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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).

 

Physics

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

  • 2024

  • Hallacy T, Yonar A, Ringstad N, Ramanathan S. 2024. Compressed sensing based approach identifies modular neural circuitry driving learned pathogen avoidance. bioRxiv : the preprint server for biology. Pubmed: 39464156 DOI:10.1101/2024.04.10.588911
    Read Abstract
  • Li C, Brenner J, Boesky A, Ramanathan S, Kreiman G. 2024. Neuron-level Prediction and Noise can Implement Flexible Reward-Seeking Behavior. bioRxiv : the preprint server for biology. Pubmed: 38826332 DOI:10.1101/2024.05.22.595306
    Read Abstract
  • Brissette B, Ficaro L, Li C, Jones DR, Ramanathan S, Ringstad N. 2024. Chemosensory detection of polyamine metabolites guides to nutritive microbes. Science advances. 10(12):eadj4387. Pubmed: 38517971 DOI:10.1126/sciadv.adj4387
    Read Abstract

  • 2023

  • 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
    Read Abstract
  • 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
    Read Abstract
  • Fok A, Brissette B, Hallacy T, Ahamed H, Ho E, Ramanathan S, Ringstad N. 2023. High-fidelity encoding of mechanostimuli by tactile food-sensing neurons requires an ensemble of ion channels. Cell reports. 42(5):112452. Pubmed: 37119137 DOI:S2211-1247(23)00463-1
    Read Abstract

  • 2021

  • Valcourt JR, Huang RE, Kundu S, Venkatasubramanian D, Kingston RE, Ramanathan S. 2021. Modulating mesendoderm competence during human germ layer differentiation. Cell reports. 37(6):109990. Pubmed: 34758327 DOI:S2211-1247(21)01469-8
    Read Abstract
  • Read Abstract

  • 2019

  • Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S. 2019. A compressed sensing framework for efficient dissection of neural circuits. Nature methods. 16(1):126-133. Pubmed: 30573831 DOI:10.1038/s41592-018-0233-6
    Read Abstract
  • Zhang Z, Zwick S, Loew E, Grimley JS, Ramanathan S. 2019. Mouse embryo geometry drives formation of robust signaling gradients through receptor localization. Nature communications. 10(1):4516. Pubmed: 31586065 DOI:10.1038/s41467-019-12533-7
    Read Abstract

  • 2018

  • Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S. 2018. A compressed sensing framework for efficient dissection of neural circuits. Nature Methods. 16(1). DOI:10.1038/s41592-018-0233-6
    Read Abstract

  • 2017

  • Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E. 2017. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. Neuron. 93(5):1035-1048.e5. Pubmed: 28279351 DOI:S0896-6273(17)30098-3
    Read Abstract
  • Furchtgott LA, Melton S, Menon V, Ramanathan S. 2017. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife. 6. Pubmed: 28296636 DOI:10.7554/eLife.20488
    Read Abstract
  • Yao Z, Mich JK, Ku S, Menon V, Krostag AR, Martinez RA, Furchtgott L, Mulholland H, Bort S, Fuqua MA, Gregor BW, Hodge RD, Jayabalu A, May RC, Melton S, Nelson AM, Ngo NK, Shapovalova NV, Shehata SI, Smith MW, Tait LJ, Thompson CL, Thomsen ER, Ye C, Glass IA, Kaykas A, Yao S, Phillips JW, Grimley JS, Levi BP, Wang Y, Ramanathan S. 2017. A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. Cell stem cell. 20(1):120-134. Pubmed: 28094016 DOI:S1934-5909(16)30340-X
    Read Abstract
  • Furchtgott LA, Melton S, Menon V, Ramanathan S. 2017. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife. DOI:10.7554/eLife.20488
    Read Abstract
  • Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S. 2017. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. eLife. DOI:10.7554/eLife.20487
    Read Abstract
  • Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E. 2017. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. Neuron. 93(5). DOI:10.1016/j.neuron.2017.02.014
    Read Abstract
  • Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E. 2017. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. Neuron. 96(4):949. Pubmed: 29144976 DOI:S0896-6273(17)30992-3
  • Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S. 2017. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. eLife. 6. Pubmed: 28296635 DOI:10.7554/eLife.20487
    Read Abstract

