Physics 434, 2014: Information Processing in Biology
Back to the main Teaching page.
- 1 News
- 2 Logistics
- 3 Lecture Notes
- 4 Homework assignments
- 5 References
- 5.1 Textbooks
- 5.2 Sensory Ecology and Corresponding Evolutionary Adaptations
- 5.3 Transcriptional regulation
- 5.4 Signal Processing in Vision
- 5.5 Bacterial chemotaxis
- 5.6 Eukaryotic chemotaxis
- 5.7 Random walks
- 5.8 Information theory
- 5.9 Noise in biochemistry, population biology, and neuroscience
- 5.10 Memory in noisy environments
- 5.11 Adaptation
- 5.12 Robustness
- 5.13 Learning
- 5.14 Eukaryotic signaling
- Project reports are due December 18, end of the day. Ilya 08:59, 04 December 2014 (EDT)
- Project presentations are scheduled on Dec 4. There's no class on December 9. We will need more than 1hr 15 min for your presentations. Please arrange your schedule to give us about 2 hours (11:30-1:30) for this class. Ilya 22:14, 05 November 2014 (EDT)
- There won't be a class on Nov 13th. The replacement class will be on Nov 18 at 5pm. Ilya 22:04, 05 November 2014 (EDT)
- We have missed two classes last week. The replacement classes will be on Nov 10 and 17 at 2:00pm. Ilya 22:02, 05 November 2014 (EDT)
- Projects now available. Please let me know which ones you will work on. Ilya 23:13, 04 November 2014 (EDT)
- Projects will be distributed by about October 21. Ilya 23:29, 15 October 2014 (EDT)
- Midterm scheduled for November 6. Ilya 23:29, 15 October 2014 (EDT)
- No classes on Oct 28, 30. Classes will be rescheduled at a later date. Ilya 23:29, 15 October 2014 (EDT)
- No homework due on Sep 24. Ilya 15:54, 21 September 2014 (EDT)
- Extra office hours: Friday, Sep 5, 2-3pm; Monday, Sep 8, 3:30-4:30pm. Added by: Ilya 10:01, 5 September 2014 (EDT)
- Homework assignments will be distributed on Tuesdays, and will be due on Wednesdays the following week. Added by: Ilya 10:00, 5 September 2014 (EDT)
- Welcome to the class!
- Syllabus -- we will deviate from it in the course of the class
- Installing Octave on your PC and Mac.
- Weekly office hours: Monday, 2:00-3:30, Thu 4:00-5:00.
- Introduction: Introduction, Aug 28, (last edited on 09/11).
- Block one: Biological information processing is probabilistic
- Discrete randomness: introducing the quantities to describe stochasticity in biology, basic probability theory of discrete random variables, Sep 2, 4, 9 (last edited on 10/21).
- Continuous randomness, Sep 16, (last edited on 10/21).
- Central limit theorem, Sep 18, (last edited on 10/27).
- Random walk and diffusion, Sep 23, 25, 30, (last edited 11/05).
- Search and first passage times, Oct 2, 7, 9, (last edited 11/06).
- Stochastic chemical kinetics, Oct 16, 21.
Download all the scripts and data files we used in class.
- HW 1, Due Sep 10.
- HW 2, Due Sep 17.
- HW 3, Due Oct 1.
- HW 4, Due Oct 8.
- HW 5, Due Oct 22.
- HW 6, Due Nov 5.
- HW 7, Due Nov 19.
- HW 8, Due Dec 9.
The list is far from being complete now. Stay tuned.
- P Nelson, Physical Modeling of Living Systems, WH Freeman, Dec 2014
- R Phillips, J Kondev, J Theriot. Physical Biology of the Cell (Garland Science, 2008)
- Sizing up E. coli. PDF
- CM Grinstead and JL Snell, Introduction to Probability.
- W Bialek, Biophysics: Searching for Principles (2011).
- Information theory overview is in Chapter 4.
- For information about Wiener processes and diffusion, a good source is: Wiener Process article in Wikipedia.
- The most standard textbook on information theory is: T Cover and J Thomas, Elements of Information Theory, 2nd ed (Wiley Interscience, 2006).
Sensory Ecology and Corresponding Evolutionary Adaptations
- T Cronin, N Shashar, R Caldwell. Polarization vision and its role in biological signaling. Integrative and Comparative Biology 43(4):549-558, 2003. PDF.
- D Stavenga, Visual acuity of fly photoreceptors in natural conditions--dependence on UV sensitizing pigment and light-controlling pupil. J Exp Biol 207 (Pt 10) pp. 1703-13, 2004. PDF.
- O Berg and P von Hippel. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol. 193(4):723-50, 1987. PDF.
- O Berg et al. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20(24):6929-48, 1981. PDF.
- C Guet, M Elowitz, W Hsing, S Leibler. Combinatorial synthesis of genetic networks. Science 296:1466, 2002. PDF.
- M Slutsky and L Mirny. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophysical J 87(6):4021-35, 2004. PDF.
