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Items: 1 to 20 of 152


Eleven grand challenges in single-cell data science.

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 B, 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 TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A.

Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6. Review.


Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.

Czech L, Barbera P, Stamatakis A.

Bioinformatics. 2020 Feb 4. pii: btaa070. doi: 10.1093/bioinformatics/btaa070. [Epub ahead of print]


Synergistic effects of early life mild adversity and chronic social defeat on rat brain microglia and cytokines.

Ferle V, Repouskou A, Aspiotis G, Raftogianni A, Chrousos G, Stylianopoulou F, Stamatakis A.

Physiol Behav. 2020 Mar 1;215:112791. doi: 10.1016/j.physbeh.2019.112791. Epub 2019 Dec 21.


A Fast and Memory-Efficient Implementation of the Transfer Bootstrap.

Lutteropp S, Kozlov AM, Stamatakis A.

Bioinformatics. 2019 Nov 22. pii: btz874. doi: 10.1093/bioinformatics/btz874. [Epub ahead of print]


Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.

Zanni G, Goto S, Fragopoulou AF, Gaudenzi G, Naidoo V, Di Martino E, Levy G, Dominguez CA, Dethlefsen O, Cedazo-Minguez A, Merino-Serrais P, Stamatakis A, Hermanson O, Blomgren K.

Mol Psychiatry. 2019 Nov 14. doi: 10.1038/s41380-019-0584-0. [Epub ahead of print]


Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity.

Jamy M, Foster R, Barbera P, Czech L, Kozlov A, Stamatakis A, Bending G, Hilton S, Bass D, Burki F.

Mol Ecol Resour. 2019 Nov 9. doi: 10.1111/1755-0998.13117. [Epub ahead of print]


Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV.

Serdari D, Kostaki EG, Paraskevis D, Stamatakis A, Kapli P.

PeerJ. 2019 Oct 25;7:e7754. doi: 10.7717/peerj.7754. eCollection 2019.


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. 2020 Jan 30;100(2):732-743. doi: 10.1002/jsfa.10076. Epub 2019 Nov 13.


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, Looz MV, Rokas A.

Syst Biol. 2020 Mar 1;69(2):308-324. doi: 10.1093/sysbio/syz058.


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. 2020 Jan 1;37(1):291-294. doi: 10.1093/molbev/msz189.


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 Nov 1;35(21):4453-4455. doi: 10.1093/bioinformatics/btz305.


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.

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