Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets, Wanxin Li, Jules Mirone, Ashok Prasad, Nina Miolane, Carine Legrand, Khanh Dao Duc, Frontiers in Bioinformatics, Volume 3, 1211819, 2023 https://doi.org/10.3389/fbinf.2023.1211819
Exact distribution of the vesicle burst size in synaptic transmission, Krishna Rijal, Nicolas I.C. Müller, Eckhard Friauf, Abhyudai Singh, Ashok Prasad, Dibyendu Das, bioRxiv 2022.12.28.522121; doi: https://doi.org/10.1101/2022.12.28.522121
Li W, Prasad A, Miolane N, Dao Duc K, editors. Using an Elastic Metric for Statistical Analysis of Tumor Cell Shape Heterogeneity. Geometric Science of Information, 6th International Conference; 2023; St. Malo, France. (Peer reviewed conference proceedings)
Tahtamouni L, Alzghoul A, Alderfer S, Sun J, Ahram M, Prasad A, Bamburg J. The role of activated androgen receptor in cofilin phospho-regulation depends on the molecular subtype of TNBC cell line and actin assembly dynamics. PLoS One. 2022 Dec 30;17(12):e0279746. doi: 10.1371/journal.pone.0279746. PMID: 36584207; PMCID: PMC9803305.
Alderfer S, Sun J, Tahtamouni L, Prasad A. Morphological signatures of actin organization in single cells accurately classify genetic perturbations using CNNs with transfer learning. Soft Matter. 2022 Nov 9;18(43):8342-8354. doi: 10.1039/d2sm01000c.
Phogat R, Parmananda P, Prasad A. Intensity dependence of sub-harmonics in cortical response to photic stimulation. J Neural Eng. 2022 Jul 29;19(4). doi: 10.1088/1741-2552/ac817f. PMID: 35839731.
Rijal, Krishna and Prasad, Ashok and Singh, Abhyudai and Das, Dibyendu, Exact Distribution of Threshold Crossing Times for Protein Concentrations: Implication for Biological Timekeeping, Phys. Rev. Lett. 128 (4), 048101 (2022) IF=9.16
Zahran, S.; Altringer, L.; Prasad, A. The Longevity-Frailty Hypothesis: Evidence from COVID-19 Death Rates in Europe. Int. J. Environ. Res. Public Health 2022, 19, 2434. https://doi.org/10.3390/ijerph19042434
Mannheimer, J.D., Prasad, A. & Gustafson, D.L. Predicting chemosensitivity using drug perturbed gene dynamics. BMC Bioinformatics 22, 15 (2020). https://doi.org/10.1186/s12859-020-03947-y
Krishna Rijal, Ashok Prasad, and Dibyendu Das, Protein hourglass: Exact first passage time distributions for protein thresholds, Phys. Rev. E 102, 052413 (2020) https://doi.org/10.1103/PhysRevE.102.052413
Elaheh Alizadeh, Jordan Castle, Analia Quirk, Cameron Taylor, Wenlong Xu, Ashok Prasad. Cellular morphological features are predictive markers of cancer cell state. Computers in Biology and Medicine, Nov;126:104044 (2020) doi: 10.1016/j.compbiomed.2020.104044; PMID: 33049477.
Werner A, Broeckling CD, Prasad A, Peebles CAM. A comprehensive time-course metabolite profiling of the model cyanobacterium Synechocystis sp. PCC 6803 under diurnal light:dark cycles. Plant J. 99(2):379-88. (2019)
Mannheimer JD, Duval DL, Prasad A, Gustafson DL. A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies. BMC Medical Genomics. 12(1):87. (2019)
Alizadeh E, Xu W, Castle J, Foss J, Prasad A., “TISMorph: A tool to quantify texture, irregularity and spreading of single cells. PLoS One. 14(6):e0217346, (2019).
Prasad, Ashok and Alizadeh, Elaheh, Cell form and function: interpreting and controlling the shape of adherent cells, Trends in Biotechnology, 37(4), 347-357, April 01, (2019)
Xu, Wenlong, Alizadeh, Elaheh, Prasad, Ashok, “,Force Spectrum Microscopy Using Mitochondrial Fluctuations of Control and ATP-Depleted Cells, Biophysical Journal, 114(12), 2933-2944, (2018)
Joshi CJ, Peebles C, Prasad A. Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction. Algal Research, v27, pp295-310, (2017)
Prasad, A., If Life Keeps Throwing Curveballs, You’ve Probably Reached a Wall.
