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Ramanathan Lab

Ramanathan Lab Publications

Signaling, Development and Fate Decisions

Anand GM, Megale HC, Murphy SH, Weis T, Lin Z, He Y, Wang X, Liu J, Ramanathan S. 2023. Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation<. Cell. 186(3):497-512.e23. PUBMED: 36657443 DOI:S0092-8674(22)01586-0

Yaman YI, Ramanathan S. 2023. Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves. Cell. 186(3):513-527.e19. PUBMED: 36657441 DOI:S0092-8674(22)01585-9

James R. Valcourt, Roya Huang, Sharmistha Kundu, Divya Venkatasubramanian, Robert E. Kingston, Sharad Ramanathan. Changing the Waddington landscape to control mesendoderm competence. bioRxiv 2019.12.06.867010 doi: https://doi.org/10.1101/867010.

Zhang Z, Zwick S, Loew E, Grimley JS, Ramanathan S. Mouse embryo geometry drives formation of robust signaling gradients through receptor localization. Nat Commun. 2019 10 04; 10(1):4516.

Close J, Yao Z, Levi B, Miller J, Bakken T, Menon V, Ting J, Wall A, Krostag A, Thomsen E, et al. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. Neuron. 2017;93 (5) :1035–1048.e5.

Jang S, Furchtgott L, Choubey S, Zou L-N, Doyle A, Menon V, Loew E, Krostag A-R, Martinez RA, Madisen L, et al. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. eLife [Internet]. 2017;6:e20487. Publisher’s Version

Yao Z, Menon V, Mich JK, Ku S, Krostag A, Martinez RA, Furchtgott L, Mulholland H, Bort S, Fuqua MA, et al. A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. Cell Stem Cell. 2016;20 (1) :120-134.

Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, et al. Fixed single-cell transcriptomic characterization of human radial glial diversity. Nat Methods. 2016;13 (1) :87-93.Abstract

Müller P, Rogers KW, Jordan BM, Lee JS, Robson D, Ramanathan S, Schier AF. Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science. 2012;336 (6082) :721-4.Abstract

McClean MN, Hersen P, Ramanathan S. Measuring in vivo signaling kinetics in a mitogen-activated kinase pathway using dynamic input stimulation. Methods Mol Biol. 2011;734 :101-19.Abstract

Thomson M, Liu SJ, Zou L-N, Smith Z, Meissner A, Ramanathan S. Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell. 2011;145 (6) :875-89.Abstract

Nachman I, Ramanathan S. HIV-1 positive feedback and lytic fate. Nat Genet. 2008;40 (4) :382-3.

Hersen P, McClean M, Ramanathan S. [Dynamic analysis of cell signalling: the example of the Saccharomyces cerevisiae osmotic response]. Med Sci (Paris). 2008;24 (12) :1020-2.

Hersen P, McClean MN, Mahadevan L, Ramanathan S. Signal processing by the HOG MAP kinase pathway. Proc Natl Acad Sci U S A. 2008;105 (20) :7165-70.Abstract

McClean MN, Hersen P, Ramanathan S. In vivo measurement of signaling cascade dynamics. Cell Cycle. 2009;8 (3) :373-6.Abstract

Mody A, Weiner J, Ramanathan S. Modularity of MAP kinases allows deformation of their signalling pathways. Nat Cell Biol. 2009;11 (4) :484-91.Abstract

McClean MN, Mody A, Broach JR, Ramanathan S. Cross-talk and decision making in MAP kinase pathways. Nat Genet. 2007;39 (3) :409-14.Abstract

Nachman I, Regev A, Ramanathan S. Dissecting timing variability in yeast meiosis. Cell. 2007;131 (3) :544-56.Abstract

Hallatschek O, Hersen P, Ramanathan S, Nelson DR. Genetic drift at expanding frontiers promotes gene segregation. Proc Natl Acad Sci U S A. 2007;104 (50) :19926-30.Abstract

Ramanathan S, Swain PS. Tracing the sources of cellular variation. Dev Cell. 2005;9 (5) :576-8.Abstract


Computation, Data Analysis and Modeling

Molecular and cellular pathology of monogenic Alzheimer’s disease at single
cell resolution Federica Marinaro , Moritz Haneklaus, Zhechun Zhang, Alessio Strano, Louis-François Handfield, Natalie S Ryan, Nick C Fox , Martin Hemberg, Sharad Ramanathan and Frederick J. Livesey (under review)

