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Reed Cartwright

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Biodesign CPD RC
Assistant Professor
Faculty, TEMPE Campus, Mailcode 6401
School of Life Sciences
Assistant Professor
Faculty, TEMPE Campus, Mailcode 6401
Biodesign Center for Personalized Diagnostics
Assistant Professor
Faculty, TEMPE Campus, Mailcode 6401
Biodesign Center for Mechanisms of Evolution
Associate Faculty
Faculty, TEMPE Campus, Mailcode 6401
Biodesign Center for Personalized Diagnostics, Human and Comparative Genomics Lab
Assistant Professor
Faculty, TEMPE Campus, Mailcode 6401
Biography

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.

CV
Binary Data Curriculum Vitae
Education

 Ph.D. University of Georgia 2006

Research Website
https://cartwrig.ht/lab
Google Scholar
Google Scholar Profile
Research Interests

computational evolutionary genomics, population genetics, biological theory, bioinformatics, biology education
 

Publications

  • 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.

Research Activity

  • 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

 

 

 

Teaching Website
https://cartwrig.ht/
Spring 2020
Course NumberCourse Title
MBB 355Intro to Computation Molec Bio
MAT 355Intro to Computation Molec Bio
BIO 355Intro to Computation Molec Bio
BIO 492Honors Directed Study
MBB 493Honors Thesis
BIO 493Honors Thesis
MBB 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Fall 2019
Course NumberCourse Title
BIO 493Honors Thesis
BIO 494Special Topics
BIO 598Special Topics
BDE 792Research
BDE 799Dissertation
Spring 2019
Course NumberCourse Title
BIO 492Honors Directed Study
MBB 493Honors Thesis
BIO 493Honors Thesis
MBB 495Undergraduate Research
BIO 498Pro-Seminar
BIO 591Seminar
BIO 598Special Topics
BDE 792Research
BDE 799Dissertation
Fall 2018
Course NumberCourse Title
BIO 340General Genetics
BIO 394Special Topics
BIO 492Honors Directed Study
BIO 495Undergraduate Research
MBB 495Undergraduate Research
BIO 499Individualized Instruction
Spring 2018
Course NumberCourse Title
BIO 493Honors Thesis
MBB 493Honors Thesis
BIO 494Special Topics
EVO 598Special Topics
Fall 2017
Course NumberCourse Title
BIO 340General Genetics
BIO 394Special Topics
BIO 492Honors Directed Study
MBB 495Undergraduate Research
BIO 499Individualized Instruction
Spring 2017
Course NumberCourse Title
MBB 493Honors Thesis
BIO 493Honors Thesis
Fall 2016
Course NumberCourse Title
BIO 189Life Sciences Career Paths
BIO 340General Genetics
BIO 492Honors Directed Study
MBB 495Undergraduate Research
BIO 499Individualized Instruction
Spring 2016
Course NumberCourse Title
MBB 493Honors Thesis
BIO 493Honors Thesis
BIO 494Special Topics
MBB 494Special Topics
BIO 499Individualized Instruction
MCB 598Special Topics
BIO 598Special Topics
EVO 598Special Topics
Fall 2015
Course NumberCourse Title
BIO 340General Genetics
BIO 492Honors Directed Study
MBB 495Undergraduate Research
BIO 499Individualized Instruction
Presentations
  • Reed A. Cartwright, Rachel Schwartz, Megan Howell, Alexandra Merry. Strong Selection is Necessary for Repeated Evolution of Blindness in Cavefish. SOLS Symposium on Genomics (Dec 2014).
  • Reed A. Cartwright, Rachel Schwartz, Megan Howell, Alexandra Merry. Strong Selection is Necessary for Repeated Evolution of Blindness in Cavefish. Southern California Evolutionary Genetics & Genomics Meeting (Nov 2014).
  • Reed Cartwright and Melissa Wilson Sayres. Symposium --- Mutation: the Ultimate Source of Molecular Variation. Society for Molecular Biology and Evolution Conference (Jun 2014).
  • Rachel Schwartz and Reed Cartwright. Phylogenies from Next-Generation Sequence without Assembly or Alignment. Society forMolecular Biology and Evolution Conference (Jun 2014).
