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Interactive effects of salinity and silicon application on Solanum lycopersicum growth, physiology and shelf life of fruit produced hydroponically.

Costan A, Stamatakis A, Chrysargyris A, Petropoulos SA, Tzortzakis N.

J Sci Food Agric. 2019 Oct 9. doi: 10.1002/jsfa.10076. [Epub ahead of print]


Functional Quality, Mineral Composition and Biomass Production in Hydroponic Spiny Chicory (Cichorium spinosum L.) Are Modulated Interactively by Ecotype, Salinity and Nitrogen Supply.

Chatzigianni M, Ntatsi G, Theodorou M, Stamatakis A, Livieratos I, Rouphael Y, Savvas D.

Front Plant Sci. 2019 Aug 30;10:1040. doi: 10.3389/fpls.2019.01040. eCollection 2019.


Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence.

Zhou X, Lutteropp S, Czech L, Stamatakis A, von Looz M, Rokas A.

Syst Biol. 2019 Aug 29. pii: syz058. doi: 10.1093/sysbio/syz058. [Epub ahead of print]


ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models.

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T.

Mol Biol Evol. 2019 Aug 20. pii: msz189. doi: 10.1093/molbev/msz189. [Epub ahead of print]


A Novel Approach to Chemical Mixture Risk Assessment-Linking Data from Population-Based Epidemiology and Experimental Animal Tests.

Bornehag CG, Kitraki E, Stamatakis A, Panagiotidou E, Rudén C, Shu H, Lindh C, Ruegg J, Gennings C.

Risk Anal. 2019 Oct;39(10):2259-2271. doi: 10.1111/risa.13323. Epub 2019 Jun 7.


Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.

Czech L, Stamatakis A.

PLoS One. 2019 May 28;14(5):e0217050. doi: 10.1371/journal.pone.0217050. eCollection 2019. Erratum in: PLoS One. 2019 Jul 11;14(7):e0219925.


Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.

Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH.

Mol Biol Evol. 2019 Sep 1;36(9):2086-2103. doi: 10.1093/molbev/msz122.


RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference.

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A.

Bioinformatics. 2019 May 9. pii: btz305. doi: 10.1093/bioinformatics/btz305. [Epub ahead of print]


Gestational exposure to an epidemiologically defined mixture of phthalates leads to gonadal dysfunction in mouse offspring of both sexes.

Repouskou A, Panagiotidou E, Panagopoulou L, Bisting PL, Tuck AR, Sjödin MOD, Lindberg J, Bozas E, Rüegg J, Gennings C, Bornehag CG, Damdimopoulou P, Stamatakis A, Kitraki E.

Sci Rep. 2019 Apr 23;9(1):6424. doi: 10.1038/s41598-019-42377-6.


Increased Anxiety-Related Behavior, Impaired Cognitive Function and Cellular Alterations in the Brain of Cend1-deficient Mice.

Segklia K, Stamatakis A, Stylianopoulou F, Lavdas AA, Matsas R.

Front Cell Neurosci. 2019 Jan 29;12:497. doi: 10.3389/fncel.2018.00497. eCollection 2018.


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

Morel B, Kozlov AM, Stamatakis A.

Bioinformatics. 2019 May 15;35(10):1771-1773. doi: 10.1093/bioinformatics/bty839.


Methods for automatic reference trees and multilevel phylogenetic placement.

Czech L, Barbera P, Stamatakis A.

Bioinformatics. 2019 Apr 1;35(7):1151-1158. doi: 10.1093/bioinformatics/bty767.


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. 2019 Mar 1;68(2):365-369. doi: 10.1093/sysbio/syy054.


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.


Simultaneous Optogenetics and Cellular Resolution Calcium Imaging During Active Behavior Using a Miniaturized Microscope.

Stamatakis AM, Schachter MJ, Gulati S, Zitelli KT, Malanowski S, Tajik A, Fritz C, Trulson M, Otte SL.

Front Neurosci. 2018 Jul 24;12:496. doi: 10.3389/fnins.2018.00496. eCollection 2018.


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 Aug;25(24):23845-23856. doi: 10.1007/s11356-018-2434-z. Epub 2018 Jun 7.


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. Review.


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 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25.


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.


The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.

Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, Collins GE, deWaard J, Dean J, Flint OS Jr, Hausmann A, Hendrich L, Hess M, Hogg ID, Kondratieff BC, Malicky H, Milton MA, Morinière J, Morse JC, Mwangi FN, Pauls SU, Gonzalez MR, Rinne A, Robinson JL, Salokannel J, Shackleton M, Smith B, Stamatakis A, StClair R, Thomas JA, Zamora-Muñoz C, Ziesmann T, Kjer KM.

Philos Trans R Soc Lond B Biol Sci. 2016 Sep 5;371(1702). pii: 20160025. doi: 10.1098/rstb.2016.0025.


Early Signs of Pathological Cognitive Aging in Mice Lacking High-Affinity Nicotinic Receptors.

