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General Information

Textbooks

	Physical Biology of the Cell (2nd ed) by Phillips, Kondev, Theriot and Garcia ISBN: 0815344503
	A Feeling for the Numbers in Biology by Ron Milo and Rob Phillips This book is in the early stages of being written and is meant to complement the recently developed BioNumbers website.  We will be periodically posting pdfs from this book for you to read.

 

Tentative Syllabus

DATE	TOPIC
1/7	No class
1/9	No class
1/11	No class
1/14	No class
1/16	Course introduction, Biology by the numbers 1	HW1 handed out
1/18
1/21	No class (holiday)
1/23		HW1 due HW2 handed out
1/25	No class
1/28
1/30	No class
2/1	No class
2/4	No class
2/6	Gene regulation 1	HW4 handed out
2/8	Models of Transcription
2/11	Genetic Switches and Oscillators
2/13		HW4 due HW5 handed out
2/15	No class
2/18
2/20	Clock and wavefront model
2/22	Beam bending and membrane deformation
2/25	No class
2/27	Curvature and dynamin polymerization	HW6 due HW7 handed out
3/1
3/4
2/6
2/8

Two additional make-up lectures will be announced later.

 

Readings

1. A Feeling for the Numbers in Biology
   
   
   • Required Reading:
   
   
   • PBoC Chap. 2, 3
   
   
   • Lecture 1 (Thinking Up E. coli)
   
   Additional reading and useful links for Lecture 1:
   • Lee et al. (2006) DNA primase acts as a molecular brake in DNA replication
     This beautiful paper describes a single-molecule measurement of DNA replication.
   • Rosenfeld et al. (2005) Gene regulation at the single-cell level
     This excellent paper shows how to count proteins by using the statistics of partitioning during cell division.
   • Gotta, Miller, French (1991) rRNA Transcription Rate in Escherichia coli
     This paper is relevant to problem 3.4 of PBoC2 and discusses how the rate of transcription was cleverly measured using electron microscopy.
   • SnapShot: Key Numbers in Biology
     This paper is full of useful numbers for making simple estimates in molecular and cell biology.
   • Street Fighting Mathematics (by Sanjoy Mahajan)
     This book provides some beautiful examples of how to use simple, approximate mathematics to address real-world problems of interest.
   • Dobzhansky, T.  (1973) Nothing in biology makes sense except in the light of evolution.  The American Biology Teacher, 125-129.
     This is the essay mentioned in class that argues for the role of evolution as the prism through which biological phenomena are viewed.
   • Eden 2011.pdf, Eden 2011 SI
     This is the paper that is referred to in homework 2 (problem 1) which introduces a clever new method of measuring the degradation time of proteins in human cells.
   
   
   • Lecture 2 (Chemotaxis)
   
   Additional reading and useful links for Lecture 2:
   • Hamdan et. al (2009) Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis
     This paper describes an anaylsis of replication rate by observing the dynamics of tetherd replication forks.
   
   
   • Lecture 6
   
   Additional reading and useful links for Lecture 6:
   • F. C. Niedhardt (1999) Bacterial Growth: Constant Obsession with dN/dt
     
   
   
   • Final Lecture
   
   Additional reading and useful links for the final lecture:
   • Churchman & Weissman (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution
     
   • Costas et al. (2011) Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks
     
   • Li, Oh & Weissman (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
     
   • Zhang & Pugh (2011) High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin
     These papers all describe modern biophysical uses of sequencing.

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