I will joining the Department of Anthropology at the University of Utah as an assistant professor in January 2019. More details will follow, but please feel free to contact with me if you are interested in collaborating or joining the lab as a graduate student or postdoc.
I am currently a postdoctoral researcher in the School of Life Sciences at Arizona State University, where my research focuses on population genomics and sex chromosome evolution. I am particularly interested in understanding the genomic signals of speciation, adaptation, and sex-biased demography in primates.
July 18, 2018 – Our preprint, “Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data”, is available at bioRxiv! The software we describe, XYalign, is available on Github.
July 2, 2018 – The paper describing Bioconda, “Bioconda: sustainable and comprehensive software distribution for the life sciences”, is now online at Nature Methods!
May 22, 2018 – I’ll be joining the Department of Anthropology at the University of Utah as an assistant professor in January 2019.
October 21, 2017 – The Bioconda preprint, “Bioconda: A sustainable and comprehensive software distribution for the life sciences,” is now online at bioRxiv.
September 25, 2017 – We just released XYalign version 1.0 (Github, documentation, Google group)! We’re putting the finishing touches on a preprint that should be online before the end of October. In the meantime, check out the documentation for more information and contact me with any questions you might have.
September 19, 2017 – Our preprint, “Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1″ is online at PeerJ Preprints!
March 6, 2017 – We were awarded a Heritage Grant by the Arizona Game and Fish Department for our project, “Characterizing the Sonoran Desert tortoise through genomic analyses of hybrids and speciation.”
December 7, 2016 – I presented a poster, titled “XYalign: Inferring and Correcting for Sex Chromosome Ploidy in Next-Generation Sequencing Data” (co-authors: Tanya Phung, Madeline Couse, Bruno Grande, Eric Karlins, Phillip Richmond, Whitney Whitford, and Melissa Wilson Sayres), at the Evolutionary Genomics of Sex meeting in Tempe, AZ (Nov 17-19). It’s now up on Figshare. You can also check out the XYalign Github repository for more information.
November 11, 2016 – I recently put together a tutorial on reproducible reference-based genome assembly and variant calling for BIO598 here at ASU. I’ve put the full tutorial and associated files up on Github. If they’re at all useful, please feel free to use, modify, etc. the materials. Let me know if you run into any issues, have any questions/suggestions, or just want to let me know that you’re using the tutorial.
November 9, 2016 – Our article “Evolution of dosage compensation in Anolis carolinensis, a reptile with XX/XY chromosomal sex determination” in Genome Biology and Evolution is now available online (with Shawn Rupp, Kimberly Olney, Elizabeth Hutchins, Kenro Kusumi, and Melissa Wilson Sayres). Scripts for differential expression are available here and I’ve put together a walk through of variant calling and X/A diversity analyses here.
October 15-17, 2016 – I participated in Hackseq, a genomics/bioinformatics hackathon in Vancouver, BC. Our group designed XYalign, a tool that (1) quickly identifies sex chromosome ploidy (e.g., XX, XY, XXY, XO, XYY, etc.), (2) remaps sequencing reads based on inferred ploidy, and (3) calculates a number of metrics across the sex chromosomes both before and after correction. The tool isn’t quite finished yet, but our corrections already seem to improve variant calling (see our presentation for more information), and got us second place at the Hackseq People’s Choice Awards! It was great working with such a fantastic team (Madeline Couse, Bruno Grande, Eric Karlins, Tanya Phung, Phillip Richmond, Whitney Whitford, and Melissa Wilson Sayres)!
September 5, 2016 – Our article “Genomic signatures of sex-biased demography: progress and prospects” in Current Opinions in Genetics and Development is now available online (co-author: Melissa Wilson Sayres).
August 28, 2016 – I had two presentations at the 2016 joint meeting of the American Society of Primatologists and the International Primatological Society in Chicago: an oral presentation titled “The Genomic Landscape of Divergence Across the Macaque Radiation” (with Brenda Bradley) and a poster presentation titled “A Network Analysis of Social Preferences in Wild Black-and-White Ruffed Lemurs” (with Andrea Baden). You can find abstracts and more details about the conference here.
