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Items: 29


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]


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.


Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis.

Czech L, Höppner A, Kobus S, Seubert A, Riclea R, Dickschat JS, Heider J, Smits SHJ, Bremer E.

Sci Rep. 2019 Jan 23;9(1):364. doi: 10.1038/s41598-018-36247-w.


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.


Clarifying the Relationships between Microsporidia and Cryptomycota.

Bass D, Czech L, Williams BAP, Berney C, Dunthorn M, Mahé F, Torruella G, Stentiford GD, Williams TA.

J Eukaryot Microbiol. 2018 Nov;65(6):773-782. doi: 10.1111/jeu.12519. Epub 2018 Apr 28.


Sex Genotyping of Archival Fixed and Immunolabeled Guinea Pig Cochleas.

Depreux FF, Czech L, Whitlon DS.

Sci Rep. 2018 Mar 26;8(1):5156. doi: 10.1038/s41598-018-23491-3.


Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis.

Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E.

Genes (Basel). 2018 Mar 22;9(4). pii: E177. doi: 10.3390/genes9040177. Review.


With a pinch of extra salt-Did predatory protists steal genes from their food?

Czech L, Bremer E.

PLoS Biol. 2018 Feb 2;16(2):e2005163. doi: 10.1371/journal.pbio.2005163. eCollection 2018 Feb.


Tinkering with Osmotically Controlled Transcription Allows Enhanced Production and Excretion of Ectoine and Hydroxyectoine from a Microbial Cell Factory.

Czech L, Poehl S, Hub P, Stöveken N, Bremer E.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01772-17. doi: 10.1128/AEM.01772-17. Print 2018 Jan 15.


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.


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.


EctD-mediated biotransformation of the chemical chaperone ectoine into hydroxyectoine and its mechanosensitive channel-independent excretion.

Czech L, Stöveken N, Bremer E.

Microb Cell Fact. 2016 Jul 20;15(1):126. doi: 10.1186/s12934-016-0525-4.


Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus.

Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, Riclea R, Dickschat JS, Heider J, Bremer E.

Environ Microbiol. 2016 Apr;18(4):1227-48. doi: 10.1111/1462-2920.13156. Epub 2016 Jan 18.


Regulation of hypoxia-induced pulmonary hypertension by vascular smooth muscle hypoxia-inducible factor-1α.

Ball MK, Waypa GB, Mungai PT, Nielsen JM, Czech L, Dudley VJ, Beussink L, Dettman RW, Berkelhamer SK, Steinhorn RH, Shah SJ, Schumacker PT.

Am J Respir Crit Care Med. 2014 Feb 1;189(3):314-24. doi: 10.1164/rccm.201302-0302OC.


Isolation of pulmonary artery smooth muscle cells from neonatal mice.

Lee KJ, Czech L, Waypa GB, Farrow KN.

J Vis Exp. 2013 Oct 19;(80):e50889. doi: 10.3791/50889.


Developmental differences in hyperoxia-induced oxidative stress and cellular responses in the murine lung.

Berkelhamer SK, Kim GA, Radder JE, Wedgwood S, Czech L, Steinhorn RH, Schumacker PT.

Free Radic Biol Med. 2013 Aug;61:51-60. doi: 10.1016/j.freeradbiomed.2013.03.003. Epub 2013 Mar 14.


Cyclic stretch induces inducible nitric oxide synthase and soluble guanylate cyclase in pulmonary artery smooth muscle cells.

Shah MR, Wedgwood S, Czech L, Kim GA, Lakshminrusimha S, Schumacker PT, Steinhorn RH, Farrow KN.

Int J Mol Sci. 2013 Feb 21;14(2):4334-48. doi: 10.3390/ijms14024334.


Increased p22(phox)/Nox4 expression is involved in remodeling through hydrogen peroxide signaling in experimental persistent pulmonary hypertension of the newborn.

