Readings
Day 1
-
Flagellar Length Control System, Testing a Simple Model Based on Intraflagellar Transport and Turnover by Wallace F. Marshall, Hongmin Qin, Monica Rodrigo Brenni, and Joel L. Rosenbaum (2005) Flagellum experiment: cut one of the two flagella and watch it regrow. The cut flagellum grows while the uncut one shrinks, until both reach the same length.
-
Flagellar Elongation and Shortening in Chlamydomonas, The Use of Cycloheximide and Colchicine to Study the Synthesis and Assembly of Flagellar Proteins by Joel L. Rosenbaum, John E. Moulder, and David L. Ringo (1969) Classic paper describing the flagellum regrowth/shortening experiment.
-
Mouvement brownien et grandeurs moléculaires by Jean Perrin (1909) Reports Brownian motion and the altitude distribution of particles in air, consistent with the Boltzmann distribution.
-
Investigations on the Theory of the Brownian Movement by Albert Einstein (1906) Derivation of the vertical distribution of molecules in the atmosphere and key results on Brownian motion.
-
Duration of urination does not change with body size by Patricia J. Yang, Jonathan Pham, Jerome Choo, and David L. Hu (2014) Mammals heavier than ~3 kg have an approximately constant urination time (~21 ± 13 s): flow rate is gravity-dominated so T ≈ V/Q. For smaller mammals, capillary and viscous forces complicate the scaling.
-
A study of tissue culture cells by electron microscopy by Keith R. Porter, Albert Claude, and Ernest F. Fullam (1944) Foundational paper for electron microscopy of cells.
-
Physical Biology of the Cell YouTube Channel. by Rob Phillips. (2021) Rob’s collection of pre-recorded vignettes. (Note: clicking the link opens a pdf containing a followable url https://www.youtube.com/@physicalbiologyofthecellca307/videos)
-
BioNumbers. by Milo Lab. (2021) A database of useful biological numbers (https://bionumbers.hms.harvard.edu).
-
Cell Biology by the Numbers. by Ron Milo, Rob Phillips. (2015) “This book describes many of the estimates we will do in class and is a useful resource for finding key numbers that characterize biological phenomena. (http://book.bionumbers.org/)”
Day 2
Day 3
-
Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling by Jonathan Rodenfels, Karla M. Neugebauer, Jonathon Howard (2019) Energy dissipation during development.
-
Search for the Wreckage of Air France Flight AF 447 by Lawrence D. Stone, Colleen M. Keller, Thomas M. Kratzke and Johan P. Strumpfer (2014) Shows how Bayesian analysis pinpointed AF447’s wreckage, found within a week.
Day 4
-
Statistics Lectures by Joe Blitzstein (2013) Youtube Videos of Statistics Lectures of Joe Blitzstein. This is the link (https://www.youtube.com/playlist?list=PL2SOU6wwxB0uwwH80KTQ6ht66KWxbzTIo)
-
Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation by Clifford P. Brangwynne, Christian R. Eckmann, David S. Courson, Agata Rybarska, Carsten Hoege, Jöbin Gharakhani, Frank Jülicher, Anthony A. Hyman (2009) Phase transition in biology.
-
Polymer physics of intracellular phase transitions by Clifford P. Brangwynne, Peter Tompa and Rohit V. Pappu (2015) Phase transition in biology.
-
Measuring mechanical stress in living tissues by Manuel Gómez-González, Ernest Latorre, Marino Arroyo and Xavier Trepat (2020) Tissue Mechanics.
Day 5
- Scientist: Four golden lessons by Steven Weinberg (2003) Swim in the rough scientific waters.
Useful links
-
Course on Bayesian Inference Website of a Bayesian Inference class taught by Justin Bois at Caltech
-
Distribution Explorer Website regrouping most of the common probability distributions, their properties and physical description by Justin Bois at Caltech.