Reed Cartwright is a geneticist who develops computational and statistical methodologies to explore evolutionary questions. Much of his research focuses on mutation — the raw material of evolution — and its impact on biological systems. Using techniques from biology, statistics and computer science, Cartwright and his research team use genetics- and genomics-based approaches to analyze mutation patterns in various organisms.
Professor Cartwright develops software that detects mutations from the genetic data of related individuals, focusing on next-generation sequencing technology. He also develops programs for sequence simulation, alignment, phylogenetics, and population genetics analysis. Using various computational approaches to scientific programming, he and his collaborators develop new methods that improve our ability to understand the evolutionary relationships between organisms.
Ph.D. University of Georgia 2006
computational evolutionary genomics, population genetics, biological theory, bioinformatics, biology education
Ashkenazy H et al. (2017) SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Res. doi:10.1093/nar/gkx322.
Cartwright RA et al. (2017) The importance of selection in the evolution of blindness in cavefish. BMC Evolutionary Biology, 17:45. doi:10.1186/s12862-017-0876-4.
Karin EL et al. (2017) Inferring rates and length-distributions of indels using approximate Bayesian computation. Genome Biology and Evolution, 9:1280–1294. doi:10.1093/gbe/evx084.
Sievert C et al. (2017) Experimental evolution reveals a novel avenue to release catabolite repression via mutations in XylR. Proc Natl Acad Sci U S A, 114:7349–7354. doi:10.1073/pnas.1700345114.
Wu SH et al. (2017) Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions. Bioinformatics, 33:2322–2329. doi:10.1093/bioinformatics/btx133.
Furstenau TN and Cartwright RA (2016) The effect of the dispersal kernel on isolation-by-distance in a continuous population. PeerJ, 4:e1848. doi:10.7717/peerj.1848.
Harkins K et al. (2016) Phylogenomic reconstruction supports supercontinent origins for Leishmania. Infection, Genetics, and Evolution, 38:101–109. doi:10.1016/j.meegid.2015.11.030.
Lofgren ET et al. (2016) Equations of the end: Teaching mathematical modeling using the zombie apocalypse. Microbiology and Biology Education, 17:137–142. doi:10.1128/jmbe.v17i1.1066.
Long H et al. (2016) Low base-substitution mutation rate in the ciliate Tetrahymena thermophila. Genome Biology and Evolution, 8:3629–3639. doi:10.1093/gbe/evw223.
Crusoe M et al. (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Research, 4:900. doi:10.12688/f1000research.6924.1.
Karin EL et al. (2015) Inferring indel parameters using a simulation-based approach. Genome Biology and Evolution, 7:3226–3238. doi:10.1093/gbe/evv212.
Schwartz RS et al. (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.
Ramu A et al. (2013) DeNovoGear: de novo indel and point mutation discovery and phasing. Nature Methods, 10:985–987. doi:10.1038/nmeth.2611.
Cartwright RA et al. (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. doi:10.2202/1544-6115.1713.
Hufford MB et al. (2012) Comparative population genomics of maize
domestication and improvement. Nature Genetics, 44:808–811. doi:10.1038/ng.2309.
Cartwright RA (2011) Bards, poets, and cliques: Frequency-dependent selection and the evolution of language genes. Bulletin of Mathematical Biology, 73:2201–2212. doi:10.1007/s11538-010-9619-z.
Cartwright RA and Graur D (2011) The multiple personalities of Watson and Crick strands. Biology Direct, 6:7. doi:10.1186/1745-6150-6-7.
Cartwright RA et al. (2011) History can matter: Non-Markovian behavior of ancestral lineages. Systematic Biology, 60:276–290. doi:10.1093/sysbio/syr012.
Conrad DF et al. (2011) Variation in genome-wide mutation rates within and between human families. Nature Genetics, 43:712–714. doi:10.1038/ng.862.
Lücking R et al. (2011) PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination. BMC Bioinformatics, 12:10. doi:10.1186/1471-2105-12-10.
Price N et al. (2011) Neutral evolution of robustness in Drosophila microRNA precursors. Molecular Biology and Evolution, 28:2115–2123. doi:10.1093/molbev/msr029.
The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature, 467:1061–1073. doi:10.1038/nature09534.
Cartwright RA (2009) Problems and solutions for estimating indel rates and length distributions. Molecular Biology and Evolution, 26:473–480. doi:10.1093/molbev/msn275.
