Reading assignments

Week 1: Rougier, et al. Ten simple rules for better figures; see also original Python code to generate figures in the paper.
Week 2: Wickham, Tidy Data

Wickham, Split-apply-combine
Week 3: Chapter 23 in MacKay
Week 4: Dan White's intro to image processing
Week 5: Sections 10.2, 10.3, 10.4, 11.1, and 11.2 of Efron and Tibshirani

Nuzzo, Statistical errors
Week 6: Eddy, What is Bayesian statistics?
Week 7: Betancourt, A Conceptual Introduction to Hamiltonian Monte Carlo and/or watch this video
Week 8: Vehtari, Gelman, and Gabry, Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC.
Week 9: Betancourt, Towards a Principled Bayesian Workflow.; Talts, et al., Validating Bayesian Inference Algorithms with Simulation-Based Calibration (optional).

Source papers for data sets

Kleinteich and Gorb, Tongue adhesion in the horned frog Ceratophrys sp., Sci. Rep., 4, 5225, 2014
Gardner, Zanic, et al., Depolymerizing kinesins Kip3 and MCAK shape cellular microtubule architecture by differential control of catastrophe, Cell, 147, 1092-1103, 2011
Prober, et al., Hypocretin/Orexin overexpression induces an insomnia-like phenotype in zebrafish, J. Neurosci., 26, 13400-13410, 2006
Gandhi, et al., Melatonin is required for the circadian regulation of sleep Neuron, 85, 1193-1199, 2015
Nath, Bedbrook, Abrams, et al., The jellfish Cassiopea exhibits a sleep-like state, Curr. Biol., 27, 2984-2990, 2017
Goehring, et al., FRAP analysis of membrane-associated proteins: lateral diffusion and membrane-cytoplasmic exchange Biophys. J., 99, 2443-2452, 2010
Iwer-Biswas, et al., Scaling laws governing stochastic growth and division of single bacterial cells PNAS, 111, 15912-15917, 2014
Good, et al., Cytoplasmic volume modulates spindle size during embryogenesis, Science, 342, 856-860, 2013
Reeves, Trisnadi, et al., Dorsal-ventral gene expression in the Drosophila embryo reflects the dynamics and precision of the Dorsal nuclear gradient, Dev. Cell, 22, 544-557, 2012
Singer, et al., Dynamic heterogeneity and DNA methylation in embryonic stem cells, Molec. Cell, 55, 319-331, 2014

Books

Gelman, et al., Bayesian Data Analysis, Third Ed., CRC Press, 2014. "BDA3" is kind of a bible for Bayesian data analysis.
The Think X series by Allen Downey are excellent pedagogical books for learning basic programming and statistics. They are available for free online. The most useful are Think Stats, Think Bayes, and Think Python.
Bradley Efron and Trevor Hastie, Computer Age Statistical Inference, Cambridge University Press, 2016. This book gives a nice historical perspective on the development of modern tools, which provides a nice overview of how everything fits together.
Richard McElreath, Statistical Rethinking, CRC Press, 2015. This book is a clear, delightful read about Bayesian statistics.
Blitzstein and Hwang, Introduction to Probability, Chapman and Hall/CRC, 2014. This is a beautiful book explaining fundamental concepts in probability.
D. S. Sivia, Data Analysis: A Bayesian Tutorial, 2nd Ed., Oxford University Press, 2006. Good pedagogical introduction to Bayesian analysis. It is also available in electronic form (though you cannot download the entire book as a PDF) here.
Gonzalez and Woods, Digital Image Processing, 3rd Ed., Prentice-Hall, 2007. This is the standard book for the basics of image processing.
Phil Gregory, Bayesian Logical Data Analysis for the Physical Sciences, Cambridge University Press, 2005. This goes into more depth on many of the topics covered in Sivia. It also has an addendum.
David MacKay, Information Theory, Inference, and Learning Algorithms, Cambridge University Press, 2003. This excellent book beautifiully ties together three related areas of science in a clear, pedagogical, and sometimes humorous manner. (Available for free online from the link.)