Konsolaki E, Tsakanikas P, Polissidis AV, Stamatakis A, Skaliora I.

Front Aging Neurosci. 2016 Apr 27;8:91. doi: 10.3389/fnagi.2016.00091. eCollection 2016.


Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.

Nucleic Acids Res. 2016 Jun 20;44(11):5022-33. doi: 10.1093/nar/gkw396. Epub 2016 May 10.


Does the choice of nucleotide substitution models matter topologically?

Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A.

BMC Bioinformatics. 2016 Mar 24;17:143. doi: 10.1186/s12859-016-0985-x.


Computing the Internode Certainty and Related Measures from Partial Gene Trees.

Kobert K, Salichos L, Rokas A, Stamatakis A.

Mol Biol Evol. 2016 Jun;33(6):1606-17. doi: 10.1093/molbev/msw040. Epub 2016 Feb 25.


Loss of UBE3A from TH-expressing neurons suppresses GABA co-release and enhances VTA-NAc optical self-stimulation.

Berrios J, Stamatakis AM, Kantak PA, McElligott ZA, Judson MC, Aita M, Rougie M, Stuber GD, Philpot BD.

Nat Commun. 2016 Feb 12;7:10702. doi: 10.1038/ncomms10702.


Lateral Hypothalamic Area Glutamatergic Neurons and Their Projections to the Lateral Habenula Regulate Feeding and Reward.

Stamatakis AM, Van Swieten M, Basiri ML, Blair GA, Kantak P, Stuber GD.

J Neurosci. 2016 Jan 13;36(2):302-11. doi: 10.1523/JNEUROSCI.1202-15.2016.


Prediction of missing sequences and branch lengths in phylogenomic data.

Darriba D, Weiß M, Stamatakis A.

Bioinformatics. 2016 May 1;32(9):1331-7. doi: 10.1093/bioinformatics/btv768. Epub 2016 Jan 5.


Neural stem/progenitor cells differentiate into oligodendrocytes, reduce inflammation, and ameliorate learning deficits after transplantation in a mouse model of traumatic brain injury.

Koutsoudaki PN, Papastefanaki F, Stamatakis A, Kouroupi G, Xingi E, Stylianopoulou F, Matsas R.

Glia. 2016 May;64(5):763-79. doi: 10.1002/glia.22959. Epub 2015 Dec 29.


The levels of the GluN2A NMDA receptor subunit are modified in both the neonatal and adult rat brain by an early experience involving denial of maternal contact.

Manatos V, Stylianopoulou F, Stamatakis A.

Neurosci Lett. 2016 Jan 26;612:98-103. doi: 10.1016/j.neulet.2015.12.005. Epub 2015 Dec 8.


Exposure to a mildly aversive early life experience leads to prefrontal cortex deficits in the rat.

Stamatakis A, Manatos V, Kalpachidou T, Stylianopoulou F.

Brain Struct Funct. 2016 Nov;221(8):4141-4157. Epub 2015 Dec 7.


Tag1 deficiency results in olfactory dysfunction through impaired migration of mitral cells.

Bastakis GG, Savvaki M, Stamatakis A, Vidaki M, Karagogeos D.

Development. 2015 Dec 15;142(24):4318-28. doi: 10.1242/dev.123943. Epub 2015 Nov 2.


Using RAxML to Infer Phylogenies.

Stamatakis A.

Curr Protoc Bioinformatics. 2015 Sep 3;51:6.14.1-14. doi: 10.1002/0471250953.bi0614s51.


Effects of a Neonatal Experience Involving Reward Through Maternal Contact on the Noradrenergic System of the Rat Prefrontal Cortex.

Kalpachidou T, Raftogianni A, Melissa P, Kollia AM, Stylianopoulou F, Stamatakis A.

Cereb Cortex. 2016 Sep;26(9):3866-3877. doi: 10.1093/cercor/bhv192. Epub 2015 Aug 26.


An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees.

Aberer AJ, Stamatakis A, Ronquist F.

Syst Biol. 2016 Jan;65(1):161-76. doi: 10.1093/sysbio/syv051. Epub 2015 Jul 30.


INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B.

Science. 2015 Jul 31;349(6247):487. doi: 10.1126/science.aaa7136.


Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

Leaché AD, Banbury BL, Felsenstein J, de Oca AN, Stamatakis A.

Syst Biol. 2015 Nov;64(6):1032-47. doi: 10.1093/sysbio/syv053. Epub 2015 Jul 29.


Impacts of Terraces on Phylogenetic Inference.

Sanderson MJ, McMahon MM, Stamatakis A, Zwickl DJ, Steel M.

Syst Biol. 2015 Sep;64(5):709-26. doi: 10.1093/sysbio/syv024. Epub 2015 May 20.


ExaML version 3: a tool for phylogenomic analyses on supercomputers.

Kozlov AM, Aberer AJ, Stamatakis A.

Bioinformatics. 2015 Aug 1;31(15):2577-9. doi: 10.1093/bioinformatics/btv184. Epub 2015 Mar 29.

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