Papers to Read

 

The papers provided here are meant to provide an entry point into the literature for going more deeply into various topics covered in class. These papers have been picked either because they provide interesting and provocative experimental measurements of particular biological phenomena or because they show how to go about constructing theoretical models in the physical biology spirit described in the course. The papers that of most direct relevance to what we will cover in class are linked on the "Syllabus" part of the website.

Biology by the numbers:

- Uri Moran etal., (2010), SnapShot: Key Numbers in Biology, Cell, 141, 1262. List of key numbers in biology, such as the quantity and size of cellular components and the rates of cellular processes.

- Rob Phillips and Ron Milo, (2009), A Feeling for the numbers in Biology,PNAS, 106, 21465-71. This paper describes the role of biological numeracy in thinking about a variety of problems.

- Sean Eddy, (2004), What is Bayesian statistics?, Nature Biotechnology, 22, 1177-178.This paper gives a compact but beautiful example of the power of Bayesian methods for figuring out the probability of some hypothesis given the data.

Hernan Garcia, etal., (2007), A First Exposure to Statistical Mechanics for Life Scientists This paper is a brief introduction to ideas from statistical mechanics that can be used to analyze a variety of problems in biology.

Regulatory biology:

- Hernan Garcia and Rob Phillips, (20011), Quantitative dissection of the simple repression input-output function, PNAS, 108, 29, 12173-8.This paper demonstrates that thermodynamic models can make quantitative predictions about the level of gene expression as a a function of repressor copy number and operator strength.

- Lacromioara Bintu, etal., (2005), Transcriptional regulation by the numbers: models, Current Opinions in Genetics and Development, 15, 116-124. This paper outlines an approach to creating quantitative models of gene expression using thermodynamics of the binding of transcription factors and RNA polymerase to DNA.

- Lacramioara Bintu etal., (2005), Transcriptional regulation by the numbers: applications, Current Opinions in Genetics and Development, 15, 125-35. This paper outlines an approach of applying thermodynamic models to gene regulation.

- Ido Golding, (2005), Real-time kinetics of gene activity in individual bacteria, Cell, 123, 1025-036.This paper clearly demonstrates that the process by which mRNA is produced in the E.coli cell is stochastic in nature. A surprising observation is that the mRNA distribution is not Poisson, characterized by bursts in mRNA production. To this day the source of the stochasticity remains a mystery.

- Victor Sourjik and Howard C. Berg, (2002), Receptor sensitivity in bacterial chemotaxis, PNAS, 99, 123-127. and Victor Sourjik and Howard C. Berg, (2002), Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer, PNAS, 99, 12669-12674. These two papers use the method of FRET to examine the relation between chemoattractant concentration and the chemical reactions within cells that control the frequency of tumbles.

- Juan Keymer etal.,(2006), Chemosensing in Escherichia coli: Two regimes of two-state receptors, PNAS, 103, 1786-1791. and Bernardo A. Mello and Yuhai Tu, (2005), An allosteric model for heterogeneous receptor complexes: Understanding bacterial chemotaxis responses to multiple stimuli, PNAS, 99, 12669-12674. Theory of chemotaxis: These two papers show how simple ideas from equilibrium statistical mechanics can be used to understand the chemotactic response of E. coli to different concentrations of chemoattractant.

Biophysics of Vision:

Reading suggestions will be posted during the course.

The Physics of Genome Management:

- Roger Kornberg and Lubert Stryer, (1988), Statistical distibutions of nucleosome: nonrandom locations by a stochastic mechanism, Nucleic Acids Research, 16, 6677-6690.This paper shows how a simple model of excluded volume predicts how nucleosomes will be organized around promoters.

- Eran Segal etal., (2006), A genomic code for nucleosome positioning, Nature, 442, 772-778. This paper describe work aimed at determining genome wide nucleosome positioning preferences.

Noam Kaplan etal., (2009), The DNA-encoded nucleosome organization of a euakryotic genome, Nature, 458, 362-366. This paper describe work aimed at determining genome wide nucleosome positioning preferences.

- Paul Wiggins etal., (2010), Strong intranucleoid interactions organize the E. coli chromosome into a nucleoid filament, PNAS, 107, 4991-5. This paper looks at the spatial organization of the genome in a cell.

- Douglas Smith etal., (2001), The bacteriophage phi29 portal motor can package DNA against a large interanl force, Nature, 413, 748-752. In this paper, optical tweezers are used to study the forces needed to package double-stranded DNA into a viral capsid.

- Alexander Tsankov etal., (2010), The role of nucleosome positioning in the evolution of gene regulation, PLoS Biology, 8, e1000414. This interesting paper examines the genome-wide nucleosome positions in 12 different yeast species. This data provides an excellent jumping off point for models of nucleosome positioning.

- K.J. Polach and J. Widom, (1995), Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation, JMB, 254, 130-149. This paper examines how different sites within nucleosomes grant access to DNA binding proteins and quantifies how this accessibility depends upon the depth of the sites of interest within the nucleosome.

Pattern formation in biology:

- Thomas Gregor, etal., (2005), Diffusion and scaling during early embryonic pattern formation, PNAS, 102, 18403-407.Quantitative analysis reveals that diffusion based mechanism cannot account for morphogen gradient scaling in early embryos across closely related fly species.

- Feng Liu, etal., (2013), Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network, PNAS, 110, 6724-29.This paper explores how patterning in the fly embryo depends upon the dosage of bicoid.

 

Papers brought up during the class

 

Monday

http://beta.milolab.webfactional.com/proteomaps/

Protein census in the cell- this collection of papers shows how modern methods are being used to take the protein census of different cell types.

Wigner - Unreasonable effectiveness of mathematics

Mahajan - Street fighting mathematics

Whitman - The unseen majority

Tuesday

Single-molecule techniques were used to measure the rate of replication

The rate of transcription was measured using electron microscopy

How long it takes for proteins to move along a nerve cell

Friday

A modern treatment of how bicoid gene dosage affects spatial patterning.

Wednesday 2

Fygenson, Phase diagram for microtubules.

Thursday 2

Varga 2006, Varga 2009. - These two excellent papers describe beautiful experiments on how microtubule length is controlled by molecular motors.