  • 2016

  • Yao Z, Mich JK, Ku S, Menon V, Krostag AR, Martinez RA, Furchtgott L, Mulholland H, Bort S, Fuqua MA, Gregor BW, Hodge RD, Jayabalu A, May RC, Melton S, Nelson AM, Ngo NK, Shapovalova NV, Shehata SI, Smith MW, Tait LJ, Thompson CL, Thomsen ER, Ye C, Glass IA, Kaykas A, Yao S, Phillips JW, Grimley JS, Levi BP, Wang Y, Ramanathan S. 2016. A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. Cell Stem Cell. 20. DOI:10.1016/j.stem.2016.09.011
    Read Abstract
  • Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, Ramanathan S. 2016. Fixed single-cell transcriptomic characterization of human radial glial diversity. Nature methods. 13(1):87-93. Pubmed: 26524239 DOI:10.1038/nmeth.3629
    Read Abstract

  • 2015

  • Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, Ramanathan S. 2015. Fixed single-cell transcriptomic characterization of human radial glial diversity. Nature Methods. 13(1). DOI:10.1038/nmeth.3629
    Read Abstract

  • 2012

  • Müller P, Rogers KW, Jordan BM, Lee JS, Robson D, Ramanathan S, Schier AF. 2012. Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science (New York, N.Y.). 336(6082):721-4. Pubmed: 22499809 DOI:10.1126/science.1221920
    Read Abstract
  • Kocabas A, Shen CH, Guo ZV, Ramanathan S. 2012. Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour. Nature. 490(7419):273-7. Pubmed: 23000898 DOI:10.1038/nature11431
    Read Abstract

  • 2011

  • McClean MN, Hersen P, Ramanathan S. 2011. Measuring in vivo signaling kinetics in a mitogen-activated kinase pathway using dynamic input stimulation. Methods in molecular biology (Clifton, N.J.). 734:101-19. Pubmed: 21468987 DOI:10.1007/978-1-61779-086-7_6
    Read Abstract
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  • 2009

  • McClean MN, Hersen P, Ramanathan S. 2009. In vivo measurement of signaling cascade dynamics. Cell cycle (Georgetown, Tex.). 8(3):373-6. Pubmed: 19177008
    Read Abstract
  • Read Abstract
  • Mody A, Weiner J, Ramanathan S. 2009. Modularity of MAP kinases allows deformation of their signalling pathways. Nature cell biology. 11(4):484-91. Pubmed: 19295513 DOI:10.1038/ncb1856
    Read Abstract

  • 2008

  • Hersen P, McClean MN, Mahadevan L, Ramanathan S. 2008. Signal processing by the HOG MAP kinase pathway. Proceedings of the National Academy of Sciences of the United States of America. 105(20):7165-70. Pubmed: 18480263 DOI:10.1073/pnas.0710770105
    Read Abstract

  • 2007

  • Nachman I, Regev A, Ramanathan S. 2007. Dissecting timing variability in yeast meiosis. Cell. 131(3):544-56. Pubmed: 17981121
    Read Abstract
  • Hallatschek O, Hersen P, Ramanathan S, Nelson DR. 2007. Genetic drift at expanding frontiers promotes gene segregation. Proceedings of the National Academy of Sciences of the United States of America. 104(50):19926-30. Pubmed: 18056799
    Read Abstract
  • McClean MN, Mody A, Broach JR, Ramanathan S. 2007. Cross-talk and decision making in MAP kinase pathways. Nature genetics. 39(3):409-14. Pubmed: 17259986
    Read Abstract

  • 2005

  • Ramanathan S, Detwiler PB, Sengupta AM, Shraiman BI. 2005. G-protein-coupled enzyme cascades have intrinsic properties that improve signal localization and fidelity. Biophysical journal. 88(5):3063-71. Pubmed: 15681646
    Read Abstract
  • Ramanathan S, Swain PS. 2005. Tracing the sources of cellular variation. Developmental cell. 9(5):576-8. Pubmed: 16256732
    Read Abstract
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