  • David Winter, Allan CHang, Ricardo Azevedo, Rebecca Zufall, Reed Cartwright. Directly measuring the rate of spontaneous mutation in Tetrahymena thermophila. Society forMolecular Biology and Evolution Conference (Jun 2014).
  • David Winter, Allan Chang, Ricardo Azevedo, Rebecca Zufall, Reed Cartwright. Accurate Detection of Mutations from Short-Read Sequencing. Evolution Meeting (Jun 2014).
  • Rachel Schwartz and Reed Cartwright. Inferring Phylogenies from Next-Generation Sequence Data. Evolution Meeting (Jun 2014).
  • Tara Furstenau and Reed Cartwright. The Effect of the Dispersal Distribution on Isolation-by-Distance in a Continuous Population. Evolution Meeting (Jun 2014).
  • Reed A. Cartwright and Donald F. Conrad. Probabilistic Models for De Novo Mutation Detection. Society forMolecular Biology and Evolution Conference (Jul 2013).
  • Nathan D. Palmer, Rachel S. Schwartz, Reed A. Cartwright. Sampling Tree-Space Effectively Using Distance Methods. Society for Molecular Biology and Evolution Conference (Jul 2013).
  • Kelly Harkins, Rachel S. Schwartz, Reed A. Cartwright, and Anne Stone. Phylogenomic Investigation of the Origins and Evolutionary History of Leishmania. Society forMolecular Biology and Evolution Conference (Jul 2013).
  • Nathan D. Palmer, Rachel S. Schwartz, and Reed A. Cartwright. Sampling Tree-Space Effectively Using Distance Methods. Evolution Conference (Jun 2013).
  • Rachel S. Schwartz and Reed A. Cartwright. Phylogenies from next-gen sequencing data without assembly. Evolution Conference (Jun 2013).
  • Reed A. Cartwright and Donald F. Conrad. Probabilistic Models for De Novo Mutation Detection. Biological Sequence Analysis and Probabilistic Models (Mar 2013).
  • Reed A. Cartwright. N/A. Teaching Phylogenetics to Undergraduates, Curriculum Development Workshop (Mar 2013).
  • Rachel Schwartz and Reed A. Cartwright. A mixture model for bias and error in genomic data reduces false positive identification of heterozygotes. Mechanisms of Protein Evolution (Feb 2013).
  • Akash Khare and Reed A. Cartwright. Estimating Indel Models via Simulation and Optimization. Mechanisms of Protein Evolution (Feb 2013).
  • Jessica Albanese and Reed A. Cartwright. LLAMBDA: Estimating Indel Rates and Length Distributions from a Multiple Sequence Alignment. Mechanisms of Protein Evolution (Feb 2013).
  • Reed A. Cartwright. Evolutionary Models of Mutation and Variation for Genomic Data. Molecular & Cellular Biology Colloquium and Genome@asu Joint Seminar (Nov 2012).
  • Patrick L Smith and Reed A. Cartwright. Hobnail: A program for identifying transposable element families from shotgun sequencing. Personal Genomes & Medical Genomics (Cold Spring Harbor Laboratory) (Nov 2012).
  • Reed A. Cartwright. Dawg 2.0: New Methods for Simulating Sequence Evolution. Society for Molecular Biology and Evolution Conference (Dublin, Ireland) (Jun 2012).
  • Reed A. Cartwright, Carolin Kosiol, and Alexandros Stamatakis. Symposium: Estimating and simulating models of molecular evolution. Society for Molecular Biology and Evolution Conference (Dublin, Ireland) (Jun 2012).
  • Reed A. Cartwright. Dawg 2.0: New Methods for Simulating Sequence Evolution. Mathematical and Computational Evolutionary Biology (Montpellier, France) (Jun 2012).
  • Reed A. Cartwright. Evolutionary Models of Mutation and Variation for Genomic Data. UC Davis Seminar, hosted by both the Genome Center and the Genetics Graduate Group (May 2012).
  • Reed A. Cartwright. N/A. SMBE Satellite Symposium on Phylomedicine (ASU) (Mar 2012).
  • Reed A. Cartwright. N/A. BioQUEST/SCALE-IT Curriculum Development Workshop (University of Tennessee) (Jan 2012).
Expertise Areas
Bioinformatics
Evolution and Developmental Biology
Genomics
Genetics
Statistics
Modeling
Phylogenetics