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The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus.

Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE.

Mol Ecol. 2018 Nov;27(22):4397-4416. doi: 10.1111/mec.14877. Epub 2018 Oct 16.


accuMUlate: a mutation caller designed for mutation accumulation experiments.

Winter DJ, Wu SH, Howell AA, Azevedo RBR, Zufall RA, Cartwright RA.

Bioinformatics. 2018 Aug 1;34(15):2659-2660. doi: 10.1093/bioinformatics/bty165.


The impact of self-incompatibility systems on the prevention of biparental inbreeding.

Furstenau TN, Cartwright RA.

PeerJ. 2017 Nov 24;5:e4085. doi: 10.7717/peerj.4085. eCollection 2017.


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 Jul 3;45(W1):W453-W457. doi: 10.1093/nar/gkx322.


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 Aug 1;33(15):2322-2329. doi: 10.1093/bioinformatics/btx133.


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;38:101-109. 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.


PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.

Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA.

BMC Bioinformatics. 2011 Jan 7;12:10. doi: 10.1186/1471-2105-12-10.


Bards, poets, and cliques: frequency-dependent selection and the evolution of language genes.

Cartwright RA.

Bull Math Biol. 2011 Sep;73(9):2201-12. doi: 10.1007/s11538-010-9619-z. Epub 2010 Dec 30.


Platelet receptor polymorphisms do not influence Staphylococcus aureus-platelet interactions or infective endocarditis.

Daga S, Shepherd JG, Callaghan JG, Hung RK, Dawson DK, Padfield GJ, Hey SY, Cartwright RA, Newby DE, Fitzgerald JR.

Microbes Infect. 2011 Mar;13(3):216-25. doi: 10.1016/j.micinf.2010.10.016. Epub 2010 Oct 29.


Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation.

Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay JA, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penadés JR, Fitzgerald JR.

Genome Biol Evol. 2010 Jul 12;2:454-66. doi: 10.1093/gbe/evq031.


Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus.

Lowder BV, Guinane CM, Ben Zakour NL, Weinert LA, Conway-Morris A, Cartwright RA, Simpson AJ, Rambaut A, Nübel U, Fitzgerald JR.

Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19545-50. doi: 10.1073/pnas.0909285106. Epub 2009 Nov 2.


Antagonism between local dispersal and self-incompatibility systems in a continuous plant population.

Cartwright RA.

Mol Ecol. 2009 Jun;18(11):2327-36. doi: 10.1111/j.1365-294X.2009.04180.x. Epub 2009 Apr 23.


Problems and solutions for estimating indel rates and length distributions.

Cartwright RA.

Mol Biol Evol. 2009 Feb;26(2):473-80. doi: 10.1093/molbev/msn275. Epub 2008 Nov 28.


Topical chloramphenicol and the risk of acute leukaemia in adults.

Smith AG, Dovey GJ, Cartwright RA.

Pharmacoepidemiol Drug Saf. 2000 May;9(3):215-9. doi: 10.1002/1099-1557(200005/06)9:3<215::AID-PDS497>3.0.CO;2-K.


Ngila: global pairwise alignments with logarithmic and affine gap costs.

Cartwright RA.

Bioinformatics. 2007 Jun 1;23(11):1427-8. Epub 2007 Mar 25.


Logarithmic gap costs decrease alignment accuracy.

Cartwright RA.

BMC Bioinformatics. 2006 Dec 5;7:527.


DNA assembly with gaps (Dawg): simulating sequence evolution.

Cartwright RA.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8.


A toxic mutator and selection alternative to the non-Mendelian RNA cache hypothesis for hothead reversion.

Comai L, Cartwright RA.

Plant Cell. 2005 Nov;17(11):2856-8. No abstract available.


Frequency-dependent selection with dominance: a window onto the behavior of the mean fitness.

Asmussen MA, Cartwright RA, Spencer HG.

Genetics. 2004 May;167(1):499-512.


Epidemiology of Hodgkin's disease: a review.

Cartwright RA, Watkins G.

Hematol Oncol. 2004 Mar;22(1):11-26. Review.


Bladder cancer in patients with spinal cord injuries.

Subramonian K, Cartwright RA, Harnden P, Harrison SC.

BJU Int. 2004 Apr;93(6):739-43.


Occupational exposure to electromagnetic fields and acute leukaemia: analysis of a case-control study.

Willett EV, McKinney PA, Fear NT, Cartwright RA, Roman E.

Occup Environ Med. 2003 Aug;60(8):577-83.


Childhood cancers and radon.

Cartwright RA, Miles JC, Kendall GM.

Lancet. 2003 May 10;361(9369):1658. No abstract available.


Leukaemia incidence near coastal features.

Lloyd F, Gilman EA, Law GR, Cartwright RA.

J Public Health Med. 2002 Dec;24(4):255-60.


Sex ratios and the risks of haematological malignancies.

Cartwright RA, Gurney KA, Moorman AV.

Br J Haematol. 2002 Sep;118(4):1071-7.


Patients entered into MRC AML trials are biologically representative of the totality of the disease in the UK.

Moorman AV, Roman E, Cartwright RA, Morgan GJ.

Clin Lab Haematol. 2002 Aug;24(4):263-5. No abstract available.


Polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes and risk of adult acute lymphocytic leukemia.

Skibola CF, Smith MT, Hubbard A, Shane B, Roberts AC, Law GR, Rollinson S, Roman E, Cartwright RA, Morgan GJ.

Blood. 2002 May 15;99(10):3786-91.


Age-specific incidence rates for cytogenetically-defined subtypes of acute myeloid leukaemia.

Moorman AV, Roman E, Cartwright RA, Morgan GJ.

Br J Cancer. 2002 Apr 8;86(7):1061-3.


The onset of the excess of childhood cancer in Seascale, Cumbria.

Cartwright RA, Dovey GJ, Kane EV, Gilman EA.

J Public Health Med. 2001 Dec;23(4):314-22.


Smoking and the risk of acute myeloid leukaemia in cytogenetic subgroups.

Moorman AV, Roman E, Cartwright RA, Morgan GJ.

Br J Cancer. 2002 Jan 7;86(1):60-2.


Polymorphism in glutathione S-transferase P1 is associated with susceptibility to chemotherapy-induced leukemia.

Allan JM, Wild CP, Rollinson S, Willett EV, Moorman AV, Dovey GJ, Roddam PL, Roman E, Cartwright RA, Morgan GJ.

Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11592-7. Epub 2001 Sep 11. Erratum in: Proc Natl Acad Sci U S A 2001 Dec 18;98(26):15394.


Epstein-Barr Virus and HLA-DPB1-*0301 in young adult Hodgkin's disease: evidence for inherited susceptibility to Epstein-Barr Virus in cases that are EBV(+ve).

Alexander FE, Jarrett RF, Cartwright RA, Armstrong AA, Gokhale DA, Kane E, Gray D, Lawrence DJ, Taylor GM.

Cancer Epidemiol Biomarkers Prev. 2001 Jun;10(6):705-9.

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