As the course progresses, we will post links to treadings relevant to what we've talked about in class

Useful links

Street Fighting Mathematics This book by Sanjoy Mahajan is about the rules of sloppy mathematical reasoning that we will often advocate.
Cell Biology by the Numbers A book that performs a surfeit of order-of-magnitude estimates in the context of cell biology.
The BioNumbers Database This database has over 20,000 numbers pertinent to biology, ranging from protein concentrations, to extinction rates, to agriculture.
The Human Impacts Database. This website has a variety of useful numbers that will be helpful either in formulating or checking our estimates about the interactions of humans with the flora and fauna that surround us as well as the oceans, the land and the atmosphere.
Flukebook: AI for Cetacean Research Facebook for whales. A database of images of individual whales to track population size and migrations.
Learn how to Build Neural Networks from Scratch in Python for Digit Recognition A more detailed treatment of image processing using machine learning, coding up a multi-layer neural network from scratch.
Introduction to basic image processing A series of Python tutorials on basic image processing, with a little more detail than what we did in class.
Interactive Proteomics Explorer A web app for quantitatively exploring the abundance of different proteins and protein complexes in E. coli as a function of growth rate.
Physical Biology of the Cell on Youtube A youtube channel with a surfeit of videos covering topics in physical biology taught by Rob at Caltech over zoom.
Blitzstein’s Statistics 110 Course Joe Blitzstein’s online course on introductory statistics

Daily Suggested Reading

Day 1

Terrestrial animal tracking as an eye on life and planet by Roland Kays, Margaret C. Crofoot, Walter Jetz, and Martin Wikelski. (2015) This very insightful article gives a wide ranging introduction to the modern state of the art in animal tracking. Every figure tells an important story.
Estimation of forage biomass and vegetation cover in grasslands using UAV imagery by Jérôme Théau, Étienne Lauzier-Hudon, Lydiane Aubé, and Nicolas Devillers. (2021) This paper is a useful resource for thinking about the biomass of grasslands, relevant to our thinking for both the migration of wildebeest and the grazing of our cattle.
Challenges and solutions for studying collective animal behaviour in the wild by Lacey F. Hughey, Andrew M. Hein, Ariana Strandburg-Peshkin, and Frants H. Jensen. (2017) This paper gives a very insightful overview of the technologies that are needed to study collective motions of animals.
Distinguishing technology from biology:a critical review of the use of GPS telemetry data in ecology by Mark Hebblewhite and Daniel T. Haydon (2010) This paper takes a critical look at the generation of “big data” associated with animal movements. Though we are incredibly enthusiastic about GPS tracking, the arguments here remind us of our own thinking on the way that DNA sequencing and structural biology have created a similar big data pressure head in the molecular interpretation of life that might be similarly misleading.
From single steps to mass migration:the problem of scale in the movementecology of the Serengeti wildebeest by Colin J. Torney, J. Grant C. Hopcraft, Thomas A. Morrison, Iain D. Couzin, and Simon A. Levin (2017) If you are to read one paper from our list on the fascinating and inspiring topic of animal movements (and the wildebeest in particular), this is it. The paper ranges from how measurements are done, to the kinds of data that result to the kinds of models that are needed to come to terms with that data
What Is Mathematics For? by Underwood Dudley. (2010) This is just a fun little excursion into where mathematics fits in our education. I find it a refreshing antidote to specious arguments about the role (i.e. non role) of mathematics in our daily lives.
Patterns of predation in a diverse predator–prey system by Tony Sinclair, Simon Mduma, and Justin Brashares. (2003) This is an incredible paper which quantitatively explores predator-prey dynamics of the Serengeti ecosystem, showing that ≈100% of impala die from predation.
A comparison of deep learning and citizen science techniques for counting wildlife in aerial survey images by Colin J. Torney, David J. Lloyd-Jones, Mark Chevallier, David C. Moyer, Honori T. Maliti, Machoke Mwita, Edward M. Kohi, Grant C. Hopcraft (2019) This is a fun paper that does a systematic comparison between deep learning for detection of animals and human annotation by citizen scientists.