- E Ozbudak, M Thattai, H Lim, B Shraiman, A van Oudenaarden. Multistability in the lactose utilization network of Escherichia coli. Nature 427: 737, 2004. PDF.
- D Dreisigmeyer, J Stajic, I Nemenman, W Hlavacek, and M Wall. Determinants of bistability in induction of the Escherichia coli lac operon. IET Syst Biol 2:293-303, 2008. PDF.
Signal Processing in Vision
- P Detwiler et al. Engineering aspects of enzymatic signal transduction: Photoreceptors in the retina. Biophys. J., 79:2801-2817, 2000. PDF.
- A Pumir et al. Systems analysis of the single photon response in invertebrate photoreceptors. Proc Natl Acad Sci USA 105 (30) pp. 10354-9, 2008. PDF.
- F Rieke and D Baylor. Single photon detection by rod cells of the retina. Rev Mod Phys 70, 1027-1036, 1998. PDF.
- T Doan, A Mendez, P Detwiler, J Chen, F Rieke. Multiple phosphorylation sites confer reproducibility of the rod's single-photon responses. Science 313, 530-533, 2006. PDF.
- J Adler. Chemotaxis in bacteria. Annu Rev Biochem 44 pp. 341-56, 1975. PDF
- H Berg and D Brown. Chemotaxis in Escherichia coli analysed by three-dimensional tracking. Nature 239 (5374) pp. 500-4, 1972. PDF.
- E Budrene and H Berg. Dynamics of formation of symmetrical patterns by chemotactic bacteria. Nature 376 (6535) pp. 49-53, 1995. PDF
- E Budrene and H Berg. Complex patterns formed by motile cells of Escherichia coli. Nature 349 (6310) pp. 630-3, 1991. PDF
- E Purcell. Life at low Reynolds number. Am J Phys 45 (1) pp. 3-11, 1977. PDF
- H Berg. Motile behavior of bacteria. Phys Today 53 (1) pp. 24-29, 2000. PDF
- C Rao and A Arkin. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol 2 (2) pp. E49, 2004. PDF
- C Rao et al. The three adaptation systems of Bacillus subtilis chemotaxis. Trends Microbio l16 (10) pp. 480-7, 2008. PDF.
- A Celani and M Vergassola. Bacterial strategies for chemotaxis response. Proc Natl Acad Sci USA107, 1391-6, 2010. PDF.
- J Franca-Koh et al. Navigating signaling networks: chemotaxis in Dictyostelium discoideum. Curr Opin Genet Dev 16 (4) pp. 333-8, 2006. PDF.
- W-J Rappel et al. Establishing direction during chemotaxis in eukaryotic cells. Biophysical Journal 83 (3) pp. 1361-7, 2002. PDF.
- G Bel, B Munsky, and I Nemenman. The simplicity of completion time distributions for common complex biochemical processes. Physical Biology 7 016003, 2010. PDF.
- J Ziv and A Lempel. A Universal Algorithm for Sequential Data Compression. IEEE Trans. Inf. Thy 3 (23) 337, 1977. PDF.
- N Tishby, F Pereira, and W Bialek. The information bottleneck method. arXiv:physics/0004057v1, 2000. PDF.
- E Ziv, I Nemenman, and C Wiggins. Optimal signal processing in small stochastic biochemical networks. PLoS ONE 2: e1077, 2007. PDF.
- S Strong, R Koberle, R de Ruyter van Steveninck, and W Bialek. Entropy and information in neural spike trains. Phys Rev Lett 80:197–200, 1998. PDF.
- R Cheong, A Rhee, CJ Wang, I Nemenman, and A Levchenko. Information Transduction Capacity of Noisy Biochemical Signaling Networks. Science doi:10.1126/science.1204553, 2011. PDF.
- A Margolin, I Nemenman, K Basso, U Klein, C Wiggins, G Stolovitzky, Riccardo D Favera, and A Califano. ARACNE: An algorithm for reconstruction of genetic networks in a mammalian cellular context. BMC Bioinformatics, 7 (Suppl. 1):S7, 2006. PDF
Noise in biochemistry, population biology, and neuroscience
- S Luria and M Delbruck. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28, 491-511, 1943. PDF.
- E Schneidman, B Freedman, and I Segev. Ion channel stochasticity may be critical in determining the reliability and precision of spike timing. Neural Comp. 10, p.1679-1704, 1998. PDF.
- T Kepler and T Elston. Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations. Biophys J. 81, 3116-3136, 2001. PDF.
- M Elowitz, A Levine, E Siggia & P Swain. Stochastic gene expression in a single cell. Science 207, 1183, 2002. PDF.
- W Blake, M Kaern, C Cantor, and J Collins. Noise in eukaryotic gene expression. Nature 422, 633-637, 2003. PDF.
- J Raser and E O’Shea. Control of stochasticity in eukaryotic gene expression. Science 304, 1811-1814, 2004. PDF.
- G Lahav. et al. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet 36, 147–150, 2004. PDF.
