopoulou C, Pavlidis P (2026). <a href=\"https:\/\/doi.org\/10.1186\/s13059-026-03968-5\"><span class=\"publication-title\">Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis<\/span><\/a>, Genome Biol <span style=\"color:#ddd; font-size:12px\">2241<\/span><\/li><li>Arapitsas NP, Christakis CA, Paragkamian S, Soultatos S, Reden F, Psarologaki C, Avramakis E, Stamatakis A, Markakis EA, Sarris PF (2026). <a href=\"https:\/\/doi.org\/10.64898\/2026.02.06.704400\"><span class=\"publication-title\">Unravelling the genomic and functional arsenal of\n                  <i>Bacilli<\/i>\n                  endophytes from plants with different lifestyles<\/span><\/a>, Preprint. https:\/\/doi.org\/10.64898\/2026.02.06.704400 <span style=\"color:#ddd; font-size:12px\">2240<\/span><\/li><li>Stelz C, H\u00fcbner L, Stamatakis A (2026). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btag044\"><span class=\"publication-title\">Bit-reproducible parallel phylogenetic tree inference<\/span><\/a>, Bioinformatics 42(2):btag044. <span style=\"color:#ddd; font-size:12px\">2230<\/span><\/li><li>H\u00e4user L, J\u00e4ger G, Stamatakis A (2026). <a href=\"https:\/\/doi.org\/10.12688\/openreseurope.20351.3\"><span class=\"publication-title\">A systematic exploration of current limitations of cognate-based phylogenetic inference<\/span><\/a>, Open Res Europe 5:258. <span style=\"color:#ddd; font-size:12px\">2229<\/span><\/li><\/ul><h2 id=\"publication-year-2025\">2025<\/h2><ul class=\"publications-list\"><li>Bettisworth B, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.11.24.690345\"><span class=\"publication-title\">bigrig: A range simulator for the DEC[+J] model<\/span><\/a>, Preprint. https:\/\/doi.org\/10.1101\/2025.11.24.690345 <span style=\"color:#ddd; font-size:12px\">2236<\/span><\/li><li>Huang W, Dombrowski N, Mahendrarajah TA, Wahl N, Stamatakis A, Szollosi GJ, Williams TA, Spang A (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.11.11.687807\"><span class=\"publication-title\">Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages<\/span><\/a>, Preprint. https:\/\/doi.org\/10.1101\/2025.11.11.687807 <span style=\"color:#ddd; font-size:12px\">2238<\/span><\/li><li>Togkousidis A, Gascuel O, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.10.07.680876\"><span class=\"publication-title\">A Systematic Investigation of Overfitting in Maximum Likelihood Phylogenetic Inference<\/span><\/a>, biorxiv;2025.10.07.680876v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">2095<\/span><\/li><li>Psonis N, Tabakaki E, Vassou D, Papadantonakis S, Souleles A, Nafplioti A, Tsampazis GK, Papadopoulou A, Xanthopoulos K, Panailidis P, Georgiadou A, Papakosta D, Koursioti S, Evangelinou M, Papadopoulou V, Evaggeloglou P, Korka E, Christidis I, Ioannou M, Kontogianni T, Arkoumanis A, Stamatakis A, Poulakakis N, Papageorgopoulou C, Pavlidis P (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.07.01.662689\"><span class=\"publication-title\">Genetic affinities between an ancient Greek colony and its metropolis: the case of Amvrakia in western Greece<\/span><\/a>, biorxiv;2025.07.01.662689v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">2109<\/span><\/li><li>H\u00e4user L, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2507.00911\"><span class=\"publication-title\">The Cognate Data Bottleneck in Language Phylogenetics<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">2100<\/span><\/li><li>Stelz C, H\u00fcbner L, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.06.02.656320\"><span class=\"publication-title\">Bit-Reproducible Phylogenetic Tree Inference under Varying Core-Counts via Reproducible Parallel Reduction Operators<\/span><\/a>, biorxiv;2025.06.02.656320v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">2108<\/span><\/li><li>Togkousidis A, Stamatakis A, Gascuel O (2025). <a href=\"https:\/\/doi.org\/10.1093\/sysbio\/syaf043\"><span class=\"publication-title\">Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization<\/span><\/a>, Systematic Biology,syaf043 <span style=\"color:#ddd; font-size:12px\">2096<\/span><\/li><li>Dav\u00edn AA, Woodcroft BJ, Soo RM, Morel B, Murali R, Schrempf D, Clark JW, \u00c1lvarez-Carretero S, Boussau B, Moody ERR, Sz\u00e1nth\u00f3 LL, Richy E, Pisani D, Hemp J, Fischer WW, Donoghue PCJ, Spang A, Hugenholtz P, Williams TA, Sz\u00f6ll\u0151si GJ (2025). <a href=\"https:\/\/doi.org\/10.1126\/science.adp1853\"><span class=\"publication-title\">A geological timescale for bacterial evolution and oxygen adaptation<\/span><\/a>, Science 388(6742),eadp1853 <span style=\"color:#ddd; font-size:12px\">2097<\/span><\/li><li>Haag J, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.03.25.645182\"><span class=\"publication-title\">Pythia 2.0: New Data, New Prediction Model, New Features<\/span><\/a>, biorxiv;2025.03.25.645182v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">2098<\/span><\/li><li>Wahl NA, Koutsovoulos G, Bettisworth B, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.1101\/2025.03.11.642618\"><span class=\"publication-title\">raxtax: A k-mer-based non-Bayesian Taxonomic Classifier<\/span><\/a>, biorxiv;2025.03.11.642618v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">2107<\/span><\/li><li>H\u00e4user L, List J (2025). <a href=\"https:\/\/doi.org\/10.15475\/calcip.2025.1.2\"><span class=\"publication-title\">Lexibench: Towards an Improved Collection of Benchmark Data for Computational Historical Linguistics<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">2101<\/span><\/li><li>Bettisworth B, Psonis N, Poulakakis N, Pavlidis P, Stamatakis A (2025). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msaf006\"><span class=\"publication-title\">Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads<\/span><\/a>, Molecular Biology and Evolution 42(2),msaf006 <span style=\"color:#ddd; font-size:12px\">2106<\/span><\/li><li>Gavriilidou A, Stamatakis A, Kupczok A, Bista I, Jiggins CD, Fern\u00e1ndez R, Skourtanioti E, Amoutzias G, Delneri D, Kyrpides N, Nikolaou C, Pittis AA, Manousaki T, Vakirlis N (2025). <a href=\"https:\/\/doi.org\/10.1093\/bioadv\/vbaf223\"><span class=\"publication-title\">Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course \u201cEvolutionary and Comparative Genomics\u201d<\/span><\/a>, Bioinformatics Advances 5(1),vbaf223 <span style=\"color:#ddd; font-size:12px\">2111<\/span><\/li><\/ul><h2 id=\"publication-year-2024\">2024<\/h2><ul class=\"publications-list\"><li>H\u00f6hler D, Haag J, Kozlov AM, Morel B, Stamatakis A (2024). <a href=\"https:\/\/doi.org\/10.1093\/bioadv\/vbaf300\"><span class=\"publication-title\">Performance assessment of phylogenetic inference tools using PhyloSmew<\/span><\/a>, Bioinformatics Advances 5(1):vbaf300. <span style=\"color:#ddd; font-size:12px\">2237<\/span><\/li><li>Uhl TN, Schimek M, H\u00fcbner L, Hespe D, Kurpicz F, Seemaier D, Stelz C, Sanders P (2024). <a href=\"https:\/\/doi.org\/10.1109\/SC41406.2024.00050\"><span class=\"publication-title\">KaMPIng: Flexible and (Near) Zero-Overhead C++ Bindings for MPI<\/span><\/a>, SC24: International Conference for High Performance Computing, Networking, Storage and Analysis,pp.1-21,IEEE <span style=\"color:#ddd; font-size:12px\">1901<\/span><\/li><li>Stamatakis A, Tsakalides P, Tamiolaki M (2024). <a href=\"https:\/\/doi.org\/10.3389\/fpos.2024.1471002\"><span class=\"publication-title\">Necessary reforms in the Greek academic system<\/span><\/a>, Front. Polit. Sci. 6,1471002 <span style=\"color:#ddd; font-size:12px\">2105<\/span><\/li><li>Kotsakiozi P, Antoniou A, Psonis N, Sagonas \u039a, Karameta E, Ilgaz \u00c7, Kumluta\u015f Y, Avc\u0131 A, Jablonski D, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N (2024). <a href=\"https:\/\/doi.org\/10.1016\/j.ympev.2024.108091\"><span class=\"publication-title\">Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region<\/span><\/a>, Molecular Phylogenetics and Evolution 197:108091 <span style=\"color:#ddd; font-size:12px\">2103<\/span><\/li><li>Togkousidis A, Stamatakis A, Gascuel O (2024). <a href=\"https:\/\/doi.org\/10.1101\/2024.07.04.602058\"><span class=\"publication-title\">Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to evade (Over-)optimization<\/span><\/a>, biorxiv;2024.07.04.602058v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1879<\/span><\/li><li>H\u00e4user L, J\u00e4ger G, Stamatakis A (2024). <a href=\"https:\/\/aclanthology.org\/2024.scil-1.16\/\"><span class=\"publication-title\">Computational Approaches for Integrating out Subjectivity in Cognate Synonym Selection<\/span><\/a>, Luise H\u00e4user, Gerhard J\u00e4ger, and Alexandros Stamatakis. 