Day 2

The quantitative and condition-dependent Escherichia coli proteome by Alexander Schmidt, Karl Kochanowski, Silke Vedelaar, Erik Ahrné, Benjamin Volkmer, Luciano Callipo, Kèvin Knoops, Manuel Bauer, Ruedi Aebersold, and Matthias Heinemann (2016) One of our favorite papers using quantitative mass spectrometry to simply measure the protein abundances in E. coli across a gamut of growth conditions.
Models in biology: ‘accurate descriptions of our pathetic thinking’ by Jeremy Gunawardena (2014) An excellent piece touching on the utility of models in biology.
Spatially Ordered Dynamics of theBacterial Carbon Fixation Machinery by Dave Savage, Bruno Afonso, Anna H. Chen, and Pamela A. Silver (2010) This paper examines how carboxysomes are partitioned in dividing cyanobacteria and uses one of the great probability distributions to assess whether inheritance is random or active.

Day 3

The depolymerizing kinesin MCAK uses lattice diffusion to rapidly target microtubule ends by Jonne Helenius, Gary Brouhard, Yannis Kalaidzidis, Stefan Diez, and Jonathon Howard (2006) In this study, Jo Howard and his crew measure the waiting time distribution of kinesins walking on microtubules.
In Memoriam: Jacques Monod (1910–1976) by Agnes Ullmann (2011) An excellent tribute to the life of Jacques Monod.
Nothing in biology makes sense except in the light of evolution by Theodosius Dobzhansky (1973) A classsic paper presenting evolution as one of biology’s central organizing principles.
Schrödinger’s ‘What is Life?’ at 75 by Rob Phillips (2021) An article by Rob on the state of “what is life?” after 75 years.

Day 4

Be Prospective, not Retrospective: A Philosophy for Advancing Reproducibility in Modern Biological Research by Griffin Chure (2022) An article by Griffin presenting his philosophy for performing reproducible research. See also the links for a GitHub Template and a template repository for turning your repository into a reproducible website.
Whence cometh the allosterome? by Janet Lindsley and Jared Rutter. (2006) A favorite paper of ours that outlines the vast chasm in our knowledge of what the allosteric effectors are that regulate the myriad proteins in biology.

Day 5

Multistability in the lactose utilization network of Escherichia coli by Ertugrul M. Ozbudak, Mukund Thattai, Han N. Lim, Boris I. Shraiman, and Alexander van Oudenaarden. (2004) This paper demonstrates hysteresis and multistability in a simple genetic network.
Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction by Manuel Razo-Mejia, Stephanie Barnes, Nathan Bellieveau, Griffin Chure, Tal Einav, Mitchell Lewis, and Rob Phillips. (2018) One of our papers applying the MWC model to understand transcriptional regulation in E. coli.

Day 6

Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner by Vladimir Varga, Jonne Helenius, Kozo Tanaka, Anthony A. Hyman, Tomoyuki U. Tanaka, and Jonathon Howard. (2004) A paper by Jo Howard and company which show that a specific kinesin depolymerizes microtubules by ripping a monomer off the end.
Anthroponumbers.org: A quantitative database of human impacts on Planet Earth by Griffin Chure, Rachel A. Banks, Avi I. Flamholz, Nicholas S. Sarai, Mason Kamb, Ignacio Lopez-Gomez, Yinon Bar-On, Ron Milo, and Rob Phillips. () This is our paper presenting and using the Human Impacts Database.

Day 7

Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates by Anatol W. Fritsch, Andres F. Diaz-Delgadillo, Omar Adame-Aranac, Carsten Hoege, Matthaus Mittasch, Moritz Kreysing, Mark Leaver ,Anthony A. Hyman, Frank Jülicher, and Christoph A. Weber. (2021) A paper containing some excellent estimates in the context of phase separation.
Reasoning for results by Dennis Bray (2001)
Life’s code script by Sydney Brenner (2012)
Biology must generate ideas as well as data by Paul Nurse (2021)
Four golden lessons by Steven Weinberg (2003)