Publications

Papers in Review

• Thoduvayil S, Chatterjee A, Weerakkody J, Coleman J, Ramakrishnan S*. Distinct protein ID secretory vesicles controlling biphasic insulin secretion. In Review.
• Ramakrishnan S*, Nair A, Pichurin J, Thoduvayil S, Radhakrishnan A, Gowtham S, Chatterji A, Kyrikides T, Gunasekara RW. Programmable Light-Driven Platform for Rapid Isolation and Fractionation of Extracellular, Cell membrane and Biomimetic Lipid Vesicles for Scalable Gene Therapy Applications. In Review at Advanced Materials.
• Acharya P, Carr AJ, Hajicek N, Thoduvayil S, Cannon K, KalyanaSundaram V, Zhang Q, Baker R, Ramakrishnan S, Sondek J, Zhang Q. Simultaneous monitoring phosphatidylinositol 4,5-bisphosphate, diacylglycerol, and inositol 1,4,5-triphosphate with a small molecule reporter for the phospholipase C isozymes. In Review at Cell Chemical Biology.

• Bera M, Kalyana Sundaram V, Thoduvayil S, Coleman J, Pincet F, Ramakrishnan S*. Highly Stable Planar Asymmetric Suspended Membranes for Investigating Protein Dynamics and Membrane Fusion. Nature Protocols, 2025.
• Mion D, Bunel L, Ramakrishnan S, Heo P, Pincet F. Biomimetic membrane in a microfluidic chip for the electrical and optical monitoring of biological reactions. Nature Protocols, 2025.

• Weerakkody J, Tseng T, Topper M, Thoduvayil S, Radhakrishnan A, Kyriakides T, Gunasekara R, Ramakrishnan S*. Photosensitive Nanoprobes for Size-Specific Isolation and Enrichment of Synthetic and Extracellular Vesicle Subpopulations. Advanced Functional Materials, 2024 (Cover).

• Bera M, Radhakrishnan A, Coleman J, Kalyana Sundaram V, Ramakrishnan S, Pincet F, Rothman JE. Synaptophysin Chaperones the Assembly of 12 SNAREpins under each Ready-Release Vesicle. PNAS, 2023.
• Panda A, Giska F, Duncan A, Welch A, Brown C, McAllister A, Parameswaran H, Coleman J, Ramakrishnan S, Guan L, Krishnakumar S, Sansom M, Rothman JE, Gupta K. Lipid vesicle native mass spectrometry for direct determination of oligomeric organization of integral membrane proteins and lipids from bilayer. Nature Methods, 2023 (Cover).
• Thoduvayil S, Weerakkody JS, Kalyana Sundaram V, Topper M, Bera M, Coleman J, Li X, Mariappan M, Ramakrishnan S*. Rapid Quantification of First and Second Phase Insulin Secretion Dynamics using an In vitro Platform for Improving Insulin Therapy. Cell Calcium, 2023.
• Kalyana Sundaram V, Chatterjee A, Bera M, Grushin K, Panda A, Li F, Coleman J, Lee S, Ramakrishnan S, Ernst AM, Gupta K, Rothman JE, Krishnakumar SS. Roles for diacylglycerol in synaptic vesicle priming and release revealed by complete reconstitution of core protein machinery. PNAS, 2023.

• Kalyana Sundaram V, Bera M, Coleman J, Weerakkody J, Krishnakumar SS, Ramakrishnan S*. Native Planar Asymmetric Suspended Membrane for Single-Molecule Investigations: Plasma Membrane on a Chip. Small, 2022 (Cover).
• Ramakrishnan S*, Weerakkody J. Suspended Lipid Bilayer: A Versatile Platform for Nextgen Drug Discovery and Biomedical Applications. Accounts of Materials Research, 2022 (Cover, Invited).
• Bera M, Ramakrishnan S, Coleman J, Rothman JE, Krishnakumar SS. Molecular Determinants of Complexin Clamping and Activation Function. eLife, 2022.

