CME Group
Computational Molecular Evolution

Publications

2020

2019

2018

  • Darriba D, Flouri T, Stamatakis A (2018). The state of software for evolutionary biology, Molecular Biology and Evolution, 35(5):1037–1046 322
  • Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation, BMC Evolutionary Biology, 18(1):11 323
  • Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, others (2018). Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system, Molecular Phylogenetics and Evolution, 125:100–115 324
  • Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology 68(2):365-369 325
  • Johnson KP, Dietrich CH, Friedrich F, Beutel RG, Wipfler B, Peters RS, Allen JM, Petersen M, Donath A, Walden KK, others (2018). Phylogenomics and the evolution of hemipteroid insects, Proceedings of the National Academy of Sciences, pp. advance online access 326
  • Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, others (2018). A roadmap for global synthesis of the plant tree of life, American Journal of Botany, 105(3):614–622 327
  • Bass D, Czech L, Williams BA, Berney C, Dunthorn M, Mahé F, Torruella G, Stentiford GD, Williams TA (2018). Clarifying the Relationships between Microsporidia and Cryptomycota, Journal of Eukaryotic Microbiology, pp. 773-782 328
  • Pauli T, Burt TO, Meusemann K, Bayless K, Donath A, Podsiadlowski L, Mayer C, Kozlov A, Vasilikopoulos A, Liu S, others (2018). New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae), Systematic Entomology, 43(3):447–459 329
  • Sann M, Niehuis O, Peters RS, Mayer C, Kozlov A, Podsiadlowski L, Bank S, Meusemann K, Misof B, Bleidorn C, others (2018). Phylogenomic analysis of Apoidea sheds new light on the sister group of bees, BMC Evolutionary Biology, vol. 18(1), p. 71 330
  • Peters RS, Niehuis O, Gunkel S, Bläser M, Mayer C, Podsiadlowski L, Kozlov A, Donath A, Noort Sv, Liu S, others (2018). Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success, Molecular Phylogenetics and Evolution, 120:286–296 331
  • Czech L, Stamatakis A (2018). Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement, Bioinformatics, pp. advance online access 332
  • Czech L, Stamatakis A (2018). Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements, bioRxiv, p. 346353 333
  • Morel B, Kozlov AM, Stamatakis A (2018). ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes., Bioinformatics 35(10):1771-1773 334
  • Stamatakis A (2018). Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges, In Population Genomics, Springer 335
  • Trefzer A, Stamatakis A (2018). Compressing Streams of Phylogenetic Trees, bioRxiv, p. 440644 336
  • Kozlov A, Darriba D, Flouri T, Morel B, Stamatakis A (2018). RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference, bioRxiv, p. 447110 337

2017

  • Morel B, Flouri T, Stamatakis A (2017). A novel heuristic for data distribution in massively parallel phylogenetic inference using site repeats, In Proceedings of 19th Conference on High Performance Computing and Communications (HPCC), Bangkok, Thailand., IEEE, Dec 2017 217
  • Czech L, Huerta-Cepas J, Stamatakis A (2017). A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits, Molecular Biology and Evolution 34(6):1535-1542 113
  • Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, others (2017). UniEuk: Time to Speak a Common Language in Protistology!, Journal of Eukaryotic Microbiology, 64(3):407-411 212
  • Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SD, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, others (2017). HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences, AIDS Research and Human Retroviruses, 33(11):1083-1098 213
  • Zhou X, Lutteropp S, Czech L, Stamatakis A, Looz Mv, Rokas A (2017). Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence, biorxiv;168526v1,[Preprint] 214
  • Flouri T, Zhang J, Czech L, Kobert K, Stamatakis A (2017). An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties, In Algorithms for Next-Generation Sequencing Data, pp. 299-325, Springer 215
  • Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A (2017). Two C++ Libraries for Counting Trees on a Phylogenetic Terrace, biorxiv;211276v1,[Preprint] 216
  • Bank S, Sann M, Mayer C, Meusemann K, Donath A, Podsiadlowski L, Kozlov A, Petersen M, Krogmann L, Meier R, others (2017). Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae), Molecular Phylogenetics and Evolution, 116:213-226 218
  • Peters RS, Krogmann L, Mayer C, Donath A, Gunkel S, Meusemann K, Kozlov A, Podsiadlowski L, Petersen M, Lanfear R, others (2017). Evolutionary history of the Hymenoptera, Current Biology, 27(7):1013-1018 219
  • Šmíd J, Moravec J, Gvoždík V, Štundl 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). Cutting the Gordian Knot: Phylogenetic and ecological diversification of the Mesalina brevirostris species complex (Squamata, Lacertidae), Zoologica Scripta, 46(6):649-664 220
  • Ahmadzadeh F, Lymberakis P, Pirouz RS, Kapli P (2017). The evolutionary history of two lizards (Squamata: Lacertidae) is linked to the geological development of Iran, Zoologischer Anzeiger – A Journal of Comparative Zoology, 270(Supplement C):49-56 221
  • Grímsson F, Kapli P, Hofmann C, Zetter R, Grimm G (2017). Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family, PeerJ, 5:e3373 222