Discovering a sparse set of pairwise discriminating features in high dimensional data
Samuel Melton, Sharad Ramanathan arXiv:1910.05814 [stat.ML]

Furchtgott L, Melton S, Menon V, Ramanathan S. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife [Internet]. 2017;2017;6:e20488. Publisher’s Version

Ramanathan S, Detwiler PB, Sengupta AM, Shraiman BI. G-protein-coupled enzyme cascades have intrinsic properties that improve signal localization and fidelity. Biophys J. 2005;88 (5) :3063-71.Abstract

Detwiler, P.B., Ramanathan, S., Sengupta, A., Shraiman, B.I., Engineering aspects of enzymatic signal transduction: photoreceptors in the retina, Biophys J., 79(6):2801-17 (2000).

Ramanathan, S., Shakhnovich, E. I., Statistical Mechanics of proteins with evolutionarily selected sequences, Phys. Rev. E., (50) 130 (1994). PMID: 9962094


C.elegans Neural Networks

Chenguang Li, Gabriel Kreiman, Sharad Ramanathan. Integrating artificial and biological neural networks to improve animal task performance using deep reinforcement learning. bioRxiv 2022.09.19.508590; doi: https://doi.org/10.1101/2022.09.19.508590

Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S. A compressed sensing framework for efficient dissection of neural circuits. Nat Methods. 2019 01; 16(1):126-133.

Kocabas A, Shen C-H, Guo ZV, Ramanathan S. Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour. Nature. 2012;490 (7419) :273-7.Abstract

Guo ZV, Hart AC, Ramanathan S. Optical interrogation of neural circuits in Caenorhabditis elegans. Nat Methods. 2009;6 (12) :891-6.Abstract


Communications and Data Networks 

Mach P, Kerbage C, Ramanathan S, Windeler RS, Eggleton BJ, Rogers JA. Influence of scattering on transmission through long-period fiber gratings and tunable microstructure fibers. Appl Opt. 2002;41 (33) :7018-24.Abstract

Basu. A., Boshes, B., Mukherjee, S., Ramanathan, S., Network Deformation: traffic-aware algorithms for dynamically reducing end-to-end delay in multi-hop wireless networks, Proceedings of IEEE ACM MobiCom, 100-113 (2004).

Basu, A., Dutta, D., Ramanathan, S., Characteristic Timescales: Analyzing end-to-end delay in networks under high loads, Bell Laboratories Technical Memorandum, ITD-03-44953M (2004).

Basu, A., Lin, A., Ramanathan, S., Routing using potentials: Dynamic Traffic Aware Routing Algorithms, Proceedings of IEEE ACM SigComm, 37-48 (2003).

D’Souza, R., Temple Lang, D., Ramanathan, S., Query time-scale distribution in Adhoc Networks, Proceedings of IEEE Infocom (2003).

Mach, P., Kerbage, C., Ramanathan, S., Windler, R., Eggleton, B., Rogers, J., Influence of Scattering on Transmission through Long-period Fiber Gratings and Tunable Microstructure Fibers, Optics Letters, 33: 7018-7024 (2002).



Bouchaud, E., Bouchaud, J. P., Fisher, D. S., Ramanathan, S. and Rice, J. R., Can crack front waves explain the roughness of cracks, J. Mech. Phys. Solids 50, 1703 (2002).

Ramanathan, S., Fisher D.S., Onset of crack propagation in heterogeneous media, Phys. Rev. B., 58, 6026 – 6046 (1998).

Fisher, DS, Dahmen, K., Ramanathan, S., Ben-Zion, Y., Statistics of Earthquakes in simple models of heterogeneous faults, Phys. Rev. Lett., 78, 4885-4888 (1997).

Ramanathan, S., Ertas, D. and Fisher, D. S., Quasistatic crack propagation in heterogeneous media, Phys. Rev. Lett., 79, 873 (1997).

Ramanathan, S., and Fisher, D. S., Dynamics and instabilities of planar tensile cracks in heterogeneous media, Phys. Rev. Lett., 79, 877, (1997).


All Publications

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