Publications

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2020

  1. Orr AJg, Padovan A, Kainer D, Külheim C, Bromham L, Carlos Bustos-Segura, Foley W, Ha  T, Hsieh JF, Morales- Suarez A, Cartwright RA*, and Lanfear R* (2020) A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant. Proceedings of the Royal Society B, p. 20192364. doi:10.1098/rspb.2019.2364.


2019

  1. Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Kim BY, McKenzie P, Messer PW, Noskova E, Ortega- Del Vecchyo D, Struck TJ, Gravel S, Gutenkunst RN, Ralph PL, Schrider DR, Siepel A, Kelleher J, and Kern AD (2019) A community-maintained standard library of population genetic models. bioRxiv, p. 885129. doi:10.1101/2019.12.20.885129.

  2. Malukiewicz Jp, Cartwright RA, Dergam JA, Igayara CS, Kessler S, Moreira SB, Nash LT, Nicola PA, Pereira LC, Pissinati A, Ruiz-Miranda CR, Ozga AT, Roos C, Silva DL, Stone AC, and Grativol AD (2019) The e ects of host taxon, hybridization, and environment on the gut microbiome of Callithrix marmosets. bioRxiv, p. 708255. doi:10.1101/708255.

  3. Kurgan G, Sievert Cp, Flores A, Schneider A, Billings T, Panyon L, Morris C, Taylor E, Kurgan L, Cartwright R, and Wang X (2019) Parallel experimental evolution reveals a novel repressive control of GalP on xylose fermentation in Escherichia coli. Biotechnology and Bioengineering. doi:10.1002/bit.27004.


2018

  1. Castillo AI, Roos B Hu, Rosenberg M S, Cartwright RA*, and Wilson Sayres MA*(2018)Genie: Aninteractivereal- time simulation for teaching genetic dri. bioRxiv, p. 268672. doi:10.1101/268672.

  2. Palmer N Du and Cartwright RA (2018) Strong episodic selection for natural competence due to host-pathogen dynamics. bioRxiv, p. 275651. doi:10.1101/275651.

  3. Herman A, Brandvain Y, Weagley J, Je ery WR, Keene AC, Kono TJY, Bilandižja 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, and McGaugh SE (2018) The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Molecular Ecology. doi:10.1111/mec.14877.

  4. Winter D Jp, Wu S Hp, Howel lA Au,g, Azevedo RB, Zufall RA, and Cartwright RA(2018) accuMUlate: Amutation caller designed for mutation accumulation experiments. Bioinformatics, 34:2659–2660. doi:10.1093/bioinfor- matics/bty165.


2017

  1. Ashkenazy H, Karin EL, Mertens Zt, Cartwright RA*,and PupkoT* (2017) SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Research. doi:10.1093/nar/gkx322.

  2. Cartwright RA, Schwartz RSp, Merry ALu, and Howell MMu (2017) The importance of selection in the evolution of blindness in cavefish. BMC Evolutionary Biology, 17:45. doi:10.1186/s12862-017-0876-4.

  3. Furstenau TNg and Cartwright RA (2017) The impact of self-incompatibility systems on the prevention of biparental inbreeding. PeerJ, 5:e4085. doi:10.7717/peerj.4085.

  4. Karin EL, Shkedy D, Ashkenazy H, Cartwright RA, and Pupko T (2017) Inferring rates and length- distributions of indels using approximate Bayesian computation. Genome Biology and Evolution, 9:1280–1294. doi:10.1093/gbe/evx084.

  5. Sievert Cp, Nieves LM, Panyon LA, Loe ler T, Morris C, Cartwright RA*, and Wang X*(2017)Experimental evolution reveals a novel avenue to release catabolite repression via mutations in XylR. Proceedings of the National Academy of Sciences of the United States of America, 114:7349–7354. doi:10.1073/pnas.1700345114.

  6. Wu S Hp, Schwartz R Sp, Winter D Jp, Conrad DF, and Cartwright RA(2017) Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions. Bioinformatics, 33:2322–2329. doi:10.1093/bioinformatics/btx133.


2016

  1. Furstenau TNg and Cartwright RA (2016) The e ect of the dispersal kernel on isolation-by-distance in a continuous population. PeerJ, 4:e1848. doi:10.7717/peerj.1848.

  2. Harkins K, Schwartz R Sp, Cartwright RA, and Stone AC (2016) Phylogenomicre construction supports supercontinent origins for Leishmania. Infection, Genetics, and Evolution, 38:101–109. doi:10.1016/j.meegid.2015.11.030.

  3. Lofgren ET, Collins K, SmithTC, and Cartwright RA (2016) Equationsoftheend: Teaching mathematical modeling using the zombie apocalypse. Microbiology and Biology Education, 17:137–142. doi:10.1128/jmbe.v17i1.1066.

  4. Long H*, Winter D Jp*, Chang AY, Jung W, Wu SHp, Balboa M, Azevedo RB, Cartwright RA, Lynch M, and Zufall RA (2016) Low base-substitution mutation rate in the ciliate Tetrahymena thermophila. Genome Biology and Evolution, 8:3629–3639. doi:10.1093/gbe/evw223.


