Day 1

More Is Different. by Phil Anderson. (1972) This very influential paper discusses the importance of different levels of reductionism when thinking of problems at various scales.
Street-Fighting mathematics. by Sanjoy Mahajan. (2010) Rules for making estimates. Chapter 5 goes through the mathematics of using one and few. Punch your opponent in the mouth while they are discussing the rules.
The quantitative and condition-dependent Escherichia coli proteome. by Schmidt et al. (2016) Mass-spec study of E. coli, counting the abundance of every protein per cell across a set of varying growth conditions.
Challenges and solutions for studying collective animal behaviour in the wild. by Hughey et al. (2017) Review on tracking behavior of animals on all different scales, from funghi to fish to wildebeest.
Challenges and solutions for studying collective animal behaviour in the wild. by Sinclair et al. (2003) An amazing paper about the correlation of herbivores sizes and their state of predation, e.g., the number of predators and percentage of animals killed by predation.
Models in biology: “accurate descriptions of our pathetic thinking” by Jeremy Gunawardena (2014) A Review discussing the role of Mathematics in Biology and how the reliance on assumptions requires models to be falsifiable.

Day 2

An Application of the Poisson Distribution by R. D. Clarke (1946) A study of how often neighborhoods in London were hit by bombs during the second world war.
An Application of the Poisson Distribution by Peter Buri (1956) An experiment about genetic drift. A heterozygotic population of flies with orange eyes is mated randomly for more than 100 generations and the populations end up being either all red or all white.

Day 3

The great ideas of biology by Sir Paul Nurse (2003) A description of the great ideas of biology, such as the concept of cells, genes as the mechanisms of heredity and subsequently evolution as well as life as chemistry.
Nothing in Biology makes Sense but in the Light of Evolution by Theodosius Dobzhansky (1972)
Why whales are big but not bigger: Physiological drivers and ecological limits in the age of ocean giants by Goldbogen et al. (2019)
Patterning and growth control in vivo by an engineered GFP gradient by Stapornwongkul et al. (2020) A group designed a receptor to recognize GFP as a morphogen in development of drosophila embryos.
Organelle Size Equalization by a Constitutive Process by Ludington et al. (2012) An amazing experiment about length control of flagella in the organism Chlamydomonas reinhardtii. One flagella was cut using lasers and the recovery of its length.
Wave Propagation along Flagella by K. E. MACHIN (1958) A study of the different types of bending for flagella of sperms shows that these flagella have to contain active elements instead of being passive elements whose motion is driven by a motor at the base.
Asymmetric distribution and spatial switching of dynein activity generates ciliary motility by Jianfeng Lin and Daniela Nicastro (2018) A time-resolved Cryo-EM study of moving flagella showing how the activity of the active elements depends on the shape of the flagella, as predicted in the Machin paper.
Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner by Varga et al. (2006) Motors walking down a mictrotubule destabilize the microtubule, therefore, actively controlling the length of the microtubule.
Key biology you should have learned in physics class: Using ideal-gas mixtures to understand biomolecular machines by Daniel M Zuckerman. (2020) Discussion of sugar transporters using elementary ideas of statistical mechanics.

Day 4

Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules by Sanchez et al. (2011) Single-molecule fluorescence microscopy is used to study how the lac repressor inhibits expression when binding to DNA

Day 5

Construction of a genetic toggle switch in Escherichia coli by Timothy S. Gardner, Charles R. Cantor & James J. Collins (2000) Construction of the first synthetic genetic toggle switch using a system of two repressors that repress each other.
A synthetic oscillatory network of transcriptional regulators by Michael Ellowitz & Stanislas Leibler (2000) Synthetic gene circuit of three repressors that leads to oscillation in the expression levels of fluorescent proteins.
Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation by Brangwynne et al. (2009) Discovery of liquid like droplets in C. elegans embryos formed by RNA and RNA-binding proteins.
Liquid-Liquid Phase Separation in Biology by Anthony A. Hyman, Christoph A. Weber & Frank J/”ulicher (2014) A theoretical and mathematical description of phase separation.
Polymer physics of intracellular phase transitions by Clifford P. Brangwynne, Peter Tompa & Rohit V. Pappu (2015) A theoretical discussion of phase transitions using the Flory–Huggins free energy.

Useful links

BioNumbers. Database of useful biological numbers.
Human Impacts Database. A collection of useful numbers for quantifying the impacts of the human presence on Earth.
Flukebook. Facebook for whales. Database for tracking and description of whales in the wild.
The Serengeti Rules - Book. An amazing documentary about five pioneer scientists that discovered the importance of keystone species.
The Serengeti Rules - Movie. An amazing documentary about five pioneer scientists that discovered the importance of keystone species.
A Shadow History of Demons in Science A book about the history of demons in science.
Physical Biology of the Cell - Youtube Channel A set of vignettes recorded for the class Aph161 at Caltech.
Github template for reproducible research A template for Github repositories, making it easier to keep organized and allow other scientist to reproduce your results.
Nonlinear Dynamics and Chaos - Steven Strogatz, Cornell University
Introduction to Data Analysis in the Biological Sciences Caltech course taught by Justin Bois about how to use Python as a tool in biological sciences.