Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki E, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A (2020). Phylogenetic analysis of SARS-CoV-2 data is difficult, Molecular Biology and Evolution,msaa314 1157
Lähnemann D, Köster 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, Mölder 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, Schönhuth A (2020). Eleven grand challenges in single-cell data science, Genome Biol 21(1) 1093
Laehnemann D, Köster 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, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, Ridder Jd, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A (2019). 12 Grand Challenges in Single-Cell Data Science, e27885v3,[Preprint] 481
Stamatakis A (2019). A review of approaches for optimizing phylogenetic likelihood calculations, In Bioinformatics and Phylogenetics, pp. 1–19, Springer 902
Serdari D, Kostaki E, Paraskevis D, Stamatakis A, Kapli P (2019). Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV, PeerJ 7:e7754 905
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
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
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
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
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
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
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
Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer A, Nguyen L, Minh B, Häseler AV, Stamatakis A (2015). The phylogenetic likelihood library, Systematic Biology, 64(2):356–362 71
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, others (2015). Phylogenomic analyses data of the avian phylogenomics project, GigaScience, 4(1):1–9 73
Biczok R (2019). Integration of internal and external gene expression and drug-perturbation data to empower novel immune therapies against Parkinson’s Disease (Master’s Thesis), Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) 899
Wegmann J (2019). Technical and Algorithmic Optimization of PaPaRa (Master’s Thesis), Computer Science, Karlsruhe Institute of Technology, Alexandros Stamatakis(HITS Tutor) 900
Breitling P (2019). Quantitave Analysis of Phylogenetic Quasi-Terraces (Master’s Thesis), 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 (Master’s Thesis), 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 (Master’s Thesis), 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 (Doctoral Thesis), Computer Science, Karlsruhe Institute of Technology, 2018, Alexandros Stamatakis(HITS Tutor) 321
2017
Schwaiger N (2017). MC3 für phylogenetische Bäume und molekulare Datierung (Master’s Thesis), 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 (Master’s Thesis), 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 (Master’s Thesis), Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) 109
Darriba D (2016). Selection of models of genomic evolution in HPC environments (Doctoral Thesis), 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 (Doctoral Thesis), 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 (Doctoral Thesis), Department of Biology, University of Crete, 2016, Nikolaos Poulakakis(Tutor), Alexandros Stamatakis(HITS Tutor) 112
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