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Items: 1 to 50 of 94


Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference.

Zhang C, Huelsenbeck JP, Ronquist F.

Syst Biol. 2020 Jan 27. pii: syaa002. doi: 10.1093/sysbio/syaa002. [Epub ahead of print]


BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.

Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.


Reply to Nakov et al.: Model choice requires biological insight when studying the ancestral habitat of photosynthetic eukaryotes.

Sánchez-Baracaldo P, Bianchini G, Huelsenbeck JP, Raven JA, Pisani D, Knoll AH.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10608-E10609. doi: 10.1073/pnas.1717417114. Epub 2017 Dec 5. No abstract available.


Chronic hepatitis C patients prior to broad access to interferon-free treatments in Germany.

Hüppe D, Buggisch P, Christensen S, Heiken H, Mauss S, Naumann U, Fischer C, Kleine H, Huelsenbeck J.

Z Gastroenterol. 2016 Aug;54(8):740-7. doi: 10.1055/s-0042-106731. Epub 2016 Aug 16.


Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures.

Moore BR, Höhna S, May MR, Rannala B, Huelsenbeck JP.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9569-74. doi: 10.1073/pnas.1518659113. Epub 2016 Aug 10.


RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F.

Syst Biol. 2016 Jul;65(4):726-36. doi: 10.1093/sysbio/syw021. Epub 2016 May 28.


Chronic heart damage following doxorubicin treatment is alleviated by lovastatin.

Henninger C, Huelsenbeck S, Wenzel P, Brand M, Huelsenbeck J, Schad A, Fritz G.

Pharmacol Res. 2015 Jan;91:47-56. doi: 10.1016/j.phrs.2014.11.003. Epub 2014 Nov 21.


Strepsiptera, phylogenomics and the long branch attraction problem.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP.

PLoS One. 2014 Oct 1;9(10):e107709. doi: 10.1371/journal.pone.0107709. eCollection 2014.


The fossilized birth-death process for coherent calibration of divergence-time estimates.

Heath TA, Huelsenbeck JP, Stadler T.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E2957-66. doi: 10.1073/pnas.1319091111. Epub 2014 Jul 9.


Probabilistic graphical model representation in phylogenetics.

Höhna S, Heath TA, Boussau B, Landis MJ, Ronquist F, Huelsenbeck JP.

Syst Biol. 2014 Sep;63(5):753-71. doi: 10.1093/sysbio/syu039. Epub 2014 Jun 20.


Cytolethal distending toxin (CDT) is a radiomimetic agent and induces persistent levels of DNA double-strand breaks in human fibroblasts.

Fahrer J, Huelsenbeck J, Jaurich H, Dörsam B, Frisan T, Eich M, Roos WP, Kaina B, Fritz G.

DNA Repair (Amst). 2014 Jun;18:31-43. doi: 10.1016/j.dnarep.2014.03.002. Epub 2014 Mar 25.


DNA double strand breaks as predictor of efficacy of the alpha-particle emitter Ac-225 and the electron emitter Lu-177 for somatostatin receptor targeted radiotherapy.

Graf F, Fahrer J, Maus S, Morgenstern A, Bruchertseifer F, Venkatachalam S, Fottner C, Weber MM, Huelsenbeck J, Schreckenberger M, Kaina B, Miederer M.

PLoS One. 2014 Feb 7;9(2):e88239. doi: 10.1371/journal.pone.0088239. eCollection 2014.


A phylogenetic model for the detection of epistatic interactions.

Nasrallah CA, Huelsenbeck JP.

Mol Biol Evol. 2013 Sep;30(9):2197-208. doi: 10.1093/molbev/mst108. Epub 2013 Jun 6.


Bayesian analysis of biogeography when the number of areas is large.

Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP.

Syst Biol. 2013 Nov;62(6):789-804. doi: 10.1093/sysbio/syt040. Epub 2013 Jun 4.


Expression and cytoprotective activity of the small GTPase RhoB induced by the Escherichia coli cytotoxic necrotizing factor 1.

Huelsenbeck SC, Roggenkamp D, May M, Huelsenbeck J, Brakebusch C, Rottner K, Ladwein M, Just I, Fritz G, Schmidt G, Genth H.

Int J Biochem Cell Biol. 2013 Aug;45(8):1767-75. doi: 10.1016/j.biocel.2013.05.020. Epub 2013 May 31.


Rac1 signaling protects monocytic AML cells expressing the MLL-AF9 oncogene from caspase-mediated apoptotic death.