March 31, 2016 – We’re crowdfunding the Gila monster genome! During the month of April, our project will be hosted on Experiment.com. Please visit our page if you’re interested in supporting us and for more information about the project!
March 10, 2016 – Greer Dolby and I were awarded a grant from the ASU School of Life Sciences for our project titled “Deciphering Ecological Drivers of Speciation and Local Adaptation in the Desert Tortoise Complex.”
November 25, 2015 – Our paper “Resource seasonality and reproduction predict fission-fusion dynamics in black-and-white ruffed lemurs (Varecia variegata)” is available online at the American Journal of Primatology (co-authors: Andrea Baden and Jason Kamilar).
September 1, 2015 – I joined the Wilson Sayres lab at Arizona State University as a postdoctoral scholar.
May 20, 2015 – Our paper “The origin of snakes: revealing the ecology, behavior, and evolutionary history of ancestral snakes using genomics, phenomics, and the fossil record” has been published by BMC Evolutionary Biology (co-authors: Allison Hsiang, Dan Field, Adam Behlke, Matt Davis, Rachel Racicot, and Jacques Gauthier). Here are some links to press associated with this article, most of which include a gorgeous artistic reconstruction by Julius Csotonyi: Yale Press Release, BMC Series Blog, NPR, New York Times, Smithsonian Magazine.
April 6, 2015 – The Yale University Provost’s Online Education Committee awarded the Yale Science Diplomats their “Distinguished Achievement Award” for “Science Shorts,” our new science video series featuring Yale graduate student researchers. This series features science videos and educational materials aimed at high school students. We’re currently working to polish our first video and associated materials and I’ll post the link as soon as we have it online.
January 22, 2015 – I was awarded an NSF DDRIG in support of my dissertation project titled “Genomics of a Primate Radiation: Speciation and Diversification in the Macaques” (with my advisor, David Watts).
December 6, 2014 – The Outreach Committee of the Yale Science Diplomats received an Online Education Innovation Grant from Yale University for “Science on Demand: Connecting Students and Yale Researchers through Online Videos and Activities.” This video series, aimed at high school students, will feature Yale scientists discussing their research. The goals of this series are to teach basic scientific concepts and foster student interest and enthusiasm in science and research.
November 9, 2014 – My poster “Protein evolution in Propithecus verreauxi detected using exome sequencing and de novo assembly” (co-authors Rich Lawler and Brenda Bradley) won the Best Student Poster award at the 2014 Northeastern Primate Ecology, Evolution, and Behavior Group’s inaugural meeting. Congratulations to Ari Strandburg-Peshkin for winning the Best Student Presentation award for her fantastic talk titled “Consensus decision-making when directional preferences conflict in wild baboons” !
June 12, 2014 – Our paper “Selective insectivory at Toro-Semliki, Uganda: comparative analyses suggest no ‘savanna’ chimpanzee pattern” (co-authors Bill McGrew, Linda Marchant, Charlotte Payne, and Kevin Hunt) has been published by the Journal of Human Evolution in a special issue called “The Other Faunivory: The Signiﬁcance of Insects & Insect Resources for Nonhuman Primates, Modern Humans, & Extinct Hominins.”
April 12, 2014 – I was awarded the American Association of Anthropological Genetics award for Outstanding Student Presentation for my podium presentation “Gene loss and protein evolution in Propithecus verreauxi detected using exome sequencing and de novo assembly” (co-authors Rich Lawler and Brenda Bradley) at the 2014 annual meeting of the American Association of Physical Anthropologists.
April 12, 2014 – Congratulations to co-author Sandra Winters (NYU) for winning the Sherwood Washburn prize for her excellent podium presentation “Primate camouflage as seen by felids, raptors, and conspecifics” (co-authors Jason Kamilar, Timothy Webster, Brenda Bradley, and James Higham) at the 2014 annual meeting of the American Association of Physical Anthropologists.