Cartwright RA (2009) Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. Molecular Ecology, 18:2327–2336. doi:10.1111/j.1365-294X.2009.04180.x.
Cartwright RA (2007) Ngila: global pairwise alignments with logarithmic and affine gap costs. Bioinformatics, 23:1427–1428. doi:10.1093/bioinformatics/btm095.
Cartwright RA (2006) Logarithmic gap costs decrease alignment accuracy. doi:10.1186/1471-2105-7-527. BMC Bioinformatics, 7:527.
Cartwright RA (2005) DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics, 21:iii31–iii38. doi:10.1093/bioinformatics/bti1200.
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. doi:10.1105/tpc.105.036293.
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. doi:10.1534/genetics.167.1.499.
BSF 2015247 (2016–2020): Estimating insertions and deletions across the tree of life
NSF DBI-1356548 (2014–2018): ABI Innovation: Identifying phylogenetically informative data from next-generation sequencing
NIH R01-GM101352 (2013–2018): Mutation accumulation in the ciliate Tetrahymena thermophila
NIH R01-HG007178 (2014–2019): Analysis of “de novo” mutation from sequencing of related individuals and cells
Summer 2022 | |
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Course Number | Course Title |
BDE 792 | Research |
Spring 2022 | |
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Course Number | Course Title |
BIO 492 | Honors Directed Study |
MBB 493 | Honors Thesis |
BIO 493 | Honors Thesis |
BIO 494 | Special Topics |
MBB 495 | Undergraduate Research |
BIO 598 | Special Topics |
BDE 792 | Research |
BDE 795 | Continuing Registration |
BDE 799 | Dissertation |
Fall 2021 | |
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Course Number | Course Title |
LIA 194 | Special Topics |
BIO 493 | Honors Thesis |
BIO 494 | Special Topics |
BIO 598 | Special Topics |
BDE 792 | Research |
BDE 799 | Dissertation |
Summer 2021 | |
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Course Number | Course Title |
BDE 792 | Research |
Spring 2021 | |
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Course Number | Course Title |
BIO 492 | Honors Directed Study |
MBB 493 | Honors Thesis |
BIO 493 | Honors Thesis |
MBB 495 | Undergraduate Research |
BDE 792 | Research |
BDE 799 | Dissertation |
Fall 2020 | |
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Course Number | Course Title |
BIO 493 | Honors Thesis |
BDE 792 | Research |
BDE 799 | Dissertation |
Summer 2020 | |
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Course Number | Course Title |
BDE 792 | Research |
Spring 2020 | |
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Course Number | Course Title |
MBB 355 | Intro to Computation Molec Bio |
MAT 355 | Intro to Computation Molec Bio |
BIO 355 | Intro to Computation Molec Bio |
BIO 492 | Honors Directed Study |
MBB 493 | Honors Thesis |
BIO 493 | Honors Thesis |
MBB 495 | Undergraduate Research |
BDE 792 | Research |
BDE 799 | Dissertation |
Fall 2019 | |
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Course Number | Course Title |
BIO 493 | Honors Thesis |
BIO 494 | Special Topics |
BIO 598 | Special Topics |
BDE 792 | Research |
BDE 799 | Dissertation |
Spring 2019 | |
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Course Number | Course Title |
BIO 492 | Honors Directed Study |
MBB 493 | Honors Thesis |
BIO 493 | Honors Thesis |
MBB 495 | Undergraduate Research |
BIO 498 | Pro-Seminar |
BIO 591 | Seminar |
BIO 598 | Special Topics |
BDE 792 | Research |
BDE 799 | Dissertation |
Fall 2018 | |
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Course Number | Course Title |
BIO 340 | General Genetics |
BIO 394 | Special Topics |
BIO 492 | Honors Directed Study |
BIO 495 | Undergraduate Research |
MBB 495 | Undergraduate Research |
BIO 499 | Individualized Instruction |
Spring 2018 | |
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Course Number | Course Title |
BIO 493 | Honors Thesis |
MBB 493 | Honors Thesis |
BIO 494 | Special Topics |
EVO 598 | Special Topics |
Fall 2017 | |
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Course Number | Course Title |
BIO 340 | General Genetics |
BIO 394 | Special Topics |
BIO 492 | Honors Directed Study |
MBB 495 | Undergraduate Research |
BIO 499 | Individualized Instruction |