- J Paulsson. Summing up the noise in gene networks. Nature 427, 415, 2004. PDF, Supplement.
- J Pedraza and A van Oudenaarden. Noise propagation in gene networks, Science 307, 1965-1969, 2005. PDF.
- N Rosenfeld, J Young, U Alon, P Swain, M Elowitz. Gene Regulation at the Single-Cell Level. Science 307, 1962, 2005. PDF.
- B Averbeck et al. Neural correlations, population coding and computation. Nat Rev Neurosci 7, 358-66, 2006. PDF.
- D Gillespie. Stochastic Simulation of Chemical Kinetics. Ann Rev Phys Chem 58, 35-55, 2007. PDF.
- T Cağatay et al. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139:512-22, 2009. PDF, supplement.
- A Walczak, G Tkacik, and W Bialek. Optimizing information flow in small genetic networks. II. Feed-forward interactions. Phys Rev E 81, 041905, 2010. PDF.
Memory in noisy environments
- T Gardner et al. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-42, 2000. PDF
- W Bialek. Stability and noise in biochemical switches. In Todd K. Leen, Thomas G. Dietterich, and Volker Tresp, editors, Advances in Neural Information Processing Systems 13, pages 103-109. MIT Press, 2001. PDF
- E Aurell and K Sneppen. Epigenetics as a first exit problem. Phys Rev Lett 88, 048101, 2002. PDF.
- E Korobkova, T Emonet, JMG Vilar, TS Shimizu, and P Cluzel. From molecular noise to behavioural variability in a single bacterium. Nature, 438:574-578, 2004. PDF.
- N Balaban, J Merrin, R Chait, L Kowalik, S Leibler. Bacterial persistence as a phenotypic switch. Science 305:1622, 2004. PDF.
- Y Tu and G Grinstein. How white noise generates power-law switching in bacterial flagellar motors. Phys Rev Lett, 2005. PDF.
- E Kussell and S Leibler. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309:2075–2078. 2005. PDF.
- D Sprinzak et al. Cis-interactions between Notch and Delta generate mutually exclusive signalling states. Nature 465, 86–90, 2010. PDF.
- N Barkai and S Leibler. Robustness in simple biochemical networks. Nature 387, 913–917, 1997. PDF.
- U Alon, M Surette, N Barkai, and S Leibler. Robustness in bacterial chemotaxis. Nature 397, 168–171, 1999. PDF.
- N Brenner et al. Adaptive rescaling maximizes information transmission. Neuron 26, 695-702. PDF.
- P Cluzel, M Surette, and S Leibler. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science, 287:1652-1655, 2000. PDF.
- B Andrews et al. Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol 2, e154, 2006. PDF.
- T Sharpee et al. Adaptive filtering enhances information transmission in visual cortex. Nature 439, 936-42, 2006. PDF.
- A Fairhall et al. Efficiency and ambiguity in an adaptive neural code. Nature 412, 787-92, 2001. PDF.
- I Nemenman et al. Neural coding of natural stimuli: information at sub-millisecond resolution. PLoS Comput Biol 4, e1000025, 2008. PDF.
- T Friedlander and N Brenner. Adaptive response by state-dependent inactivation. Proc Natl Acad Sci USA 106, 22558-63, 2009. PDF.
- W Ma et al. Defining network topologies that can achieve biochemical adaptation. Cell 138, 760-73, 2009. PDF.
- A Eldar, D Rosin, B-Z Shilo, and N Barkai. Self-Enhanced Ligand Degradation Underlies Robustness of Morphogen Gradients. Developmental Cell, Vol. 5, 635–646, 2003. PDF.
- T Gregor, W Bialek, R de Ruyter van Steveninc, D Tank, and E Wieschaus. Diffusion and scaling during early embryonic pattern formation. PNAS 102:18403, 2005. PDF.
- T Doan, A Mendez, P Detwiler, J Chen, F Rieke. Multiple phosphorylation sites confer reproducibility of the Rod's single-photon responses. Science 313, 530-3, 2006. PDF.
- A Lander et al. The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harb Perspect Biol 1, a002022, 2009. PDF
- CR Gallistel et al. The rat approximates an ideal detector of changes in rates of reward: implications for the law of effect. J Exp Psychol Anim Behav Process 27, 354-72, 2001. PDF.
- CR Gallistel et al. The learning curve: implications of a quantitative analysis. Proc Natl Acad Sci USA 101, 13124-31, 2004. PDF.
- B Andrews and P Iglesias. An information-theoretic characterization of the optimal gradient sensing response of cells. PLoS Comput Biol 3, e153, 2007. PDF.
- M Vergassola et al. 'Infotaxis' as a strategy for searching without gradients. Nature 445, 406-9, 2007. PDF.
- C-Y Huang and J Ferrell. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 93:10078, 1996. PDF.
- N Markevich et al. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol 164:353-9, 2004. PDF.
- C Gomez-Uribe, G Verghese, and L Mirny. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol 3:e246, 2007. PDF.