2024. Computational Approaches for Integrating out Subjectivity in Cognate Synonym Selection. In Proceedings of the Society for Computation in Linguistics 2024, pages 162\u2013172, Irvine, CA. Association for Computational Linguistics. <span style=\"color:#ddd; font-size:12px\">1906<\/span><\/li><li>Agrawal K, Petrank E, Hespe D, H\u00fcbner L, Kurpicz F, Sanders P, Schimek M, Seemaier D, Uhl TN (2024). <a href=\"https:\/\/doi.org\/10.1145\/3626183.3660260\"><span class=\"publication-title\">Brief Announcement: (Near) Zero-Overhead C++ Bindings for MPI<\/span><\/a>, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures,pp.289-291,ACM <span style=\"color:#ddd; font-size:12px\">1903<\/span><\/li><li>H\u00fcbner L, Stamatakis A (2024). <a href=\"https:\/\/doi.org\/10.1101\/2024.05.23.595533\"><span class=\"publication-title\">Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests<\/span><\/a>, biorxiv;2024.05.23.595533v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1902<\/span><\/li><li>Kozlov OM, Stamatakis A (2024). <a href=\"https:\/\/doi.org\/10.23919\/ISC.2024.10528928\"><span class=\"publication-title\">EcoFreq: Compute with Cheaper, Cleaner Energy via Carbon-Aware Power Scaling<\/span><\/a>, ISC High Performance 2024 Research Paper Proceedings (39th International Conference),pp.1-12,IEEE <span style=\"color:#ddd; font-size:12px\">1904<\/span><\/li><li>Stiller J, Feng S, Chowdhury A, Rivas-Gonz\u00e1lez I, Duch\u00eane DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjelds\u00e5 J, Hosner PA, Fonseca RRd, Petersen B, Tobias JA, Sz\u00e9kely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen M, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G (2024). <a href=\"https:\/\/doi.org\/10.1038\/s41586-024-07323-1\"><span class=\"publication-title\">Complexity of avian evolution revealed by family-level genomes<\/span><\/a>, Nature <span style=\"color:#ddd; font-size:12px\">1832<\/span><\/li><li>H\u00e4user L, J\u00e4ger G, List J, Rama T, Stamatakis A (2024). <a href=\"https:\/\/aclanthology.org\/2024.sigtyp-1.11\/\"><span class=\"publication-title\">Are Sounds Sound for Phylogenetic Reconstruction?<\/span><\/a>, Luise H\u00e4user, Gerhard J\u00e4ger, Johann-Mattis List, Taraka Rama, and Alexandros Stamatakis. 2024. Are Sounds Sound for Phylogenetic Reconstruction?. In Proceedings of the 6th Workshop on Research in Computational Linguistic Typology and Multilingual NLP, pages 78\u201387, St. Julian&#8217;s, Malta. Association for Computational Linguistics. <span style=\"color:#ddd; font-size:12px\">1905<\/span><\/li><li>Haag J, Jordan AI, Stamatakis A (2024). <a href=\"https:\/\/doi.org\/10.1101\/2024.03.14.584962\"><span class=\"publication-title\">Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data<\/span><\/a>, biorxiv;2024.03.14.584962v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1833<\/span><\/li><li>Wiegert J, H\u00f6hler D, Haag J, Stamatakis A (2024). <a href=\"https:\/\/doi.org\/10.1101\/2024.03.04.583288\"><span class=\"publication-title\">Predicting Phylogenetic Bootstrap Values via Machine Learning<\/span><\/a>, biorxiv;2024.03.04.583288v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1834<\/span><\/li><li>Williams TA, Davin AA, Sz\u00e1nth\u00f3 LL, Stamatakis A, Wahl NA, Woodcroft BJ, Soo RM, Eme L, Sheridan PO, Gubry-Rangin C, Spang A, Hugenholtz P, Sz\u00f6ll\u0151si GJ (2024). <a href=\"https:\/\/doi.org\/10.1093\/ismejo\/wrae129\"><span class=\"publication-title\">Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution<\/span><\/a>, The ISME Journal 18(1),wrae129 <span style=\"color:#ddd; font-size:12px\">2104<\/span><\/li><li>Stamatakis A, Tamiolaki \ufeff (2024). <a href=\"https:\/\/esv-elibrary.de\/journal\/article\/99.160005\/ful.2024.01.17\"><span class=\"publication-title\">Substanziell unterfinanziert &#8211; Probleme der griechischen Forschungslandschaft<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">2113<\/span><\/li><\/ul><h2 id=\"publication-year-2023\">2023<\/h2><ul class=\"publications-list\"><li>Morel B, Williams TA, Stamatakis A, Sz\u00f6ll\u0151si GJ (2023). <a href=\"https:\/\/doi.org\/10.1101\/2023.10.06.561091\"><span class=\"publication-title\">AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss<\/span><\/a>, biorxiv;2023.10.06.561091v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">1751<\/span><\/li><li>Togkousidis A, Kozlov OM, Haag J, H\u00f6hler D, Stamatakis A (2023). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msad227\"><span class=\"publication-title\">Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty<\/span><\/a>, Molecular Biology and Evolution 40(10),msad227 <span style=\"color:#ddd; font-size:12px\">1750<\/span><\/li><li>Ewers I, Rajter L, Czech L, Mah\u00e9 F, Stamatakis A, Dunthorn M (2023). <a href=\"https:\/\/doi.org\/10.1111\/jeu.12990\"><span class=\"publication-title\">Interpreting phylogenetic placements for taxonomic assignment of environmental\n              DNA<\/span><\/a>, J Eukaryotic Microbiology 70(5),e12990 <span style=\"color:#ddd; font-size:12px\">1748<\/span><\/li><li>Trost J, Haag J, H\u00f6hler D, Jacob L, Stamatakis A, Boussau B (2023). <a href=\"https:\/\/doi.org\/10.1101\/2023.07.11.548509\"><span class=\"publication-title\">Simulations of sequence evolution: how (un)realistic they are and why<\/span><\/a>, biorxiv;2023.07.11.548509v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">1747<\/span><\/li><li>Togkousidis A, Chernomor O, Stamatakis A (2023). <a href=\"https:\/\/doi.org\/10.1109\/IPDPSW59300.2023.00035\"><span class=\"publication-title\">Parallel Inference of Phylogenetic Stands with Gentrius<\/span><\/a>, 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW),pp.139-148,IEEE <span style=\"color:#ddd; font-size:12px\">1746<\/span><\/li><li>Williams TA, Davin AA, Morel B, Sz\u00e1nth\u00f3 LL, Spang A, Stamatakis A, Hugenholtz P, Sz\u00f6ll\u0151si GJ (2023). <a href=\"https:\/\/doi.org\/10.1101\/2023.03.17.533068\"><span class=\"publication-title\">The power and limitations of species tree-aware phylogenetics<\/span><\/a>, biorxiv;2023.03.17.533068v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1745<\/span><\/li><li>Koptekin D, Y\u00fcnc\u00fc E, Rodr\u00edguez-Varela R, Alt\u0131n\u0131\u015f\u0131k NE, Psonis N, Kashuba N, Yorulmaz S, George R, Kazanc\u0131 DD, Kaptan D, G\u00fcr\u00fcn K, Vural KB, Gemici HC, Vassou D, Daskalaki E, Karamurat C, Lagerholm VK, Erdal \u00d6D, K\u0131rd\u00f6k E, Marangoni A, Schachner A, \u00dcst\u00fcnda\u011f H, Shengelia R, Bitadze L, Elashvili M, Stravopodi E, \u00d6zba\u015faran M, Duru G, Nafplioti A, Rose CB, Gencer T, Darbyshire G, Gavashelishvili A, Pitskhelauri K, \u00c7evik \u00d6, Vuru\u015fkan O, Kyparissi-Apostolika N, B\u00fcy\u00fckkarakaya AM, O\u011fuzhano\u011flu U, G\u00fcnel S, Tabakaki E, Aliev A, Ibrahimov A, Shadlinski V, Sampson A, K\u0131l\u0131n\u00e7 GM, Atakuman \u00c7, Stamatakis A, Poulakakis N, Erdal YS, Pavlidis P, Stor\u00e5 J, \u00d6zer F, G\u00f6therstr\u00f6m A, Somel M (2023). <a href=\"https:\/\/doi.org\/10.1016\/j.cub.2022.11.034\"><span class=\"publication-title\">Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean<\/span><\/a>, Current Biology 33(1):41-57.e15 <span style=\"color:#ddd; font-size:12px\">1742<\/span><\/li><li>Morel B, Williams TA, Stamatakis A (2023). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btac832\"><span class=\"publication-title\">Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data<\/span><\/a>, Bioinformatics 39(1),btac832 <span style=\"color:#ddd; font-size:12px\">1744<\/span><\/li><li>Haag J, H\u00fcbner L, Kozlov AM, Stamatakis A (2023). <a href=\"https:\/\/doi.org\/10.1093\/bioadv\/vbad124\"><span class=\"publication-title\">The Free Lunch is not over yet\u2014systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference<\/span><\/a>, Bioinformatics Advances 3(1),vbad124 <span style=\"color:#ddd; font-size:12px\">1749<\/span><\/li><li>Psonis N, Vassou D, Nafplioti A, Tabakaki E, Pavlidis P, Stamatakis A, Poulakakis N (2023). <a href=\"https:\/\/doi.org\/10.2139\/ssrn.4647981\"><span class=\"publication-title\">Identification of the 18 World War II Executed Citizens of Adele, Rethymnon, Crete Using an Ancient DNA Approach and Low Coverage Genomes<\/span><\/a>, [Preprint] <span style=\"color:#ddd; font-size:12px\">1752<\/span><\/li><li>Bruers B, Cruces M, Demleitner M, Duckeck G, D\u00fcren M, Eich N, En\u00dflin T, Erdmann J, Erdmann M, Fackeldey P, Felder C, Fischer B, Fr\u00f6se S, Funk S, Gasthuber M, Grimshaw A, Hadasch D, Hannemann M, Kappes A, Kleinem\u00fchl R, Kozlov OM, Kuhr T, Lupberger M, Neuhaus S, Niknejadi P, Reindl J, Schindler D, Schneidewind A, Schreiber F, Schumacher M, Schwarz K, Streit A, Cube RFv, Walker R, Walther C, Wozniewski S, Zhou K (2023). <span class=\"publication-title\">Resource-aware Research on Universe and Matter: Call-to-Action in Digital Transformation<\/span>, arXiv,physics.comp-ph,2311.01169 <span style=\"color:#ddd; font-size:12px\">1764<\/span><\/li><\/ul><h2 id=\"publication-year-2022\">2022<\/h2><ul class=\"publications-list\"><li>Haag J, H\u00f6hler D, Bettisworth B, Stamatakis A (2022). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msac254\"><span class=\"publication-title\">From Easy to Hopeless\u2014Predicting the Difficulty of Phylogenetic Analyses<\/span><\/a>, Molecular Biology and Evolution 39(12),msac254 <span style=\"color:#ddd; font-size:12px\">1740<\/span><\/li><li>H\u00f6hler D, Haag J, Kozlov AM, Stamatakis A (2022). <a href=\"https:\/\/doi.org\/10.1101\/2022.10.31.514545\"><span class=\"publication-title\">A representative Performance Assessment of Maximum Likelihood based Phylogenetic Inference Tools<\/span><\/a>, biorxiv;2022.10.31.514545v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1741<\/span><\/li><li>Hubner L, Hespe D, Sanders P, Stamatakis A (2022). <a href=\"https:\/\/doi.org\/10.1109\/FTXS56515.2022.00008\"><span class=\"publication-title\">ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms<\/span><\/a>, 2022 IEEE\/ACM 12th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS),pp.24-35,IEEE <span style=\"color:#ddd; font-size:12px\">1743<\/span><\/li><li>Haag J, H\u00fcbner L, Kozlov AM, Stamatakis A (2022). <a href=\"https:\/\/doi.org\/10.1101\/2022.07.13.499893\"><span class=\"publication-title\">The Free Lunch is not over yet \u2013 Systematic Exploration of Numerical Thresholds in Phylogenetic Inference<\/span><\/a>, biorxiv;2022.07.13.499893v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1537<\/span><\/li><li>Haag J, H\u00f6hler D, Bettisworth B, Stamatakis A (2022). <a href=\"https:\/\/doi.org\/10.1101\/2022.06.20.496790\"><span class=\"publication-title\">From Easy to Hopeless &#8211; Predicting the Difficulty of Phylogenetic Analyses<\/span><\/a>, biorxiv;2022.06.20.496790v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1536<\/span><\/li><li>Czech L, Stamatakis A, Dunthorn M, Barbera P (2022). <a href=\"https:\/\/doi.org\/10.3389\/fbinf.2022.871393\"><span class=\"publication-title\">Metagenomic Analysis Using Phylogenetic Placement\u2014A Review of the First Decade<\/span><\/a>, Front. Bioinform. 2,871393 <span style=\"color:#ddd; font-size:12px\">1534<\/span><\/li><li>Bettisworth B, Smith SA, Stamatakis A (2022). <a href=\"https:\/\/doi.org\/10.1101\/2022.04.19.488734\"><span class=\"publication-title\">Lagrange-NG: The next generation of Lagrange<\/span><\/a>, biorxiv;2022.04.19.488734v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1535<\/span><\/li><li>Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N (2022). <a href=\"https:\/\/doi.org\/10.1111\/1755-0998.13470\"><span class=\"publication-title\">SPART: A versatile and standardized data exchange format for species partition information<\/span><\/a>, Molecular Ecology Resources 22(1):430-438 <span style=\"color:#ddd; font-size:12px\">1430<\/span><\/li><\/ul><h2 id=\"publication-year-2021\">2021<\/h2><ul class=\"publications-list\"><li>H\u00f6hler D, Pfeiffer W, Ioannidis V, Stockinger H, Stamatakis A (2021). <a href=\"https:\/\/doi.org\/10.1101\/2021.10.05.463179\"><span class=\"publication-title\">RAxML Grove: An empirical Phylogenetic Tree Database<\/span><\/a>, biorxiv;2021.10.05.463179v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">1431<\/span><\/li><li>Lutteropp S, Scornavacca C, Kozlov AM, Morel B, Stamatakis A (2021). <a href=\"https:\/\/doi.org\/10.1101\/2021.08.30.458194\"><span class=\"publication-title\">NetRAX: Accurate and Fast Maximum Likelihood Phylogenetic Network Inference\n            \u22c6<\/span><\/a>, biorxiv;2021.08.30.458194v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1296<\/span><\/li><li>Mah\u00e9 F, Czech L, Stamatakis A, Quince C, Vargas Cd, Dunthorn M, Rognes T (2021). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btab493\"><span class=\"publication-title\">Swarm v3: towards tera-scale amplicon clustering<\/span><\/a>, Bioinformatics,btab493 <span style=\"color:#ddd; font-size:12px\">1297<\/span><\/li><li>Bettisworth B, Stamatakis A (2021). <a href=\"https:\/\/doi.org\/10.1101\/2021.06.24.449715\"><span class=\"publication-title\">Phylourny: Predicting the Knock-out-phase of Tournaments via Phylogenetic Methods by example of the UEFA EURO 2020<\/span><\/a>, biorxiv;2021.06.24.449715v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1279<\/span><\/li><li>Psonis N, Antoniou A, Karameta E, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N (2021). <a href=\"https:\/\/doi.org\/10.1016\/j.ympev.2021.107121\"><span class=\"publication-title\">The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics<\/span><\/a>, Molecular Phylogenetics and Evolution 159:107121 <span style=\"color:#ddd; font-size:12px\">1300<\/span><\/li><li>Barbera P, Stamatakis A (2021). <a href=\"https:\/\/doi.org\/10.1109\/IPDPSW52791.2021.00041\"><span class=\"publication-title\">Efficient Memory Management in Likelihood-based Phylogenetic Placement<\/span><\/a>, 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW),pp.218-227,IEEE <span style=\"color:#ddd; font-size:12px\">1432<\/span><\/li><li>Morel B, Schade P, Lutteropp S, Williams TA, Sz\u00f6ll\u0151si GJ, Stamatakis A (2021). <a href=\"https:\/\/doi.org\/10.1101\/2021.03.29.437460\"><span class=\"publication-title\">SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss<\/span><\/a>, biorxiv;2021.03.29.437460v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1298<\/span><\/li><li>Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N (2021). <a href=\"https:\/\/doi.org\/10.1101\/2021.03.22.435428\"><span class=\"publication-title\">SPART, a versatile and standardized data exchange format for species partition information<\/span><\/a>, biorxiv;2021.03.22.435428v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1299<\/span><\/li><li>Hodcroft EB, Maio ND, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C (2021). <a href=\"https:\/\/doi.org\/10.1038\/d41586-021-00525-x\"><span class=\"publication-title\">Want to track pandemic variants faster? Fix the bioinformatics bottleneck<\/span><\/a>, Nature 591(7848):30-33 <span style=\"color:#ddd; font-size:12px\">1302<\/span><\/li><li>H\u00fcbner L, Kozlov AM, Hespe D, Sanders P, Stamatakis A (2021). <a href=\"https:\/\/doi.org\/10.1101\/2021.01.15.426773\"><span class=\"publication-title\">Exploring Parallel MPI Fault Tolerance Mechanisms for Phylogenetic Inference with RAxML-NG<\/span><\/a>, biorxiv;2021.01.15.426773v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1301<\/span><\/li><\/ul><h2 id=\"publication-year-2020\">2020<\/h2><ul class=\"publications-list\"><li>Morel B, Barbera P, Czech L, Bettisworth B, H\u00fcbner L, Lutteropp S, Serdari D, Kostaki E, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A (2020). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msaa314\"><span class=\"publication-title\">Phylogenetic analysis of SARS-CoV-2 data is difficult<\/span><\/a>, Molecular Biology and Evolution,msaa314 <span style=\"color:#ddd; font-size:12px\">1157<\/span><\/li><li>L\u00e4hnemann D, K\u00f6ster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson Bd, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, M\u00f6lder F, Niknejad A, Raczkowski L, Reinders M, Ridder Jd, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Sch\u00f6nhuth A (2020). <a href=\"https:\/\/doi.org\/10.1186\/s13059-020-1926-6\"><span class=\"publication-title\">Eleven grand challenges in single-cell data science<\/span><\/a>, Genome Biol 21(1) <span style=\"color:#ddd; font-size:12px\">1093<\/span><\/li><li>Gornik SG, Bergheim BG, Morel B, Stamatakis A, Foulkes NS, Guse A (2020). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msaa304\"><span class=\"publication-title\">Photoreceptor diversification accompanies the evolution of Anthozoa<\/span><\/a>, Molecular Biology and Evolution,msaa304 <span style=\"color:#ddd; font-size:12px\">1158<\/span><\/li><li>Zapletal A, H\u00f6hler D, Sinz C, Stamatakis A (2020). <a href=\"https:\/\/doi.org\/10.1101\/2020.10.07.330621\"><span class=\"publication-title\">SoftWipe \u2013 a tool and benchmark to assess scientific software quality<\/span><\/a>, biorxiv;2020.10.07.330621v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">1153<\/span><\/li><li>Barbera P, Czech L, Lutteropp S, Stamatakis A (2020). <a href=\"https:\/\/doi.org\/10.1111\/1755-0998.13255\"><span class=\"publication-title\">SCRAPP\n              : A tool to assess the diversity of microbial samples from phylogenetic placements<\/span><\/a>, Mol Ecol Resour,1755-0998.13255 <span style=\"color:#ddd; font-size:12px\">1149<\/span><\/li><li>Gottschling M, Czech L, Mah\u00e9 F, Adl S, Dunthorn M (2020). <a href=\"https:\/\/doi.org\/10.1101\/2020.08.07.242388\"><span class=\"publication-title\">The windblown: possible explanations for dinophyte DNA in forest soils<\/span><\/a>, biorxiv;2020.08.07.242388v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1151<\/span><\/li><li>Edgar RC, Taylor J, Altman T, Barbera P, Meleshko D, Lin V, Lohr D, Novakovsky G, Al-Shayeb B, Banfield JF, Korobeynikov A, Chikhi R, Babaian A (2020). <a href=\"https:\/\/doi.org\/10.1101\/2020.08.07.241729\"><span class=\"publication-title\">Petabase-scale sequence alignment catalyses viral discovery<\/span><\/a>, biorxiv;2020.08.07.241729v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1152<\/span><\/li><li>Kozlov A, Alves J, Stamatakis A, Posada D (2020). <a href=\"https:\/\/doi.org\/10.1101\/2020.07.31.230292\"><span class=\"publication-title\">CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data<\/span><\/a>, biorxiv;2020.07.31.230292v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">1150<\/span><\/li><li>Lutteropp S, Kozlov AM, Stamatakis A (2020). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btz874\"><span class=\"publication-title\">A fast and memory-efficient implementation of the transfer bootstrap<\/span><\/a>, Bioinformatics 36(7):2280-2281 <span style=\"color:#ddd; font-size:12px\">1160<\/span><\/li><li>Bettisworth B, Stamatakis A (2020). <a href=\"https:\/\/doi.org\/10.1101\/2020.02.13.935304\"><span class=\"publication-title\">RootDigger\n            : a root placement program for phylogenetic trees<\/span><\/a>, biorxiv;2020.02.13.935304v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">1094<\/span><\/li><\/ul><h2 id=\"publication-year-2019\">2019<\/h2><ul class=\"publications-list\"><li>Breitling P, Stamatakis A, Chernomor O, Bettisworth B, Reszczynski L (2019). <a href=\"https:\/\/doi.org\/10.1101\/810309\"><span class=\"publication-title\">Empirical Analysis of Phylogenetic Quasi-Terraces<\/span><\/a>, biorxiv;810309v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">476<\/span><\/li><li>Comte N, Morel B, Hasic D, Gu\u00e9guen L, Boussau B, Daubin V, Penel S, Scornavacca C, Gouy M, Stamatakis A, Tannier E, Parsons DP (2019). <a href=\"https:\/\/doi.org\/10.1101\/782946\"><span class=\"publication-title\">Treerecs: an integrated phylogenetic tool, from sequences to reconciliations<\/span><\/a>, biorxiv;782946v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">477<\/span><\/li><li>Morel B, Kozlov AM, Stamatakis A, Sz\u00f6ll\u0151si GJ (2019). <a href=\"https:\/\/doi.org\/10.1101\/779066\"><span class=\"publication-title\">GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss<\/span><\/a>, biorxiv;779066v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">483<\/span><\/li><li>Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH (2019). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msz122\"><span class=\"publication-title\">Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States<\/span><\/a>, Molecular Biology and Evolution 36(9):2086-2103 <span style=\"color:#ddd; font-size:12px\">484<\/span><\/li><li>Zhou X, Lutteropp S, Czech L, Stamatakis A, Looz MV, Rokas A (2019). <a href=\"https:\/\/doi.org\/10.1093\/sysbio\/syz058\"><span class=\"publication-title\">Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence<\/span><\/a>, Systematic Biology 69(2):308\u2013324 <span style=\"color:#ddd; font-size:12px\">904<\/span><\/li><li>Laehnemann D, K\u00f6ster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson Bd, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kie\u0142basa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, M\u00f6lder F, Niknejad A, R\u0105czkowski \u0141, Reinders M, Ridder Jd, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Sch\u00f6nhuth A (2019). <a href=\"https:\/\/doi.org\/10.7287\/peerj.preprints.27885v3\"><span class=\"publication-title\">12 Grand Challenges in Single-Cell Data Science<\/span><\/a>, e27885v3,[Preprint] <span style=\"color:#ddd; font-size:12px\">481<\/span><\/li><li>Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T (2019). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msz189\"><span class=\"publication-title\">ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models<\/span><\/a>, Molecular Biology and Evolution 37(1):291-294 <span style=\"color:#ddd; font-size:12px\">478<\/span><\/li><li>Czech L, Barbera P, Stamatakis A (2019). <a href=\"https:\/\/doi.org\/10.1101\/647958\"><span class=\"publication-title\">Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data<\/span><\/a>, biorxiv;647958v3,[Preprint] <span style=\"color:#ddd; font-size:12px\">480<\/span><\/li><li>Kozlov AM, Stamatakis A (2019). <a href=\"https:\/\/doi.org\/10.20944\/preprints201905.0056.v1\"><span class=\"publication-title\">Using RAxML-NG in Practice<\/span><\/a>, [Preprint] <span style=\"color:#ddd; font-size:12px\">951<\/span><\/li><li>Jamy M, Foster R, Barbera P, Czech L, Kozlov A, Stamatakis A, Ba\u00df D, Burki F (2019). <a href=\"https:\/\/doi.org\/10.1111\/1755-0998.13117\"><span class=\"publication-title\">Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity<\/span><\/a>, Mol Ecol Resour.00:1-15 <span style=\"color:#ddd; font-size:12px\">479<\/span><\/li><li>Baar I, Hubner L, Oettig P, Zapletal A, Schlag S, Stamatakis A, Morel B (2019). <a href=\"https:\/\/doi.org\/10.1109\/IPDPSW.2019.00038\"><span class=\"publication-title\">Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning<\/span><\/a>, 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW),pp.175-184,IEEE <span style=\"color:#ddd; font-size:12px\">741<\/span><\/li><li>Stamatakis A (2019). <span class=\"publication-title\">A review of approaches for optimizing phylogenetic likelihood calculations<\/span>, In Bioinformatics and Phylogenetics, pp. 1\u201319, Springer <span style=\"color:#ddd; font-size:12px\">902<\/span><\/li><li>Serdari D, Kostaki E, Paraskevis D, Stamatakis A, Kapli P (2019). <span class=\"publication-title\">Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV<\/span>, PeerJ 7:e7754 <span style=\"color:#ddd; font-size:12px\">905<\/span><\/li><\/ul><h2 id=\"publication-year-2018\">2018<\/h2><ul class=\"publications-list\"><li>Darriba D, Flouri T, Stamatakis A (2018). <span class=\"publication-title\">The state of software for evolutionary biology<\/span>, Molecular Biology and Evolution, 35(5):1037\u20131046 <span style=\"color:#ddd; font-size:12px\">322<\/span><\/li><li>Hoang DT, Vinh LS, Flouri T, Stamatakis A, H\u00e4seler Av, Minh BQ (2018). <span class=\"publication-title\">MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation<\/span>, BMC Evolutionary Biology, 18(1):11 <span style=\"color:#ddd; font-size:12px\">323<\/span><\/li><li>Psonis N, Antoniou A, Karameta E, Leach\u00e9 AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, others  (2018). <span class=\"publication-title\">Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system<\/span>, Molecular Phylogenetics and Evolution, 125:100\u2013115 <span style=\"color:#ddd; font-size:12px\">324<\/span><\/li><li>Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A (2018). <a href=\"https:\/\/doi.org\/10.1093\/sysbio\/syy054\"><span class=\"publication-title\">EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences<\/span><\/a>, Systematic Biology 68(2):365-369 <span style=\"color:#ddd; font-size:12px\">325<\/span><\/li><li>Johnson KP, Dietrich CH, Friedrich F, Beutel RG, Wipfler B, Peters RS, Allen JM, Petersen M, Donath A, Walden KK, others  (2018). <span class=\"publication-title\">Phylogenomics and the evolution of hemipteroid insects<\/span>, Proceedings of the National Academy of Sciences, pp. advance online access <span style=\"color:#ddd; font-size:12px\">326<\/span><\/li><li>Eiserhardt WL, Antonelli A, Bennett DJ, Botigu\u00e9 LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, others  (2018). <span class=\"publication-title\">A roadmap for global synthesis of the plant tree of life<\/span>, American Journal of Botany, 105(3):614\u2013622 <span style=\"color:#ddd; font-size:12px\">327<\/span><\/li><li>Bass D, Czech L, Williams BA, Berney C, Dunthorn M, Mah\u00e9 F, Torruella G, Stentiford GD, Williams TA (2018). <span class=\"publication-title\">Clarifying the Relationships between Microsporidia and Cryptomycota<\/span>, Journal of Eukaryotic Microbiology, pp. 773-782 <span style=\"color:#ddd; font-size:12px\">328<\/span><\/li><li>Pauli T, Burt TO, Meusemann K, Bayless K, Donath A, Podsiadlowski L, Mayer C, Kozlov A, Vasilikopoulos A, Liu S, others  (2018). <span class=\"publication-title\">New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae)<\/span>, Systematic Entomology, 43(3):447\u2013459 <span style=\"color:#ddd; font-size:12px\">329<\/span><\/li><li>Sann M, Niehuis O, Peters RS, Mayer C, Kozlov A, Podsiadlowski L, Bank S, Meusemann K, Misof B, Bleidorn C, others  (2018). <span class=\"publication-title\">Phylogenomic analysis of Apoidea sheds new light on the sister group of bees<\/span>, BMC Evolutionary Biology, vol. 18(1), p. 71 <span style=\"color:#ddd; font-size:12px\">330<\/span><\/li><li>Peters RS, Niehuis O, Gunkel S, Bl\u00e4ser M, Mayer C, Podsiadlowski L, Kozlov A, Donath A, Noort Sv, Liu S, others  (2018). <span class=\"publication-title\">Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success<\/span>, Molecular Phylogenetics and Evolution, 120:286\u2013296 <span style=\"color:#ddd; font-size:12px\">331<\/span><\/li><li>Czech L, Stamatakis A (2018). <span class=\"publication-title\">Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement<\/span>, Bioinformatics, pp. advance online access <span style=\"color:#ddd; font-size:12px\">332<\/span><\/li><li>Czech L, Stamatakis A (2018). <span class=\"publication-title\">Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements<\/span>, bioRxiv, p. 346353 <span style=\"color:#ddd; font-size:12px\">333<\/span><\/li><li>Morel B, Kozlov AM, Stamatakis A (2018). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/bty839\"><span class=\"publication-title\">ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.<\/span><\/a>, Bioinformatics 35(10):1771-1773 <span style=\"color:#ddd; font-size:12px\">334<\/span><\/li><li>Stamatakis A (2018). <span class=\"publication-title\">Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges<\/span>, In Population Genomics, Springer <span style=\"color:#ddd; font-size:12px\">335<\/span><\/li><li>Trefzer A, Stamatakis A (2018). <span class=\"publication-title\">Compressing Streams of Phylogenetic Trees<\/span>, bioRxiv, p. 440644 <span style=\"color:#ddd; font-size:12px\">336<\/span><\/li><li>Kozlov A, Darriba D, Flouri T, Morel B, Stamatakis A (2018). <span class=\"publication-title\">RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference<\/span>, bioRxiv, p. 447110 <span style=\"color:#ddd; font-size:12px\">337<\/span><\/li><\/ul><h2 id=\"publication-year-2017\">2017<\/h2><ul class=\"publications-list\"><li>Morel B, Flouri T, Stamatakis A (2017). <span class=\"publication-title\">A novel heuristic for data distribution in massively parallel phylogenetic inference using site repeats<\/span>, In Proceedings of 19th Conference on High Performance Computing and Communications (HPCC), Bangkok, Thailand., IEEE, Dec 2017 <span style=\"color:#ddd; font-size:12px\">217<\/span><\/li><li>Czech L, Huerta-Cepas J, Stamatakis A (2017). <a href=\"https:\/\/doi.org\/10.1093\/molbev\/msx055\"><span class=\"publication-title\">A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits<\/span><\/a>, Molecular Biology and Evolution 34(6):1535-1542 <span style=\"color:#ddd; font-size:12px\">113<\/span><\/li><li>Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, others  (2017). <span class=\"publication-title\">UniEuk: Time to Speak a Common Language in Protistology!