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Items: 1 to 20 of 134


ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.

Morel B, Kozlov AM, Stamatakis A.

Bioinformatics. 2018 Oct 15. doi: 10.1093/bioinformatics/bty839. [Epub ahead of print]


Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement.

Czech L, Barbera P, Stamatakis A.

Bioinformatics. 2018 Aug 31. doi: 10.1093/bioinformatics/bty767. [Epub ahead of print]


EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences.

Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A.

Syst Biol. 2018 Aug 27. doi: 10.1093/sysbio/syy054. [Epub ahead of print]


Effects of an early life experience on rat brain cannabinoid receptors in adolescence and adulthood.

Vangopoulou C, Bourmpoula MT, Koupourtidou C, Giompres P, Stamatakis A, Kouvelas ED, Mitsacos A.

IBRO Rep. 2018 May 28;5:1-9. doi: 10.1016/j.ibror.2018.05.002. eCollection 2018 Dec.


A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation.

Mandalakis M, Panikov NS, Polymenakou PN, Sizova MV, Stamatakis A.

Environ Sci Pollut Res Int. 2018 Jun 7. doi: 10.1007/s11356-018-2434-z. [Epub ahead of print]


Two C++ libraries for counting trees on a phylogenetic terrace.

Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A.

Bioinformatics. 2018 Oct 1;34(19):3399-3401. doi: 10.1093/bioinformatics/bty384.


A roadmap for global synthesis of the plant tree of life.

Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, Pokorny L, Rahbek C, Sandel B, Smith SA, Stamatakis A, Vos RA, Warnow T, Baker WJ.

Am J Bot. 2018 Mar;105(3):614-622. doi: 10.1002/ajb2.1041. Epub 2018 Mar 30.


Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.

Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, Jablonski D, Crnobrnja-Isailović J, Gherghel I, Lymberakis P, Poulakakis N.

Mol Phylogenet Evol. 2018 Aug;125:100-115. doi: 10.1016/j.ympev.2018.03.021. Epub 2018 Mar 21.


MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A, Minh BQ.

BMC Evol Biol. 2018 Feb 2;18(1):11. doi: 10.1186/s12862-018-1131-3.


The State of Software for Evolutionary Biology.

Darriba D, Flouri T, Stamatakis A.

Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014.


An early experience of mild adversity involving temporary denial of maternal contact affects the serotonergic system of adult male rats and leads to a depressive-like phenotype and inability to adapt to a chronic social stress.

Diamantopoulou A, Kalpachidou T, Aspiotis G, Gampierakis I, Stylianopoulou F, Stamatakis A.

Physiol Behav. 2018 Feb 1;184:46-54. doi: 10.1016/j.physbeh.2017.11.004. Epub 2017 Nov 7.


Impact of nitrogen source and supply level on growth, yield and nutritional value of two contrasting ecotypes of Cichorium spinosum L. grown hydroponically.

Chatzigianni M, Alkhaled B, Livieratos I, Stamatakis A, Ntatsi G, Savvas D.

J Sci Food Agric. 2018 Mar;98(4):1615-1624. doi: 10.1002/jsfa.8636. Epub 2017 Sep 25.


Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests.

Mahé F, de Vargas C, 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 EAD, Seppey CVW, Egge E, Lentendu G, Wirth R, Trueba G, Dunthorn M.

Nat Ecol Evol. 2017 Mar 20;1(4):91. doi: 10.1038/s41559-017-0091.


HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C.

AIDS Res Hum Retroviruses. 2017 May 25. doi: 10.1089/AID.2017.0061. [Epub ahead of print]


Quality changes and shelf-life extension of ready-to-eat fish patties by adding encapsulated citric acid.

Bou R, Claret A, Stamatakis A, Martínez B, Guerrero L.

J Sci Food Agric. 2017 Dec;97(15):5352-5360. doi: 10.1002/jsfa.8424. Epub 2017 Jun 13.


A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.

Czech L, Huerta-Cepas J, Stamatakis A.

Mol Biol Evol. 2017 Jun 1;34(6):1535-1542. doi: 10.1093/molbev/msx055. Erratum in: Mol Biol Evol. 2017 Sep 1;34(9):2427.


UniEuk: Time to Speak a Common Language in Protistology!

Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C.

J Eukaryot Microbiol. 2017 May;64(3):407-411. doi: 10.1111/jeu.12414. Epub 2017 Apr 21. Review.


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

Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T.

Bioinformatics. 2017 Jun 1;33(11):1630-1638. doi: 10.1093/bioinformatics/btx025.


Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.

Kobert K, Stamatakis A, Flouri T.

Syst Biol. 2017 Mar 1;66(2):205-217. doi: 10.1093/sysbio/syw075.


Effects of pre- and postnatal exposure to 1880-1900MHz DECT base radiation on development in the rat.

Stasinopoulou M, Fragopoulou AF, Stamatakis A, Mantziaras G, Skouroliakou K, Papassideri IS, Stylianopoulou F, Lai H, Kostomitsopoulos N, Margaritis LH.

Reprod Toxicol. 2016 Oct;65:248-262. doi: 10.1016/j.reprotox.2016.08.008. Epub 2016 Aug 17.


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