Publications

Peer Reviewed Papers // *RXiv Preprints //Datasets // Pre-Prints // Book Chapters// Conference Proceedings // Popular Science //Hindi / Marathi writings //Miscellaneous

    Pre-Prints

  1. Basu J and Athale CA. (2024) Microtubule polymerization tuned by macromolecular crowdant size and density. Posted February 07, 2024. https://doi.org/10.1101/2024.02.02.578534
  2. Dhruv Khatri and Chaitanya A. Athale (2024) Deep learning based reconstruction of embryonic cell-division cycle from label-free microscopy time-series of evolutionarily diverse nematodes. BioRxiv https://doi.org/10.1101/2024.05.09.593369
  3. Tanvi Kale, Ryth Dasgupta, Mandar M Inamdar,  Chaitanya A Athale (2024) Mechanics of E. coli cell width homeostasis and bulging dynamics from MreB and septum inhibition. BioRXiV https://doi.org/10.1101/2024.11.22.624946
    Peer-reviewed papers (from 2009)

    2024

  1. Jashaswi Basu and Chaitanya A. Athale (2024) Collective effect of Vigna sp. (mung) tubulin GTP hydrolysis rate divergence on microtubule filament assembly. Cytoskeleton doi/10.1002/cm.21923
  2. Dhruv Khatri, Shivani A. Yadav, Chaitanya A. Athale (in press) KnotResolver: Tracking self-intersecting filaments in microscopy using directed graphs. BioInformatics [accepted] ArXiVqbio>arXiv:2404.12029 https://doi.org/10.48550/arXiv.2404.12029
  3. Tanvi Kale, Dhruv Khatri, Jashaswi Basu, Shivani A Yadav, Chaitanya A Athale (2024) Quantification of cell shape, intracellular flows and transport based on DIC object detection and tracking. J. Microsc. http://doi.org/doi: 10.1111/jmi.13295
  4. Shivani Yadav, Dhruv Khatri, Aman Soni, Neha Khetan and Chaitanya A. Athale (2024) Wave-like oscillations of clamped microtubules driven by collective dynein transport. Biophys. J. 123(4): 509-524. DOI: 10.1016/j.bpj.2024.01.016 BioRxiv 2022.09.11.507451. [News item on NatureIndia Blog] [Pudhari (marathi daily newspaper) १-मार्च २०२४]

    5. 2023

  5. Tanvi Kale, Dhruv Khatri and Chaitanya A Athale (2023)
    Allometry of Escherichia coli surface area with volume: effect of size variability, filamentation and division dynamics. Phys. Biol. 20 046007. Published 20 June 2023 DOI:10.1088/1478-3975/acdcda
    6. 2022

  6. Dhruv Khatri*, Thibault Brugiere*, Chaitanya A. Athale and Marie Delattre (2022) Evolutionary divergence of anaphase spindle mechanics in nematode embryos constrained by antagonistic pulling and viscous forces. Mol. Biol. Cell Vol 33, No 6.
  7. Kunalika Jain, Jashaswi Basu, Megha Roy, Jyoti Yadav, Shivprasad Patil, Chaitanya A. Athale (2022) Polymerization kinetics of tubulin from mung seedlings modeled as a competition between nucleation and GTP-hydrolysis rates. Cytoskeleton, Vol 78, Issue 9, p436-447 .
  8. Tanvi Kale, Shivam S. Chitnis and Chaitanya A. Athale (2022) Scaling of Cell Growth and Macromolecules* Quantitative Understanding of Cellular Size- and Time-Scales. Resonance, March 2022, Volume 27, Issue 3 pp 325-337.
    9. 2021

  9. Khetan N, Pruliere G, Hebras C, Chenevert J, Chaitanya A. Athale (2021) Self-organized optimal packing of kinesin-5-driven microtubule asters scales with cell size. J Cell Sci. 134(10):jcs257543.
  10. Kunalika Jain, Shivani A. Yadav and Chaitanya A. Athale (2021) Number Dependence of Microtubule Collective Transport by Kinesin and Dynein. J. Indian Inst. Sci. https://doi.org/10.1007/s41745-020-00212-2
  11. Kunalika Jain*, Neha Khetan*, Shivani A. Yadav, Saravanan Palani, Chaitanya A. Athale (2021) Collective Dynein Transport of the Nucleus by Pulling on Astral MTs during Saccharomyces cerevisiae. Yeast. doi.org/10.1002/yea.3552 (* joint first authors)
  12. Anushree R. Chaphalkar*, Yash K. Jawale*, Dhruv Khatri, Chaitanya A. Athale (2021) Quantifying Intracellular Particle Flows by DIC Object Tracking. Biophysical JournalVolume 120, Issue 3, 2 February 2021, Pages 393-401 https://doi.org/10.1016/j.bpj.2020.12.013. (* joint first authors)