Hinterleitner C, Huelsenbeck J, Henninger C, Wartlick F, Schorr A, Kaina B, Fritz G.

Apoptosis. 2013 Aug;18(8):963-79. doi: 10.1007/s10495-013-0842-6.


Rac1 protein signaling is required for DNA damage response stimulated by topoisomerase II poisons.

Huelsenbeck SC, Schorr A, Roos WP, Huelsenbeck J, Henninger C, Kaina B, Fritz G.

J Biol Chem. 2012 Nov 9;287(46):38590-9. doi: 10.1074/jbc.M112.377903. Epub 2012 Sep 25.


Cytoprotective effect of the small GTPase RhoB expressed upon treatment of fibroblasts with the Ras-glucosylating Clostridium sordellii lethal toxin.

Huelsenbeck J, May M, Schulz F, Schelle I, Ronkina N, Hohenegger M, Fritz G, Just I, Gerhard R, Genth H.

FEBS Lett. 2012 Oct 19;586(20):3665-73. doi: 10.1016/j.febslet.2012.08.024. Epub 2012 Sep 11.


The lipid lowering drug lovastatin protects against doxorubicin-induced hepatotoxicity.

Henninger C, Huelsenbeck J, Huelsenbeck S, Grösch S, Schad A, Lackner KJ, Kaina B, Fritz G.

Toxicol Appl Pharmacol. 2012 May 15;261(1):66-73.


MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.

Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.

Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029. Epub 2012 Feb 22.


A dirichlet process prior for estimating lineage-specific substitution rates.

Heath TA, Holder MT, Huelsenbeck JP.

Mol Biol Evol. 2012 Mar;29(3):939-55. doi: 10.1093/molbev/msr255. Epub 2011 Nov 2.


Rac1-regulated endothelial radiation response stimulates extravasation and metastasis that can be blocked by HMG-CoA reductase inhibitors.

Hamalukic M, Huelsenbeck J, Schad A, Wirtz S, Kaina B, Fritz G.

PLoS One. 2011;6(10):e26413. doi: 10.1371/journal.pone.0026413. Epub 2011 Oct 19.


BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100. Epub 2011 Oct 1.


Inhibition of Rac1 signaling by lovastatin protects against anthracycline-induced cardiac toxicity.

Huelsenbeck J, Henninger C, Schad A, Lackner KJ, Kaina B, Fritz G.

Cell Death Dis. 2011 Aug 11;2:e190. doi: 10.1038/cddis.2011.65.


Structurama: bayesian inference of population structure.

Huelsenbeck JP, Andolfatto P, Huelsenbeck ET.

Evol Bioinform Online. 2011;7:55-9. doi: 10.4137/EBO.S6761. Epub 2011 Jun 2.


Mevalonate pathway inhibitors affect anticancer drug-induced cell death and DNA damage response of human sarcoma cells.

Nilsson S, Huelsenbeck J, Fritz G.

Cancer Lett. 2011 May 1;304(1):60-9. doi: 10.1016/j.canlet.2010.12.022. Epub 2011 Feb 26.


Biologically inspired phylogenetic models strongly outperform the no common mechanism model.

Huelsenbeck JP, Alfaro ME, Suchard MA.

Syst Biol. 2011 Mar;60(2):225-32. doi: 10.1093/sysbio/syq089. Epub 2011 Jan 20.


Potential use of HMG-CoA reductase inhibitors (statins) as radioprotective agents.

Fritz G, Henninger C, Huelsenbeck J.

Br Med Bull. 2011;97:17-26. doi: 10.1093/bmb/ldq044. Epub 2011 Jan 20. Review.


Quantifying the impact of dependent evolution among sites in phylogenetic inference.

Nasrallah CA, Mathews DH, Huelsenbeck JP.

Syst Biol. 2011 Jan;60(1):60-73. doi: 10.1093/sysbio/syq074. Epub 2010 Nov 15.


In defence of model-based inference in phylogeography.

Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet JM, Huelsenbeck J, Foll M, Yang Z, Rousset F, Balding D, Excoffier L.

Mol Ecol. 2010 Feb;19(3):436-446. doi: 10.1111/j.1365-294X.2009.04515.x. Epub 2010 Jan 11.


Distinct kinetics of (H/K/N)Ras glucosylation and Rac1 glucosylation catalysed by Clostridium sordellii lethal toxin.

Huelsenbeck SC, Klose I, Reichenbach M, Huelsenbeck J, Genth H.

FEBS Lett. 2009 Oct 6;583(19):3133-9. doi: 10.1016/j.febslet.2009.09.006. Epub 2009 Sep 8.


