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Items: 1 to 20 of 185


Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR.

Sievert C, Nieves LM, Panyon LA, Loeffler T, Morris C, Cartwright RA, Wang X.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7349-7354. doi: 10.1073/pnas.1700345114. Epub 2017 Jun 27.


SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm.

Ashkenazy H, Levy Karin E, Mertens Z, Cartwright RA, Pupko T.

Nucleic Acids Res. 2017 Apr 29. doi: 10.1093/nar/gkx322. [Epub ahead of print]


Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.

Levy Karin E, Shkedy D, Ashkenazy H, Cartwright RA, Pupko T.

Genome Biol Evol. 2017 May 1;9(5):1280-1294. doi: 10.1093/gbe/evx084.


Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions.

Wu SH, Schwartz RS, Winter DJ, Conrad DF, Cartwright RA.

Bioinformatics. 2017 Mar 15. doi: 10.1093/bioinformatics/btx133. [Epub ahead of print]


The importance of selection in the evolution of blindness in cavefish.

Cartwright RA, Schwartz RS, Merry AL, Howell MM.

BMC Evol Biol. 2017 Feb 7;17(1):45. doi: 10.1186/s12862-017-0876-4.


Low Base-Substitution Mutation Rate in the Germline Genome of the Ciliate Tetrahymena thermophil.

Long H, Winter DJ, Chang AY, Sung W, Wu SH, Balboa M, Azevedo RBR, Cartwright RA, Lynch M, Zufall RA.

Genome Biol Evol. 2016 Dec 1;8(12):3629-3639. doi: 10.1093/gbe/evw223.


The effect of the dispersal kernel on isolation-by-distance in a continuous population.

Furstenau TN, Cartwright RA.

PeerJ. 2016 Mar 29;4:e1848. doi: 10.7717/peerj.1848. eCollection 2016.


Equations of the End: Teaching Mathematical Modeling Using the Zombie Apocalypse.

Lofgren ET, Collins KM, Smith TC, Cartwright RA.

J Microbiol Biol Educ. 2016 Mar 1;17(1):137-42. doi: 10.1128/jmbe.v17i1.1066. eCollection 2016 Mar.


Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia.

Winter DJ, Pacheco MA, Vallejo AF, Schwartz RS, Arevalo-Herrera M, Herrera S, Cartwright RA, Escalante AA.

PLoS Negl Trop Dis. 2015 Dec 28;9(12):e0004252. doi: 10.1371/journal.pntd.0004252. eCollection 2015 Dec.


Phylogenomic reconstruction supports supercontinent origins for Leishmania.

Harkins KM, Schwartz RS, Cartwright RA, Stone AC.

Infect Genet Evol. 2016 Mar;38:101-9. doi: 10.1016/j.meegid.2015.11.030. Epub 2015 Dec 18.


Inferring Indel Parameters using a Simulation-based Approach.

Levy Karin E, Rabin A, Ashkenazy H, Shkedy D, Avram O, Cartwright RA, Pupko T.

Genome Biol Evol. 2015 Nov 3;7(12):3226-38. doi: 10.1093/gbe/evv212.


A composite genome approach to identify phylogenetically informative data from next-generation sequencing.

Schwartz RS, Harkins KM, Stone AC, Cartwright RA.

BMC Bioinformatics. 2015 Jun 11;16:193. doi: 10.1186/s12859-015-0632-y.


DeNovoGear: de novo indel and point mutation discovery and phasing.

Ramu A, Noordam MJ, Schwartz RS, Wuster A, Hurles ME, Cartwright RA, Conrad DF.

Nat Methods. 2013 Oct;10(10):985-7. doi: 10.1038/nmeth.2611. Epub 2013 Aug 25.


Comparative population genomics of maize domestication and improvement.

Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J.

Nat Genet. 2012 Jun 3;44(7):808-11. doi: 10.1038/ng.2309.


A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data.

Cartwright RA, Hussin J, Keebler JE, Stone EA, Awadalla P.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(2). pii: /j/sagmb.2012.11.issue-2/1544-6115.1713/1544-6115.1713.xml. doi: 10.2202/1544-6115.1713.


A novel core genome-encoded superantigen contributes to lethality of community-associated MRSA necrotizing pneumonia.

Wilson GJ, Seo KS, Cartwright RA, Connelley T, Chuang-Smith ON, Merriman JA, Guinane CM, Park JY, Bohach GA, Schlievert PM, Morrison WI, Fitzgerald JR.

PLoS Pathog. 2011 Oct;7(10):e1002271. doi: 10.1371/journal.ppat.1002271. Epub 2011 Oct 13.


Genomic and surface proteomic analysis of the canine pathogen Staphylococcus pseudintermedius reveals proteins that mediate adherence to the extracellular matrix.

Bannoehr J, Ben Zakour NL, Reglinski M, Inglis NF, Prabhakaran S, Fossum E, Smith DG, Wilson GJ, Cartwright RA, Haas J, Hook M, van den Broek AH, Thoday KL, Fitzgerald JR.

Infect Immun. 2011 Aug;79(8):3074-86. doi: 10.1128/IAI.00137-11. Epub 2011 May 16.


History can matter: non-Markovian behavior of ancestral lineages.

Cartwright RA, Lartillot N, Thorne JL.

Syst Biol. 2011 May;60(3):276-90. doi: 10.1093/sysbio/syr012. Epub 2011 Mar 11.


The multiple personalities of Watson and Crick strands.

Cartwright RA, Graur D.

Biol Direct. 2011 Feb 8;6:7. doi: 10.1186/1745-6150-6-7.


Neutral evolution of robustness in Drosophila microRNA precursors.

Price N, Cartwright RA, Sabath N, Graur D, Azevedo RB.

Mol Biol Evol. 2011 Jul;28(7):2115-23. doi: 10.1093/molbev/msr029. Epub 2011 Jan 31.

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