2015

  1. Crusoe M, Alameldin H, Awad S, Boucher E, Caldwell A, Cartwright RA, Charbonneau A, Constantinides B, Edvenson G, Fay S, Fenton J, Fenzl T, Fish J, Garcia-Gutierrez L, Garland P, Gluck J, Gonzalez I, Guermond S, Guo J, Gupta A, Herr J, Howe A, Hyer A, Harpfer A, Irber L, Kidd R, Lin D, Lippi J, Mansour T, McANulty P, McDonald E, Mizzi J, Murray K, Nahum J, Nanlohy K, Nederbragt A, Ortiz-Zuazaga H, Ory J, Pell J, Pepe-Ranney C, Russ Z, Schwarz E, Scott C, Seaman J, Sievert S, Simpson J, Skennerton C, Spencer J, Srinivasan R, Standage D, Stapleton J, Steinman S, Stein J, Taylor B, Trimble W, Wiencko H, Wright M, Wyss B, Zhang Q, zyme e, and Brown C (2015) The khmer so ware package: enabling e icient nucleotide sequence analysis. F1000Research, 4:900. doi:10.12688/f1000research.6924.1.

  2. Karin EL, Rabin A, Ashkenazy H, Shkedy D, Avram O, Cartwright RA, and Pupko T (2015) Inferring indel parameters using a simulation-based approach. Genome Biology and Evolution, 7:3226–3238. doi:10.1093/gbe/evv212.

  3. Schwartz R Sp, Harkins K, Stone AC, and Cartwright RA (2015) A composite genome approach to identify phylogenetically informative data from next-generation sequencing. BMC Bioinformatics, 16:193. doi:10.1186/s12859- 015-0632-y.

  4. Winter D Jp, Pacheco MA, Vallejo AF, Schwartz R Sp, Arevalo-Herrera M, Herrera S, Cartwright RA*, and Escalante AA* (2015) Whole genome sequencing of field isolates reveals extensive genetic diversity in Plasmodium vivax from Colombia. PLoS Negl Trop Dis, 9:e0004252. doi:10.1371/journal.pntd.0004252.


2013

  1. Ramu A, Noordam MJ, Schwartz RS, Wuster A, Hurles ME, Cartwright RA, and Conrad DF (2013). DeNovoGear: de novo indel and point mutation discovery and phasing. Na-ture Methods, 10:985–987.


2012

  1. Matthew B Hufford, Xun Xu, Joost Van Heerwaarden, Tanja Pyhäjärvi, Jer-Ming Chia, Reed A Cartwright, Robert J Elshire, Jeffrey C Glaubitz, Kate E Guill, Shawn M Kaeppler, Jinsheng Lai, Peter L Morrell, Laura M Shannon, Chi Song, Nathan M Springer, Ruth A Swanson-Wagner, Peter Tiffin, Jun Wang, Gengyun Zhang, John Doebley, Michael D McMullen, Doreen Ware, Edward S Buckler, Shuang Yang, Jeffrey Ross-Ibarra. Comparative population genomics of maize domestication and improvement. Nature Genetics (2012).

  2. Reed A Cartwright, Julie Hussin, Jonathan EM Keebler, Eric A Stone, Philip Awadalla. A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data. Statistical Applications in Genetics and Molecular Biology (2012).

  3. Reed A. Cartwright. Lab Notes: The Alias Method for Sampling from Discrete Distributions. The Panda's Thumb (2012).

  4. Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, 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, and Ross-Ibarra J (2012). Comparative population genomics of maize domestication and improvement. Nature Genetics, 44:808–811.

  5. Cartwright RA, Hussin J, Keebler J, Awadalla P, and Stone EA (2012). A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data. Statistical Applications in Genetics and Molecular Biology, 11:6.


2011

  1. Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Cassals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright RA, Rouleau G, Daly M, Stone EA, Hurles ME, and Awadalla P (2011). Variation in genome-wide mutation rates within and between human families. Nature Genetics, 43:712–714.

  2. Cartwright RA, Lartillot N, and Thorne JL (2011). History can matter: Non-Markovian behavior of ancestral lineages. Systematic Biology, 60:276–290.

  3. Cartwright RA and Graur D (2011). The multiple personalities of Watson and Crick strands. Biology Direct, 6:7.

  4. Price* N, Cartwright RA*, Sabath N, Graur D, and Azevedo RBR (2011). Neutral evolution of robustness in Drosophila microRNA precursors. Molecular Biology and Evolution, 28:2115–2123.

  5. Lücking R, Hodkinson B, Stamatakis A, and Cartwright RA (2011). PICS-Ord: unlim-ited coding of ambiguous regions by pairwise identity and cost scores ordination. BMC Bioinformatics, 12:10.

  6. Cartwright RA (2011). Bards, poets, and cliques: Frequency-dependent selection and the evolution of language genes. Bulletin of Mathematical Biology, 73:2201–2212.


2010

  1. The 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing. Nature, 467:1061–1073.


Prior to 2010

  1. Cartwright RA (2009a). Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution, 26:473–480.

  2. Cartwright RA (2009b). Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. Molecular Ecology, 18:2327–2336.

  3. Cartwright RA (2007). Ngila: global pairwise alignments with logarithmic and affine gap costs. Bioinformatics, 23:1427–1428.

  4. Cartwright RA (2006). Logarithmic gap costs decrease alignment accuracy. BMC Bioin-formatics, 7:527.

  5. Comai L and Cartwright RA (2005). A toxic mutator and selection alternative to the non-mendelian, RNA cache hypothesis for hothead reversion. Plant Cell, 17:2856–2858.

  6. Cartwright RA (2005). DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics, 21(Suppl. 3):iii31–iii38.

  7. Asmussen MA, Cartwright RA, and Spencer HG (2004). Frequency-dependent selection with dominance: A window onto the behavior of the mean fitness. Genetics, 167:499–512.

*co-first authors.


Books

Cartwright RA and Zivkovic B, editors (2008). The Open Laboratory: The Best Writing on Science Blogs 2007. Lulu.com, Chapel Hill, NC.