Harvard University - Department of Molecular & Cellular Biology

SHARAD RAMANATHAN

Ramanathan
Professor of Molecular and Cellular Biology
Gordon McKay Professor of Applied Physics

Email: sharad@post.harvard.edu
Phone: 617-384-7852

Mail: NW 365.20
Northwest Building
52 Oxford St
Cambridge, MA  02138

Ramanathan Lab Website
Members of the Ramanathan Lab
List of Publications from PubMed

Courses

MCB 111. Mathematics in Biology
Catalog Number: 6444  View Course Website
Term: Spring Term 2013-2014.   Credit: Half course.
Instructors: Michael Desai, Sharad Ramanathan
Course Level: For Undergraduates and Graduates
Description: Develops the mathematics needed for quantitative understanding of biological phenomena including data analysis, simple models, and framing quantitative questions. Topics include probability, transforms and linear algebra, and dynamical systems, each motivated by current biological research.
Prerequisite(s): Mathematics 19 or higher.
Meetings: M., W., 10-11:30
MCB 198. Advanced Mathematical Techniques for Modern Biology
Catalog Number: 62117  View Course Website
Term: [Spring Term 2014-2015.]   Credit: Half course.
Instructors: Lakshminarayanan Mahadevan, Sharad Ramanathan
Course Level: For Undergraduates and Graduates
Description: How do we find biologically meaningful patterns in a large amount of data? How do animals learn to use patterns in the environment to infer information despite the ignorance of the underlying laws? The course will introduce Bayesian analysis, maximum entropy principles, hidden markov models and pattern theory in order to study DNA sequence, gene expression and neural spike train data. The relevant biological background will be covered in depth.
Prerequisite(s): A strong background in calculus, linear algebra, fourier analysis, complex analysis at the advanced undergraduate level and an introductory knowledge of probability theory is required. Knowledge of statistical mechanics and comfort with programming will b
Meetings: Tu., Th., 10-11:30, and a one-hour section meeting weekly.
MCB 305. Signaling Processing and Systems Biology
Catalog Number: 1443  View Course Website
Term: Fall Term; Repeated Spring Term 2013-2014.   Credit: Half course.
Instructor: Sharad Ramanathan
Course Level: Graduate Course
APMTH 126. Statistics and Inference in Biology
Catalog Number: 89788  View Course Website
Term: Spring Term 2013-2014.   Credit: Half course.
Instructors: Michael Desai, Sharad Ramanathan
Course Level: For Undergraduates and Graduates
Description: We often deal with incomplete information when going about our lives: recognizing a friend's face covered by a shadow, having a phone conversation where the reception is poor, reading a document with lots of spelling and grammatical errors. In such circumstances, we make good guesses to process and understand the data. How do we do this? What kind of mathematical framework do we need to interpret noisy and incomplete data? This course will develop a set of statistical tools that will help us solve such poorly posed problems. We will draw on examples from primary literature in biology to study optical illusions, text recognition, sequence alignment, decoding cryptographs, processing of chemo-attractive signals to find food, and survival strategies of bacteria in unpredictable environments to motivate the underlying mathematical framework.
Prerequisite(s): Mathematics 19a/b or Mathematics 21a/b.
Meetings: M., W., 10-11:30
BIOPHYS 334. Decision Making in Cells and Organisms
Catalog Number: 71609  View Course Website
Term: Fall Term; Repeated Spring Term 2013-2014.   Credit: Half course.
Instructor: Sharad Ramanathan
Course Level: Graduate Course
(View all MCB Courses)

Research

Our laboratory studies how cells and organisms make decisions. To arrive at a decision, organisms must measure multiple environmental signals and interpret them appropriately. The questions we are interested in are how cells and organisms interpret their environment, how this interpretation depends on prior experiences, as well as the spatial, temporal modulation and the statistics of environmental cues. We want to achieve a quantitative understanding of the underlying signaling and transcriptional circuits that lead to discrete decisions. Since our goal is to uncover general design principles of the circuits that underlie decision making, our lab works on several model systems. Our recent work has focused on the yeast Sacchromyces cerevisiae, but we are now working on circuits that make developmental decisions in mammalian cells and behavioral decisions in the worm C. elegans. We are also developing several new optical and micro-fluidic techniques to interrogate the dynamics of signaling and transcriptional networks in single cells.

Publications

Kocabas, A.1, Shen, C., Guo, Z.G., Ramanathan, S., Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behavior, Nature (2012) 490 273-277

Müller, P., Rogers, K.W., Jordan, B.M., Lee, J.S., Robson, D., Ramanathan, S., Schier, A.F., Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science (2012) 336 (6082), 721-724.

Thomson, M.W., Liu, S.J., Zou, L.N., Smith, Z., Meissner, A., Ramanathan, S., Pluripotency factors in embryonic stem cells regulate differentiation into germ layers, Cell (2011), 145(6), 875-889

Guo, Z.V., Hart, A.C., Ramanathan, S., Optical interrogation and monitoring of neural circuits in Caenorhabditis elegans, Nature Methods, 6, 891-896 (2009)

Mody A., Weiner J., Ramanathan S., (2009) Modularity of MAP kinases allows deformation of their signaling pathways. Nature Cell Biology 11, 484 - 491

Hersen P., McClean M.N., Mahadevan L., Ramanathan, S., (2008) Signal Processing by the HOG MAP kinase pathway. Proc. Natl. Acad. Sci. USA May 14, 2008, 10.1073/pnas.0710770105

Hallatschek O., Hersen, P., Ramanathan, S., and Nelson, D. (2007) Genetic drift at expanding frontiers promotes gene segregation. Proc. Natl. Acad. Sci. USA 104 (50), 19926-30

Nachman, I., Regev, A., and Ramanathan, S. (2007) Dissecting Timing Variability in Yeast Meiosis. Cell 131, 544-556.

Ramanathan, S., and Broach, J. (2007). Do cells think? Cell. Mol. Life Sci. 64, 1801-4 .

McClean, M. N., Mody, A., Broach, J., and Ramanathan, S. (2007). Decision Making in MAP Kinase pathways. Nat. Genet. 39, 409-414.

Detwiler PB., Ramanathan, S., Sengupta, A., Shraiman BI. (2000). Engineering Aspects of Enzymatic Signal Transduction: Photoreceptors in the Retina. Biophys J, December 2000, p. 2801-2817, Vol. 79, No. 6.

 

updated: 04/22/2014