I am interested in phylogenetic methods and phyloinformatics. How do we build evolutionary trees from sequence data and how do we synthesize and share information about the tree of life? More broadly, I am interested in the standards, tools, training, and communities that we need in order to make biodiversity data easily and widely available.

Peer-reviewed publications

McTavish, E. J., Drew, B. T., Redelings, B., & Cranston, K. A. (2017). How and Why to Build a Unified Tree of Life. BioEssays, 39(11). https://dx.doi.org/10.1002/bies.201700114

Stoltzfus, A., Rosenberg, M., Lapp, H., Budd, A., Cranston, K., Pontelli, E., … & Vos, R. A. (2017). Community and Code: Nine Lessons from Nine NESCent Hackathons. F1000Research, 6. http://dx.doi.org/10.12688/f1000research.11429.1

Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., \& Teal, T. K. (2017). Good enough practices in scientific computing. PLoS Comput Biol 13(6): e1005510. doi:10.1371/journal.pcbi.1005510

Rees, J., & Cranston, K. (2017). Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal, 5, e12581. doi:10.3897/BDJ.5.e12581

McTavish, E. J., Hinchliff, C. E., Allman, J. F., Brown, J. W., Cranston, K. A., Holder, M. T., … & Smith, S. A. (2015). Phylesystem: a git-based data store for community curated phylogenetic estimates. Bioinformatics, btv276. doi:10.1093/bioinformatics/btv276.

Hinchliff, C. E., Smith, S. A., Allman, J. F., Burleigh, J. G., Chaudhary, R., Coghill, L. M., … & Cranston, K. A. (2015). Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, 112(41), 12764-12769. doi:10.1073/pnas.1423041112. In the Altmetrics Top 100 for 2015 and in top 5% overall; https://www.altmetric.com/details/4529894

Ksepka, D.T., Parham, J.F., Allman, J.F., Benton, M.J., Carrano, M.T., Cranston, K.A., … & Warnock, R.C.M. (2015) The Fossil Calibration Database, A New Resource for Divergence Dating. Systematic Biology. doi:10.1093/sysbio/syv025

Teal, T. K., Cranston, K. A., Lapp, H., White, E., Wilson, G., Ram, K., Pawlik, A. (2015) Data Carpentry: Workshops to Increase Data Literacy for Researchers. International Journal of Digital Curation. 10(1):135-143. doi:10.2218/ijdc.v10i1.351

Cranston, K. A., Harmon, L. J., O’Leary, M. A., Lisle, C. (2014) Best Practices for Data Sharing in Phylogenetic Research. PLOS Currents Tree of Life. Jun 19. Edition 1. doi:10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645

Stoltzfus, A., Lapp, H., Matasci, N., Deus, H., Sidlauskas, B., Zmasek, C. M., … & Jordan, G. (2013). Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC bioinformatics, 14(1), 158. doi:10.1186/1471-2105-14-158

Rodrigo, A., Alberts, S., Cranston, K., Kingsolver, J., Lapp, H., McClain, C., … & Wiegmann, B. (2013). Science incubators: synthesis centers and their role in the research ecosystem. PloS biology, 11(1), e1001468. doi:10.1371/journal.pbio.1001468

Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., … & Kleibenstein, D. J. (2011). The iPlant collaborative: cyberinfrastructure for plant biology. Frontiers in plant science, 2. doi:10.3389/fpls.2011.0003

Evans, M. E., Hearn, D. J., Theiss, K. E., Cranston, K., Holsinger, K. E., & Donoghue, M. J. (2011). Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera). New Phytologist, 191(2), 555-563. doi:10.1111/j.1469-8137.2011.03697.x

Ammiraju, J. S., Fan, C., Yu, Y., Song, X., Cranston, K. A., Pontaroli, A. C., … & Wing, R. A. (2010). Spatiotemporal patterns of genome evolution in allotetraploid species of the genus Oryza. The Plant Journal, 63(3), 430-442. doi:10.1111/j.1365-313X.2010.04251.x

Cranston, K. A. (2010) Quantifying gene tree incongruence across varying phylogenetic depths. In L. Lacey Knowles, Laura S. Kubatko (Eds.) Estimating Species Trees: Practical and Theoretical Aspects, Wiley-Blackwell.

Cranston, K. A., Hurwitz, B., Sanderson, M. J., Ware, D., Wing, R. A., & Stein, L. (2010). Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae). Systematic botany, 35(3), 512-523. doi:10.1600/036364410792495872

Cranston, K. A., Hurwitz, B., Ware, D., Stein, L., & Wing, R. A. (2009). Species trees from highly incongruent gene trees in rice. Systematic Biology 58(5), 489-500. doi:10.1093/sysbio/syp054

Sanderson, M. J., Boss, D., Chen, D., Cranston, K. A., & Wehe, A. (2008). The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. Systematic Biology 57(3), pp. 335-346. doi:10.1080/10635150802158688

Cranston, K. A., & Rannala, B. (2007). Summarizing a posterior distribution of trees using agreement subtrees. Systematic Biology 56(4), pp. 578-590. doi:10.1080/10635150701485091

Cranston, K., & Rannala, B. (2005). Closing the gap between rocks and clocks. Heredity, 94(5), 461-462. doi:10.1038/sj.hdy.6800644

Pre-prints and other non-peer-reviewed

(published preprints not shown)

Katz, D.S., Choi, S.T., Wilkins-Diehr, N., Hong, N.C., Venters, C.C., … & Littauer, R. Report on the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2). arXiv:1507.01715

Katz, D. S., Allen, G., Hong, N. C., Cranston, K., Parashar, M., Proctor, D., … & Wilkins-Diehr, N. (2014). Second Workshop on on Sustainable Software for Science: Practice and Experiences (WSSSPE2): Submission, Peer-Review and Sorting Process, and Results. arXiv:1411.3464.

Vision, T., & Cranston, K. A. (2014) Open data for evolutionary synthesis: an introduction to the NESCent collection. Nature Scientific Data. doi:10.1038/sdata.2014.30

Cranston, K. A., Blackburn, D., Brown, J. W., Dececchi, A., Gardner, N., Greshake, B., … & Wolfe, J. (2014): Simple rules for sharing phylogenetic data. figshare. doi:10.6084/m9.figshare.997763

Rees, J. A., Cranston, K. A., Lapp, H., & Vision, T. (2013): Response to GBIF request for consultation on data licenses. figshare. doi:10.6084/m9.figshare.799766

Cranston, K. A., Vision, T., O’Meara, B., & Lapp, H. (2013): A grassroots approach to software sustainability. figshare. doi:10.6084/m9.figshare.790739