Biophysical journal. 112(6):1047-1049, (2017).
Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation, SW Smeal, MA Schmitt, RR Pereira, A Prasad, JD Fisk, Virology 500, 259-274 (2017)
Simulation of the M13 life cycle II: Investigation of the control mechanisms of M13 infection and establishment of the carrier state, SW Smeal, MA Schmitt, RR Pereira, A Prasad, JD Fisk, Virology 500, 275-284 (2017)
Measuring systematic changes in invasive cancer cell shape using Zernike moments
E Alizadeh, SM Lyons, JM Castle, A Prasad, Integrative Biology 8 (11), 1183-1193 (2016)
June I Medford, Ashok Prasad Towards programmable plant genetic circuits, The Plant Journal 87(1), 139-148, (2016)
Samanthe M. Lyons, Elaheh Alizadeh, Joshua Mannheimer, Katherine Schuamberg, Jordan Castle, Bryce Schroder, Philip Turk, Douglas Thamm, Ashok Prasad, Changes in Cell Shape Are Correlated with Metastatic Potential in Murine and Human Osteosarcomas, Biology Open 5: 289-299; doi: 10.1242/bio.013409 (2016)
Katherine A. Schaumberg, Mauricio S. Antunes, Tessema K. Kassaw, Wenlong Xu, Christopher S. Zalewski, June I. Medford, Ashok Prasad, Quantitative characterization of genetic parts and circuits for plant synthetic biology, Nature Methods, 13, 94-100 (2016).
June Medford and Ashok Prasad, Plant Synthetic Biology takes root, Invited Perspective, Science, 346 no. 6206 pp. 162-163, October (2014)
Chintan J. Joshi and Ashok Prasad, Epistatic interactions among metabolic genes depend upon environmental conditions, Molecular Biosystems, 10 (10), 2578 – 2589, doi: 10.1039/C4MB00181H (2014)
S. M. Lyons, W. Xu, J. Medford, Ashok Prasad, Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems. PLoS Computational Biology, 10(3): e1003533. doi:10.1371/journal.pcbi.1003533 (2014)
Dipjyoti Das, Dibyendu Das and Ashok Prasad, Giant number fluctuations in microbial ecologies, Journal of Theoretical Biology, 308, 96-104, (2012)
Dustin Robert Berger, Ketul Popat, Ashok Prasad, PCL Nanopillars Vs Nanofibers: A Contrast in Progenitor Cell Morphology, Proliferation, and Fate Determination, Advanced Engineering Materials, 14(6), B351-B356, (2012)
S. M. Lyons, Ashok Prasad, Cross-talk and information transfer in mammalian and bacterial signaling, PLoS ONE 7(4): e34488. doi:10.1371/journal.pone.0034488 (2012)
Ashok Prasad, Computational Modeling of Signal Transduction Networks: A Pedagogical Exposition, Chapter 10 in “Computational Modeling of Signaling Networks”, Methods of Molecular Biology Series, edited by X. Liu and M. Betterton, Springer. 2011
A. W. C. Lau, Ashok Prasad and Z. Dogic: Condensation of isolated semi-flexible filaments driven by depletion interactions, European Physical Letters 87, 48006 (2009)
http://www.iop.org/EJ/abstract/-search=69463715.6/0295-5075/87/4/48006
Ashok Prasad, Julie Zikherman, Jayajit Das, Jeroem Roose, Arthur Weiss, Arup Chakraborty: Origin of the sharp boundary that discriminates positive and negative selection in thymocytes, Proceedings of the National Academy of Sciences 106, 528-533 (2009).
Vivek B. Shenoy, Dhananjay T. Tambe, Ashok Prasad and Julie A. Theriot
A kinematic description of the trajectories of Listeria monocytogenes propelled by actin comet tails, Proceedings of the National Academy of Sciences 104, 8229 (2007).
Ashok Prasad, Howard Stone and Jane’ Kondev: Drift in Supported Membranes, Physics of Fluids, 19, 113103 (2007). http://link.aip.org/link/?PHFLE6/19/113103/1
Yuko Hori, Ashok Prasad and Jane’ Kondev: Stretching short biopolymers by fields and forces, Physical Review E 75, 041904 (2007). http://pre.aps.org/abstract/PRE/v75/i4/e041904
Ashok Prasad, Yuko Hori and Jane’ Kondev: Elasticity of semiflexible polymers in two dimensions, Physical Review E 72, 041918 (2005).
Prasad Lab at Colorado State University 