<\/span>, Journal of Eukaryotic Microbiology, 64(3):407-411 <span style=\"color:#ddd; font-size:12px\">212<\/span><\/li><li>Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SD, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, others  (2017). <span class=\"publication-title\">HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences<\/span>, AIDS Research and Human Retroviruses, 33(11):1083-1098 <span style=\"color:#ddd; font-size:12px\">213<\/span><\/li><li>Zhou X, Lutteropp S, Czech L, Stamatakis A, Looz Mv, Rokas A (2017). <a href=\"https:\/\/doi.org\/10.1101\/168526\"><span class=\"publication-title\">Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence<\/span><\/a>, biorxiv;168526v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">214<\/span><\/li><li>Flouri T, Zhang J, Czech L, Kobert K, Stamatakis A (2017). <span class=\"publication-title\">An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties<\/span>, In Algorithms for Next-Generation Sequencing Data, pp. 299-325, Springer <span style=\"color:#ddd; font-size:12px\">215<\/span><\/li><li>Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A (2017). <a href=\"https:\/\/doi.org\/10.1101\/211276\"><span class=\"publication-title\">Two C++ Libraries for Counting Trees on a Phylogenetic Terrace<\/span><\/a>, biorxiv;211276v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">216<\/span><\/li><li>Bank S, Sann M, Mayer C, Meusemann K, Donath A, Podsiadlowski L, Kozlov A, Petersen M, Krogmann L, Meier R, others  (2017). <span class=\"publication-title\">Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae)<\/span>, Molecular Phylogenetics and Evolution, 116:213-226 <span style=\"color:#ddd; font-size:12px\">218<\/span><\/li><li>Peters RS, Krogmann L, Mayer C, Donath A, Gunkel S, Meusemann K, Kozlov A, Podsiadlowski L, Petersen M, Lanfear R, others  (2017). <span class=\"publication-title\">Evolutionary history of the Hymenoptera<\/span>, Current Biology, 27(7):1013-1018 <span style=\"color:#ddd; font-size:12px\">219<\/span><\/li><li>\u0160m\u00edd J, Moravec J, Gvo\u017ed\u00edk V, \u0160tundl J, Frynta D, Lymberakis P, Kapli P, Wilms T, Schmitz A, Shobrak M, Yousefkhani S, Rastegar-Pouyani E, Castilla A, Els J, Mayer W (2017). <span class=\"publication-title\">Cutting the Gordian Knot: Phylogenetic and ecological diversification of the Mesalina brevirostris species complex (Squamata, Lacertidae)<\/span>, Zoologica Scripta, 46(6):649-664 <span style=\"color:#ddd; font-size:12px\">220<\/span><\/li><li>Ahmadzadeh F, Lymberakis P, Pirouz RS, Kapli P (2017). <span class=\"publication-title\">The evolutionary history of two lizards (Squamata: Lacertidae) is linked to the geological development of Iran<\/span>, Zoologischer Anzeiger &#8211; A Journal of Comparative Zoology, 270(Supplement C):49-56 <span style=\"color:#ddd; font-size:12px\">221<\/span><\/li><li>Gr\u00edmsson F, Kapli P, Hofmann C, Zetter R, Grimm G (2017). <span class=\"publication-title\">Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family<\/span>, PeerJ, 5:e3373 <span style=\"color:#ddd; font-size:12px\">222<\/span><\/li><\/ul><h2 id=\"publication-year-2016\">2016<\/h2><ul class=\"publications-list\"><li>Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F (2016). <span class=\"publication-title\">VSEARCH: a versatile open source tool for metagenomics<\/span>, PeerJ, 4:e2584, Oct 2016 <span style=\"color:#ddd; font-size:12px\">123<\/span><\/li><li>Mah\u00e9 F, Vargas Cd, Bass D, Czech L, Stamatakis A, Lara E, Singer D, Mayor J, Bunge J, Sernaker S, Siemensmeyer T, Trautmann I, Romac S, Berney C, Kozlov A, Mitchell EA, Seppey CVW, Egge E, Lentendu G, Wirth R, Trueba G, Dunthorn M (2016). <a href=\"https:\/\/doi.org\/10.1101\/050997\"><span class=\"publication-title\">Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites<\/span><\/a>, biorxiv;050997v3,[Preprint] <span style=\"color:#ddd; font-size:12px\">114<\/span><\/li><li>Scholl C, Kobert K, Flouri T, Stamatakis A (2016). <span class=\"publication-title\">The divisible load balance problem with shared cost and its application to phylogenetic inference<\/span>, In Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International, pp. 408\u2013417 <span style=\"color:#ddd; font-size:12px\">115<\/span><\/li><li>Darriba D, Wei\u00df M, Stamatakis A (2016). <span class=\"publication-title\">Prediction of missing sequences and branch lengths in phylogenomic data<\/span>, Bioinformatics, 32(9):1331\u20131337 <span style=\"color:#ddd; font-size:12px\">116<\/span><\/li><li>Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A (2016). <span class=\"publication-title\">Does the choice of nucleotide substitution models matter topologically?<\/span>, BMC Bioinformatics, 17(1):143 <span style=\"color:#ddd; font-size:12px\">117<\/span><\/li><li>Skourtanioti E, Kapli P, Ilgaz \u00c7, Kumluta\u015f Y, Avc\u0131 A, Ahmadzadeh F, Crnobrnja\u2013Isailovi\u0107 J, Gherghel I, Lymberakis P, Poulakakis N (2016). <span class=\"publication-title\">A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes<\/span>, Molecular Phylogenetics and Evolution, 103:199\u2013214 <span style=\"color:#ddd; font-size:12px\">118<\/span><\/li><li>Ahmadzadeh F, Flecks M, Carretero MA, B\u00f6hme W, Ihlow F, Kapli P, Miraldo A, R\u00f6dder D (2016). <span class=\"publication-title\">Separate histories in both sides of the Mediterranean: phylogeny and niche evolution of ocellated lizards<\/span>, Journal of Biogeography, 43(6):1242\u20131253 <span style=\"color:#ddd; font-size:12px\">119<\/span><\/li><li>Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M (2016). <span class=\"publication-title\">Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae<\/span>, Molecular Phylogenetics and Evolution, 98:300\u2013313 <span style=\"color:#ddd; font-size:12px\">120<\/span><\/li><li>Renner SS, Grimm GW, Kapli P, Denk T (2016). <span class=\"publication-title\">Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth\u2013death clock model<\/span>, Phil. Trans. R. Soc. B, 371(1699):20150135 <span style=\"color:#ddd; font-size:12px\">121<\/span><\/li><li>Kobert K, Stamatakis A, Flouri T (2016). <span class=\"publication-title\">Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations<\/span>, Systematic Biology <span style=\"color:#ddd; font-size:12px\">122<\/span><\/li><li>Kozlov AM, Zhang J, Yilmaz P, Gl\u00f6ckner FO, Stamatakis A (2016). <span class=\"publication-title\">Phylogeny-aware identification and correction of taxonomically mislabeled sequences<\/span>, Nucleic Acids Research, 44(11):5022\u20135033 <span style=\"color:#ddd; font-size:12px\">124<\/span><\/li><li>Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T (2016). <a href=\"https:\/\/doi.org\/10.1101\/063875\"><span class=\"publication-title\">Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo<\/span><\/a>, biorxiv;063875v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">125<\/span><\/li><li>Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, others  (2016). <span class=\"publication-title\">The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life<\/span>, Phil. Trans. R. Soc. B, vol. 371(1702), p. 20160025 <span style=\"color:#ddd; font-size:12px\">126<\/span><\/li><li>Hoang DT, Vinh LS, Flouri T, Stamatakis A, H\u00e4seler Av, Minh BQ (2016). <span class=\"publication-title\">A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation<\/span>, In Knowledge and Systems Engineering (KSE), 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE), Hanoi, 2016, pp. 1\u20136 <span style=\"color:#ddd; font-size:12px\">127<\/span><\/li><\/ul><h2 id=\"publication-year-2015\">2015<\/h2><ul class=\"publications-list\"><li>Aberer AJ, Stamatakis A, Ronquist F (2015). <a href=\"https:\/\/doi.org\/10.1093\/sysbio\/syv051\"><span class=\"publication-title\">An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees<\/span><\/a>, Syst Biol 65(1):161-176 <span style=\"color:#ddd; font-size:12px\">77<\/span><\/li><li>McTavish EJ, Hillis DM (2015). <a href=\"https:\/\/doi.org\/10.1186\/s12864-015-1469-5\"><span class=\"publication-title\">How do SNP ascertainment schemes and population demographics affect inferences about population history?