2016

  • Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016). VSEARCH: a versatile open source tool for metagenomics, PeerJ, 4:e2584, Oct 2016 123
  • Mahé 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). Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites, biorxiv;050997v3,[Preprint] 114
  • Scholl C, Kobert K, Flouri T, Stamatakis A (2016). The divisible load balance problem with shared cost and its application to phylogenetic inference, In Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International, pp. 408–417 115
  • Darriba D, Weiß M, Stamatakis A (2016). Prediction of missing sequences and branch lengths in phylogenomic data, Bioinformatics, 32(9):1331–1337 116
  • Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A (2016). Does the choice of nucleotide substitution models matter topologically?, BMC Bioinformatics, 17(1):143 117
  • Skourtanioti E, Kapli P, Ilgaz Ç, Kumlutaş Y, Avcı A, Ahmadzadeh F, Crnobrnja–Isailović J, Gherghel I, Lymberakis P, Poulakakis N (2016). A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes, Molecular Phylogenetics and Evolution, 103:199–214 118
  • Ahmadzadeh F, Flecks M, Carretero MA, Böhme W, Ihlow F, Kapli P, Miraldo A, Rödder D (2016). Separate histories in both sides of the Mediterranean: phylogeny and niche evolution of ocellated lizards, Journal of Biogeography, 43(6):1242–1253 119
  • Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M (2016). Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae, Molecular Phylogenetics and Evolution, 98:300–313 120
  • Renner SS, Grimm GW, Kapli P, Denk T (2016). Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model, Phil. Trans. R. Soc. B, 371(1699):20150135 121
  • Kobert K, Stamatakis A, Flouri T (2016). Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations, Systematic Biology 122
  • Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A (2016). Phylogeny-aware identification and correction of taxonomically mislabeled sequences, Nucleic Acids Research, 44(11):5022–5033 124
  • Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo, biorxiv;063875v1,[Preprint] 125
  • Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, others (2016). The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life, Phil. Trans. R. Soc. B, vol. 371(1702), p. 20160025 126
  • Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (2016). A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation, In Knowledge and Systems Engineering (KSE), 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE), Hanoi, 2016, pp. 1–6 127

2015

2019

  • Biczok R (2019). Integration of internal and external gene expression and drug-perturbation data to empower novel immune therapies against Parkinson’s Disease, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) 899
  • Wegmann J (2019). Technical and Algorithmic Optimization of PaPaRa, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) 900
  • Breitling P (2019). Quantitave Analysis of Phylogenetic Quasi-Terraces, Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) 901

2018

  • Rülicke L (2018). Design and Implementation of I/O-Efficient Taxa Quartets Counting in the Context of Phylogenetic Analysis, Computer Science, University of Frankfurt, 2018, Ulrich Meyer(Tutor), Alexandros Stamatakis(HITS Tutor) 319
  • Giesse S (2018). Inferring Species Trees by Minimizing Quartet-based Uncertainty, Computer Science, Karlsruhe Institute of Technology, 2018, Alexandros Stamatakis(HITS Tutor) 320
  • Kozlov A (2018). Models, Optimizations, and Tools for Large-Scale Phylogenetic Inference, Handling Sequence Uncertainty, and Taxonomic Validation, Computer Science, Karlsruhe Institute of Technology, 2018, Alexandros Stamatakis(HITS Tutor) 321

2017

  • Schwaiger N (2017). MC3 für phylogenetische Bäume und molekulare Datierung, Mathematics, Karlsruhe Institute of Technology, 2017, Alexandros Stamatakis and Tilmann Gneiting(Tutor) 210
  • Lutteropp S (2017). Error-Profile-Aware Correction of Next Generation Sequencing Read, Computer Science, Karlsruhe Institute of Technology, 2017, Alexandros Stamatakis(Tutor) 211

2016

  • Barbera P (2016). Efficient and Massively Parallel Implementation of the Evolutionary Placement Algorithm, Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) 109
  • Darriba D (2016). Selection of models of genomic evolution in HPC environments, Computer Science, University of A Coruna, 2016, Guillermo López Taboada(Tutor), Alexandros Stamatakis(HITS Tutor) 110
  • Kobert K (2016). Mathematical Problems in Molecular Evolution and Next Generation Sequencing, Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) 111
  • Psonis N (2016). Molecular Phylogeny and Phylogeography of the Podarcis tauricus (Sauria: Lacertidae) Species Subgroup, Department of Biology, University of Crete, 2016, Nikolaos Poulakakis(Tutor), Alexandros Stamatakis(HITS Tutor) 112

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