• Li F, Kalyana Sundaram V, Gatta AT, Coleman J, Ramakrishnan S, Krishnakumar SS, Pincet F, Rothman JE. Vesicle capture by discrete self-assembled clusters of membrane-bound Munc13-1. FEBS Letters, 2021.

• Ramakrishnan S, Bera M, Coleman J, Rothman JE, and Krishnakumar SS. Synergistic Roles of Synaptotagmin-1 and Complexin in Calcium Regulated Neuronal Exocytosis. eLife, 2020.
• Ramakrishnan S, Bera M, Coleman J, Krishnakumar SS, Pincet F, and Rothman JE. Synaptotagmin oligomers are necessary and can be sufficient to form a Ca²⁺‐sensitive fusion clamp. FEBS Letters, 2019.
• Heo P, Ramakrishnan S, Coleman J, Rothman J, Fleury JB, Pincet F. Highly Reproducible Physiological Asymmetric Membrane with Freely Diffusing Embedded Proteins in a 3D‐Printed Microfluidic Setup. Small, 2019.
• Coleman J, Jouannot O,# Ramakrishnan S,# Zanetti N, Wang J, Salpietro V, Houlden H, Rothman J, Krishnakumar S. PRRT2 Regulates Synaptic Fusion by Directly Moderating SNARE Complex Assembly. Cell Reports, 2018.
• Ramakrishnan S,# Gohlke A,# Li F, Coleman J, Xu W, Rothman J, Pincet F. High throughput single vesicle fusion using free-standing membranes and automated analysis. Langmuir, 2018.
• Ramakrishnan S, Martin M, Cloitre T, Agarwal V, Cusinier F, Gergely C. Porous silicon microcavities redefine colorimetric ELISA sensitivity for ultrasensitive detection of autoimmune antibodies. Sensors and Actuators B: Chemical, 2018.
• Papa Z, Ramakrishnan S, Martin M, Cloitre T, Zimayi L, Toth Z, Gergely C, Budai J. Ellipsometric behavior of patterned layers – depolarization and quasi absorption. Applied Surface Science, 2017.
• Ramakrishnan S,* Zhu J, Gergely C. Organic-Inorganic Interface simulations for new material discoveries. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2017.
• Papa Z,# Ramakrishnan S,# Martin M, Marquez J, Zimanyi L, Toth Z, Gergely C. Interactions at the silicon-peptide surfaces – Evidence of peptide multilayer assembly. Langmuir, 2016.
• Ramakrishnan S, Jebors S, Martin M, Cloitre T, Agarwal V, Mehdi A, Martinez J, Subra G, Gergely C. Engineered adhesion peptides for improved silicon adsorption. Langmuir, 2015.
• Ramakrishnan S, Martin M, Cloitre T, Firlej L, Gergely C. Design rules for metal binding biomolecules: Understanding of amino acid adsorption on platinum crystallographic facets by density functional theoretical calculations. Physical Chemistry Chemical Physics, 2015.
• Ramakrishnan S, Martin M, Cloitre T, Firlej L, Gergely C. Molecular Mechanism of Selective Binding of Peptides to Silicon Surface. Journal of Chemical Information and Modeling, 2014.
• Ramakrishnan S, Martin M, Cloitre T, Firlej L, Cuisinier FJ, Gergely C. Insights on the facet specific adsorption of amino acids and peptides towards platinum. Journal of Chemical Information and Modeling, 2013.
• Ramakrishnan S, Estephan E, Martin M, Cloitre T & Gergely C. Probing the mechanism of material specific peptides for optical sensors. Proc. SPIE 8765, Bio-MEMS and Medical Microdevices, 2013.
• Salehi H, Middendorp E, Panayotov I, Collart Dutilleul PY, Vegh AG, Ramakrishnan S, Gergely C, Cuisinier F. Confocal Raman data analysis enables identifying apoptosis of MCF-7 cells caused by anticancer drug paclitaxel. Journal of Biomedical Optics, 2013.
• Salehi H, Middendorp E, Végh AG, Ramakrishnan S, Gergely C, Cuisinier FJG. Detection of apoptosis caused by anticancer drug paclitaxel in MCF-7 cells by confocal Raman microscopy. Proceedings of SPIE, 2013.