<\/span><\/a>, BMC Genomics 16(1) <span style=\"color:#ddd; font-size:12px\">84<\/span><\/li><li>McTavish EJ, Steel M, Holder MT (2015). <a href=\"https:\/\/doi.org\/10.1016\/j.ympev.2015.07.027\"><span class=\"publication-title\">Twisted trees and inconsistency of tree estimation when gaps are treated as missing data \u2013 The impact of model mis-specification in distance corrections<\/span><\/a>, Molecular Phylogenetics and Evolution 93:289-295 <span style=\"color:#ddd; font-size:12px\">85<\/span><\/li><li>Leach\u00e9 AD, Banbury BL, Felsenstein J, Oca And, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1093\/sysbio\/syv053\"><span class=\"publication-title\">Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies<\/span><\/a>, Syst Biol 64(6):1032-1047 <span style=\"color:#ddd; font-size:12px\">76<\/span><\/li><li>McTavish EJ, Hinchliff CE, Allman JF, Brown JW, Cranston KA, Holder MT, Rees JA, Smith SA (2015). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btv276\"><span class=\"publication-title\">Phylesystem: a git-based data store for community-curated phylogenetic estimates<\/span><\/a>, Bioinformatics 31(17):2794-2800 <span style=\"color:#ddd; font-size:12px\">83<\/span><\/li><li>Sanderson MJ, McMahon MM, Stamatakis A, Zwickl DJ, Steel M (2015). <a href=\"https:\/\/doi.org\/10.1093\/sysbio\/syv024\"><span class=\"publication-title\">Impacts of Terraces on Phylogenetic Inference<\/span><\/a>, Syst Biol 64(5):709-726 <span style=\"color:#ddd; font-size:12px\">72<\/span><\/li><li>Kozlov AM, Aberer AJ, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btv184\"><span class=\"publication-title\">ExaML version 3: a tool for phylogenomic analyses on supercomputers<\/span><\/a>, Bioinformatics 31(15):2577-2579 <span style=\"color:#ddd; font-size:12px\">74<\/span><\/li><li>Flouri T, Giaquinta E, Kobert K, Ukkonen E (2015). <a href=\"https:\/\/doi.org\/10.1016\/j.ipl.2015.03.006\"><span class=\"publication-title\">Longest common substrings with k mismatches<\/span><\/a>, Information Processing Letters 115(6-8):643-647 <span style=\"color:#ddd; font-size:12px\">86<\/span><\/li><li>Barton C, Flouri T, Iliopoulos CS, Pissis SP (2015). <a href=\"https:\/\/doi.org\/10.1016\/j.tcs.2015.03.016\"><span class=\"publication-title\">Global and local sequence alignment with a bounded number of gaps<\/span><\/a>, Theoretical Computer Science 582:1-16 <span style=\"color:#ddd; font-size:12px\">87<\/span><\/li><li>Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer A, Nguyen L, Minh B, H\u00e4seler AV, Stamatakis A (2015). <span class=\"publication-title\">The phylogenetic likelihood library<\/span>, Systematic Biology, 64(2):356\u2013362 <span style=\"color:#ddd; font-size:12px\">71<\/span><\/li><li>Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, others  (2015). <span class=\"publication-title\">Phylogenomic analyses data of the avian phylogenomics project<\/span>, GigaScience, 4(1):1\u20139 <span style=\"color:#ddd; font-size:12px\">73<\/span><\/li><li>Kobert K, Salichos L, Rokas A, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1101\/022053\"><span class=\"publication-title\">Computing the Internode Certainty and related measures from partial gene trees.<\/span><\/a>, biorxiv;022053v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">75<\/span><\/li><li>Stamatakis A (2015). <span class=\"publication-title\">Using RAxML to Infer Phylogenies<\/span>, Current Protocols in Bioinformatics, pp. 6\u201314 <span style=\"color:#ddd; font-size:12px\">78<\/span><\/li><li>Flouri T, Kobert K, Rognes T, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1101\/031500\"><span class=\"publication-title\">Are all global alignment algorithms and implementations correct?<\/span><\/a>, biorxiv;031500v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">79<\/span><\/li><li>Darriba D, Flouri T, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1101\/031930\"><span class=\"publication-title\">The State of Software in Evolutionary Biology<\/span><\/a>, biorxiv;031930v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">80<\/span><\/li><li>Baudis N, Barbera P, Graf S, Lutteropp S, Opitz D, Flouri T, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1101\/033191\"><span class=\"publication-title\">Two Independent and Highly Efficient Open Source TKF91 Implementations<\/span><\/a>, biorxiv;033191v1,[Preprint] <span style=\"color:#ddd; font-size:12px\">81<\/span><\/li><li>Czech L, Stamatakis A (2015). <a href=\"https:\/\/doi.org\/10.1101\/035360\"><span class=\"publication-title\">Do Phylogenetic Tree Viewers correctly display Support Values?<\/span><\/a>, biorxiv;035360v4,[Preprint] <span style=\"color:#ddd; font-size:12px\">82<\/span><\/li><\/ul><h2 id=\"publication-year-1975\">1975<\/h2><ul class=\"publications-list\"><li>Schmoldt A, Benthe HF, Haberland G (1975). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10\"><span class=\"publication-title\">Digitoxin metabolism by rat liver microsomes.<\/span><\/a>, Biochem Pharmacol. 1975 Sep 1;24(17):1639-41. <span style=\"color:#ddd; font-size:12px\">1533<\/span><\/li><\/ul>            <\/div>\n                                <div class=\"hits-tabs--tab\">\n              <\/ul><h2 id=\"publication-year-2025\">2025<\/h2><ul class=\"publications-list\"><li>Knirsch L, Morel B, Stamatakis A (2025). <span class=\"publication-title\">Distanzbasierte Inferenz von Genb\u00e4umen unter Ber\u00fccksichtigung ihres Speziesbaumes (Bachelor&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1915<\/span><\/li><li>Haag J (2025). <span class=\"publication-title\">Novel Applications of Machine Learning and Data Science Methods in Evolutionary Genomics (PhD Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">2115<\/span><\/li><li>H\u00fcbner L (2025). <span class=\"publication-title\">Scalable Evolutionary Bioinformatics (PhD Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">2114<\/span><\/li><li>Bodynek M (2025). <span class=\"publication-title\">Quantifying Uncertainty in Protein Multiple Sequence Alignment (Bachelor&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">2116<\/span><\/li><\/ul><h2 id=\"publication-year-2024\">2024<\/h2><ul class=\"publications-list\"><li>Suhrkamp A, Stamatakis A (2024). <span class=\"publication-title\">Improving DNA-Barcoding Databases: A Framework for Error Detection and Correction in the Barcode of Life Data System (BOLD) (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1907<\/span><\/li><li>Laudemann E, Stamatakis A (2024). <span class=\"publication-title\">Validation and Cross\u2011Species Comparison of scRNA\u2011seq Trajectory Inference Algorithms (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1908<\/span><\/li><li>Borker E, Stamatakis A (2024). <span class=\"publication-title\">Effects of Systematic Errors on Phylogenetic Inference (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1909<\/span><\/li><li>Hengstler J, H\u00fcbner L, Stamatakis A (2024). <span class=\"publication-title\">Re-Engineering Genomic Tree Sequence Inference Algorithms (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1910<\/span><\/li><li>Siebelt D, H\u00fcbner L, Stamatakis A (2024). <span class=\"publication-title\">Faster Sorting of Aligned DNA-Read Files (Bachelor&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1911<\/span><\/li><li>Wiegert J, Haag J, H\u00f6hler D, Stamatakis A (2024). <span class=\"publication-title\">Use Cases of Predictive Modeling for Phylogenetic Inference