Wedgwood S, Lakshminrusimha S, Czech L, Schumacker PT, Steinhorn RH.

Antioxid Redox Signal. 2013 May 10;18(14):1765-76. doi: 10.1089/ars.2012.4766. Epub 2013 Feb 15.


Hydrocortisone normalizes oxygenation and cGMP regulation in lambs with persistent pulmonary hypertension of the newborn.

Perez M, Lakshminrusimha S, Wedgwood S, Czech L, Gugino SF, Russell JA, Farrow KN, Steinhorn RH.

Am J Physiol Lung Cell Mol Physiol. 2012 Mar 15;302(6):L595-603. doi: 10.1152/ajplung.00145.2011. Epub 2011 Dec 23.


Apocynin improves oxygenation and increases eNOS in persistent pulmonary hypertension of the newborn.

Wedgwood S, Lakshminrusimha S, Farrow KN, Czech L, Gugino SF, Soares F, Russell JA, Steinhorn RH.

Am J Physiol Lung Cell Mol Physiol. 2012 Mar 15;302(6):L616-26. doi: 10.1152/ajplung.00064.2011. Epub 2011 Dec 23.


Molecular diversity of the telson and venom components from Pandinus cavimanus (Scorpionidae Latreille 1802): transcriptome, venomics and function.

Diego-García E, Peigneur S, Clynen E, Marien T, Czech L, Schoofs L, Tytgat J.

Proteomics. 2012 Jan;12(2):313-28. doi: 10.1002/pmic.201100409. Epub 2012 Jan 4.


Mitochondrial oxidant stress increases PDE5 activity in persistent pulmonary hypertension of the newborn.

Farrow KN, Wedgwood S, Lee KJ, Czech L, Gugino SF, Lakshminrusimha S, Schumacker PT, Steinhorn RH.

Respir Physiol Neurobiol. 2010 Dec 31;174(3):272-81. doi: 10.1016/j.resp.2010.08.018. Epub 2010 Sep 6.


SOD and inhaled nitric oxide normalize phosphodiesterase 5 expression and activity in neonatal lambs with persistent pulmonary hypertension.

Farrow KN, Lakshminrusimha S, Czech L, Groh BS, Gugino SF, Davis JM, Russell JA, Steinhorn RH.

Am J Physiol Lung Cell Mol Physiol. 2010 Jul;299(1):L109-16. doi: 10.1152/ajplung.00309.2009. Epub 2010 Apr 16.


Regulation of phosphodiesterase 3 in the pulmonary arteries during the perinatal period in sheep.

Chen B, Lakshminrusimha S, Czech L, Groh BS, Gugino SF, Russell JA, Farrow KN, Steinhorn RH.

Pediatr Res. 2009 Dec;66(6):682-7. doi: 10.1203/PDR.0b013e3181bce574.


Superoxide dismutase restores eNOS expression and function in resistance pulmonary arteries from neonatal lambs with persistent pulmonary hypertension.

Farrow KN, Lakshminrusimha S, Reda WJ, Wedgwood S, Czech L, Gugino SF, Davis JM, Russell JA, Steinhorn RH.

Am J Physiol Lung Cell Mol Physiol. 2008 Dec;295(6):L979-87. doi: 10.1152/ajplung.90238.2008. Epub 2008 Sep 12.


Novel roles of formin mDia2 in lamellipodia and filopodia formation in motile cells.

Yang C, Czech L, Gerboth S, Kojima S, Scita G, Svitkina T.

PLoS Biol. 2007 Nov;5(11):e317.


Hyperoxia increases phosphodiesterase 5 expression and activity in ovine fetal pulmonary artery smooth muscle cells.

Farrow KN, Groh BS, Schumacker PT, Lakshminrusimha S, Czech L, Gugino SF, Russell JA, Steinhorn RH.

Circ Res. 2008 Feb 1;102(2):226-33. Epub 2007 Nov 8.

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