Materials

Here you will find papers and vignettes mentioned in the class. These sections will be updated as the course progresses.

Vignettes

PBoC Vignette Library - This series of vignettes expands on topics we will cover in the course. Specific suggestions for vignettes to watch will be given during the course.

Date Topic
Mon. Oct 3

1. A feeling for the organism

Tue. Oct 4
Wed. Oct 5
Thur. Oct 6
Fri. Oct 7

In-Class Readings

Monday Lectures (Day 1)

Cell Biology by the Numbers by Ron Milo and Rob Phillips. 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.

Street-Fighting Mathematics by Sanjoy Mahajan. This book elaborates on the skills we will be honing throughout the week as we try to go from the precise calculating with which we are often taught to performing quick calculations largely driven by our intuition to get to rough estimates.

Introduction to Smooth Manifolds by John M Kee. Exceptional textbook math.

Science from a Sheet of Paper by Tadashi Tokieda.

Schrödinger’s What Is Life? at 75 by Rob Phillips Cell Systems .

Post-translational modification: nature’s escape from genetic imprisonment and the basis for dynamic information encoding by Sudhakaran Prabakaran, Guy Lippens, Hanno Steen, and Jeremy Gunawardena.

SARS-CoV-2 (COVID-19) by the numbers by Yinon M. Bar-On, Avi Flamholz, Rob Phillips and Ron Milo eLife .

The quantitative and condition-dependent Escherichia coli proteome by Schmidt et al. Nature Biotechnology . Mass Spectrometry measurements of the E. coli proteome in 22 different growth conditions. Datasets are in the Supplementary.

mRNA translation by DNA Learning Center. Video about the Ribosome synthesizing a protein. Not showing proofreading.

Anthroponumbers.org: A quantitative database of human impacts on Planet Earth by Chure & Banks et al. Patterns .

Human Impacts Database by Chure & Banks et al.. Database containing an evergrowing list of curated numbers about the human impact on the planet.

Striking Graphs That Show Humanity’s Domination of the Earth by Matt Simon Wired Magazine . Article about the Human Impacts Database

How a century of ammonia synthesis changed the world by Erisman et al. Nature Geoscience .

Physical limits to magnetogenetics by Markus Meister eLife .

Tuesday Lectures (Day 2)

The Origins of Genome Complexity by Michael Lynch and John S. Conery Science .

A synthetic oscillatory network of transcriptional regulators by Micheal Ellowitz and Stanislas Leibler Nature .

Interdependence of Cell Growth and Gene Expression: Origins and Consequences by Matthew Scott et al. Science .

Emergence of robust growth laws from optimal regulation of ribosome synthesis by Matthew Scott et al. Molecular Systems Biology . Follow up paper on Scott et al., 2010, with free access.

Napoleon Is in Equilibrium by Rob Phillips Annual Reviews .

An application of the Poisson Distribution by R. D. CLARKE.

What is Bayesian statistics? by Sean R Eddy Nature Biotechnology .

Nextstrain: real-time tracking of pathogen evolution by James Hadfield et al. Bioinformatics .

Fitness flux and ubiquity of adaptive evolution by Ville Mustonen and Michael Lässig PNAS . Very thorough discussion of population genetics and fitness flux. Check out the supplementary for a discussion of mutation-selection-drift dynamics with plenty of derivations.

On the Probability if Fixation of Mutant Genes in a Population by Motoo Kimura. Derives the probability of mutations fixing in a population in the limit of low mutation rates. The equation shows how the population size and natural selection compete.

From biophysics to evolutionary genetics: statistical aspects of gene regulation by Michael Lässig. Review on population genetics.

Wednesday (Day 3)

Design Principles of Length Control of Cytoskeletal Structures by Lishibanya Mohapatra et al. Annual Reviews .

Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner by Vladimir Varga et al. Nature Cell Biology .

Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows by Mirjam Mayer et al. Nature .

Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects by Stefan Münster et al. Nature .

Epithelial Viscoelasticity Is Regulated by Mechanosensitive E-cadherin Turnover by K. Venkatesan Iyer et al. Current Biology .

Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates by Anatol W. Fritsch et al. PNAS .

A hydraulic instability drives the cell death decision in the nematode germline by Nicolas T. Chartier et al. Nature Physics .

Thursday (Day 4)

In Memoriam: Jacques Monod (1910–1976) by Agnes Ullmann Genome Biol Evol .

Nothing in Biology makes Sense Except in the Light of Evolution by Theodosius Dobzhansky National Association of Biology Teachers .

What I’d Like to Know about 2105 by N. David Mermin.

The energetics of genome complexity by Nick Lane and William Martin Nature .

The bioenergetic costs of a gene by Michael Lynch and Georgi K. Marinov PNAS .

Key biology you should have learned in physics class: Using ideal-gas mixtures to understand biomolecular machines by Daniel M. Zuckerman arXiv .

Polymerases and the Replisome: Machines within Machines by Tania A Baker and Stephen P Bell Cell .

Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity by J. J. Hopfield PNAS .