and Placements (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1912<\/span><\/li><li>Mercatoris L, Stamatakis A (2024). <span class=\"publication-title\">Quantification and Prediction of Multiple Sequence Alignment Difficulty (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1913<\/span><\/li><\/ul><h2 id=\"publication-year-2023\">2023<\/h2><ul class=\"publications-list\"><li>Wahl N, Morel B, Stamatakis A (2023). <span class=\"publication-title\">Approximating Phylogenetic Tree Distributions with Distance-Based Methods (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1914<\/span><\/li><li>H\u00e4user L, Haag J, Stamatakis A (2023). <span class=\"publication-title\">Quantitative Analysis and Characterization of Natural Language Evolution Datasets (Master&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1916<\/span><\/li><li>Strehmel J, Bettisworth B, H\u00f6hler D, Stamatakis A (2023). <span class=\"publication-title\">Is there a Correlation between the Use of Swearwords and Code Quality in Open Source Code? (Bachelor&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1917<\/span><\/li><\/ul><h2 id=\"publication-year-2022\">2022<\/h2><ul class=\"publications-list\"><li>Stelz C, H\u00fcbner L, Stamatakis A (2022). <span class=\"publication-title\">Core-Count Independent Reproducible Reduce (Bachelor&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1918<\/span><\/li><li><span class=\"publication-title\">Investigating the relationship between tree distance and model distance (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">1878<\/span><\/li><\/ul><h2 id=\"publication-year-2021\">2021<\/h2><ul class=\"publications-list\"><li>Haag J (2021). <a href=\"https:\/\/cme.h-its.org\/exelixis\/pubs\/masterJulia.pdf\"><span class=\"publication-title\">Empirical Numerical Properties of Maximum Likelihood Phylogenetic Inference (Master&#8217;s Thesis)<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">1435<\/span><\/li><\/ul><h2 id=\"publication-year-2020\">2020<\/h2><ul class=\"publications-list\"><li>Schade P (2020). <span class=\"publication-title\">Phylogenetic species tree inference from gene trees despite paralogy (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">1877<\/span><\/li><li>H\u00f6hler D (2020). <span class=\"publication-title\">Advanced Heuristics for Accelerating PaPaRa (Master&#8217;s Thesis)<\/span>,  Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">1876<\/span><\/li><li>Hubner L (2020). <span class=\"publication-title\">Load-Balance and Fault-Tolerance for Massively Parallel Phylogenetic Inference (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">1875<\/span><\/li><\/ul><h2 id=\"publication-year-2019\">2019<\/h2><ul class=\"publications-list\"><li>Biczok R (2019). <span class=\"publication-title\">Integration of internal and external gene expression and drug-perturbation data to empower novel immune therapies against Parkinson\u2019s Disease (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">899<\/span><\/li><li>Wegmann J (2019). <span class=\"publication-title\">Technical and Algorithmic Optimization of PaPaRa (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">900<\/span><\/li><li>Breitling P (2019). <span class=\"publication-title\">Quantitave Analysis of Phylogenetic Quasi-Terraces (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">901<\/span><\/li><\/ul><h2 id=\"publication-year-2018\">2018<\/h2><ul class=\"publications-list\"><li>R\u00fclicke L (2018). <span class=\"publication-title\">Design and Implementation of I\/O-Efficient Taxa Quartets Counting in the Context of Phylogenetic Analysis (Master&#8217;s Thesis)<\/span>, Computer Science, University of Frankfurt, 2018, Ulrich Meyer(Tutor), Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">319<\/span><\/li><li>Giesse S (2018). <span class=\"publication-title\">Inferring Species Trees by Minimizing Quartet-based Uncertainty (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, 2018, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">320<\/span><\/li><li>Kozlov A (2018). <span class=\"publication-title\">Models, Optimizations, and Tools for Large-Scale Phylogenetic Inference, Handling Sequence Uncertainty, and Taxonomic Validation (PhD Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, 2018, Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">321<\/span><\/li><\/ul><h2 id=\"publication-year-2017\">2017<\/h2><ul class=\"publications-list\"><li>Schwaiger N (2017). <span class=\"publication-title\">MC3 f\u00fcr phylogenetische B\u00e4ume und molekulare Datierung (Master&#8217;s Thesis)<\/span>, Mathematics, Karlsruhe Institute of Technology, 2017, Alexandros Stamatakis and Tilmann Gneiting(Tutor) <span style=\"color:#ddd; font-size:12px\">210<\/span><\/li><li>Lutteropp S (2017). <span class=\"publication-title\">Error-Profile-Aware Correction of Next Generation Sequencing Read (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, 2017, Alexandros Stamatakis(Tutor) <span style=\"color:#ddd; font-size:12px\">211<\/span><\/li><\/ul><h2 id=\"publication-year-2016\">2016<\/h2><ul class=\"publications-list\"><li>Barbera P (2016). <span class=\"publication-title\">Efficient and Massively Parallel Implementation of the Evolutionary Placement Algorithm (Master&#8217;s Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) <span style=\"color:#ddd; font-size:12px\">109<\/span><\/li><li>Darriba D (2016). <span class=\"publication-title\">Selection of models of genomic evolution in HPC environments (PhD Thesis)<\/span>, Computer Science, University of A Coruna, 2016, Guillermo L\u00f3pez Taboada(Tutor), Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">110<\/span><\/li><li>Kobert K (2016). <span class=\"publication-title\">Mathematical Problems in Molecular Evolution and Next Generation Sequencing (PhD Thesis)<\/span>, Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) <span style=\"color:#ddd; font-size:12px\">111<\/span><\/li><li>Psonis N (2016). <span class=\"publication-title\">Molecular Phylogeny and Phylogeography of the Podarcis tauricus (Sauria: Lacertidae) Species Subgroup (PhD Thesis)<\/span>, Department of Biology, University of Crete, 2016, Nikolaos Poulakakis(Tutor), Alexandros Stamatakis(HITS Tutor) <span style=\"color:#ddd; font-size:12px\">112<\/span><\/li><\/ul><h2 id=\"publication-year-1970\">1970<\/h2><ul class=\"publications-list\"><li>Morel B (1970). <a href=\"https:\/\/cme.h-its.org\/exelixis\/pubs\/dissBenoit.pdf\"><span class=\"publication-title\">Algorithms, load balancing strategies, and dynamic kernels for large-scale phylogenetic tree inference under Maximum Likelihood (PhD Thesis)<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">1436<\/span><\/li><li>Barbera P (1970). <a href=\"https:\/\/publikationen.bibliothek.kit.edu\/1000139668\"><span class=\"publication-title\">High-Performance approaches for Phylogenetic Placement, and its application to species and diversity quantification (PhD Thesis)<\/span><\/a> <span style=\"color:#ddd; font-size:12px\">1434<\/span><\/li><\/ul>            <\/div>\n                            <\/div>\n      <\/div>\n\n  <\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"featured_media":40636,"parent":46,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"page-templates\/group.php","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"hits-research-group":[1282],"class_list":["post-1352","page","type-page","status-publish","has-post-thumbnail","hentry","hits-research-group-cme-de"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Publikationen - HITS gGmbH<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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