Killing of rat basophilic leukemia cells by lethal toxin from Clostridium sordellii: critical role of phosphatidylinositide 3'-OH kinase/Akt signaling.

Dreger SC, Schulz F, Huelsenbeck J, Gerhard R, Hofmann F, Just I, Genth H.

Biochemistry. 2009 Mar 3;48(8):1785-92. doi: 10.1021/bi800708b.


Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence.

Bollback JP, Huelsenbeck JP.

Genetics. 2009 Jan;181(1):225-34. doi: 10.1534/genetics.107.085225. Epub 2008 Nov 10.


Statistical assignment of DNA sequences using Bayesian phylogenetics.

Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R.

Syst Biol. 2008 Oct;57(5):750-7. doi: 10.1080/10635150802422316.


Bayesian analysis of amino acid substitution models.

Huelsenbeck JP, Joyce P, Lakner C, Ronquist F.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3941-53. doi: 10.1098/rstb.2008.0175.


Prevention of the cytopathic effect induced by Clostridium difficile Toxin B by active Rac1.

Halabi-Cabezon I, Huelsenbeck J, May M, Ladwein M, Rottner K, Just I, Genth H.

FEBS Lett. 2008 Nov 12;582(27):3751-6. doi: 10.1016/j.febslet.2008.10.003. Epub 2008 Oct 9.


A Bayesian perspective on a non-parsimonious parsimony model.

Huelsenbeck JP, Ané C, Larget B, Ronquist F.

Syst Biol. 2008 Jun;57(3):406-19. doi: 10.1080/10635150802166046.


Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms.

Brandley MC, Huelsenbeck JP, Wiens JJ.

Evolution. 2008 Aug;62(8):2042-64. doi: 10.1111/j.1558-5646.2008.00430.x. Epub 2008 May 27.


Clostridium difficile toxins: more than mere inhibitors of Rho proteins.

Genth H, Dreger SC, Huelsenbeck J, Just I.

Int J Biochem Cell Biol. 2008;40(4):592-7. doi: 10.1016/j.biocel.2007.12.014. Epub 2008 Jan 5. Review.


Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics.

Lakner C, van der Mark P, Huelsenbeck JP, Larget B, Ronquist F.

Syst Biol. 2008 Feb;57(1):86-103. doi: 10.1080/10635150801886156.


Alignment uncertainty and genomic analysis.

Wong KM, Suchard MA, Huelsenbeck JP.

Science. 2008 Jan 25;319(5862):473-6. doi: 10.1126/science.1151532.


A nonparametric method for accommodating and testing across-site rate variation.

Huelsenbeck JP, Suchard MA.

Syst Biol. 2007 Dec;56(6):975-87.


Upregulation of the immediate early gene product RhoB by exoenzyme C3 from Clostridium limosum and toxin B from Clostridium difficile.

Huelsenbeck J, Dreger SC, Gerhard R, Fritz G, Just I, Genth H.

Biochemistry. 2007 Apr 24;46(16):4923-31. Epub 2007 Mar 31.


Clonal interference is alleviated by high mutation rates in large populations.

Bollback JP, Huelsenbeck JP.

Mol Biol Evol. 2007 Jun;24(6):1397-406. Epub 2007 Mar 22.


Inference of population structure under a Dirichlet process model.

Huelsenbeck JP, Andolfatto P.

Genetics. 2007 Apr;175(4):1787-802. Epub 2007 Jan 21.


Difference in the cytotoxic effects of toxin B from Clostridium difficile strain VPI 10463 and toxin B from variant Clostridium difficile strain 1470.

Huelsenbeck J, Dreger S, Gerhard R, Barth H, Just I, Genth H.

Infect Immun. 2007 Feb;75(2):801-9. Epub 2006 Dec 4.


Cellular stability of Rho-GTPases glucosylated by Clostridium difficile toxin B.

Genth H, Huelsenbeck J, Hartmann B, Hofmann F, Just I, Gerhard R.

FEBS Lett. 2006 Jun 12;580(14):3565-9. Epub 2006 May 22.


Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees".

Ronquist F, Larget B, Huelsenbeck JP, Kadane JB, Simon D, van der Mark P.

Science. 2006 Apr 21;312(5772):367; author reply 367.


A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

Huelsenbeck JP, Jain S, Frost SW, Pond SL.

Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6263-8. Epub 2006 Apr 10.


Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty.

Alfaro ME, Huelsenbeck JP.

Syst Biol. 2006 Feb;55(1):89-96.


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