    13. 2020

  13. Khetan N and Athale C.A. (2020) Aster Swarming by Symmetry Breaking of Cortical Dynein Transport and Coupling Kinesins. Soft Matter 2020,16, 8554-8564 DOI: 10.1039/D0SM01086C [arXiv:2005.05686]
  14. Joshi Y.J., Jawale Y.K., Athale C.A. (2020) Tunability of the Dual Feedback Genetic Oscillator Modeled by the Asymmetry in Transcription and Translation. Phys. Rev. E 101, 012417 – Published 29 January 2020 [arXiv:1905.06301] 
    15. 2019

  15. Jain K., Khetan N and Athale C.A. (2019) Collective effects of yeast cytoplasmic dynein based microtubule transport. Soft Matter, 2019,15, 1571-1581 DOI: 10.1039/C8SM01434E
    Setup of the dynein gliding assay in simulation and experiment

    Dynein Collective Transport

  16. Neha Khetan, Shagun Maheshwari, Chaitanya A. Athale (2019) Mechanics of Hydra Detachment from Subrates: The Role of Substrate Rigidity and Starvation. Proc. Ind. Natl. Sci. Acad (INSA) 58(1): 291-299 [PDF]

    17. A stereo microscope image of a Hydra magnipapillata individual
    A stereo microscope image of a Hydra magnipapillata individual (Khetan, Maheshwari and Athale)
  17. Khetan N. and Athale C.A. (in press) Flocking, swirling and spinning stars in a cell. Art of Theoretical Biology, Springer.
  18. Yash Jawale, Umakant Rapol and Chaitanya A. Athale (2019) Open Source 3D printed focussing mechanism (3DPFM) for cellphone based cellular microscopy. J. Microsc. 273(2):105-114 https://doi.org/10.1111/jmi.12765

    Cellphone Microscope with Focussing Mechanism

    Cellphone Microscope with Focussing Mechanism (Jawale et al. J. Micrscosc.)

    19. 2018

    2017

  19. Deshpande, S; Pawar, A; Dighe, A; Athale, C. A.; Sengupta, D. (2017) Role of Spatial Inhomogenity in GPCR Dimerisation Predicted by Receptor Association-Diffusion Models. Phys. Biol. Volume 14, Number 3

    Receptor dimrerization dynamics: Monte Carlo model with spatial inhomogeneities (Deshpande et al. 2017 Phys. Biol.)

  20. Gangan M.S. and Athale C.A. (2017) Threshold Effect of Growth Rate on Population Variability of Escherichia coli Cell Lengths Roy. Soc. open science DOI: 10.1098/rsos.160417 22-Feb-2017, Dataset; https://datadryad.org/stash/dataset/doi:10.5061/dryad.2bs69

    21. E. coli cells in a microfluidics channel were analyzed to obtain a division-stage depdenent cell size as seen in the histogram (REF: Gangan and Athale, 2017).

    2016

  21. Chaphalkar AR, Jain K, Gangan MS, Athale CA (2016) Automated Multi-Peak Tracking Kymography (AMTraK): A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy. PLoS ONE 11(12): e0167620. 19-Dec-2016  doi:10.1371/journal.pone.0167620 [Paper] [Software]AMTraK Quantification of vesicle transport in axons
  22. Khetan N. and Athale C.A. (2016) A Motor-Gradient and Clustering Model of the Centripetal Motility of MTOCs in Meiosis I of Mouse Oocytes PLoS Comput Biol 12(10): e1005102. 5-Oct-2016 Online full-text
    MTOC convergence in Mouse-Ocyte Meiosis I
  23. Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, et al. (2016) Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLoS ONE 11(3): e0150182. doi:10.1371/journal.pone.0150182 [the iGEM2015 team from IISER Pune is part of the consortium]
  24. Durba Sengupta, Manali Joshi, C. A. Athale, Amitabha Chattopadhyay. What can simulations tell us about GPCRs: Integrating the scales. Methods in Cell Biology. Volume 132, 2016, Pages 429Ð452 [abstract]
    25. 2015

  25. Aiswarya B. Pawar, Sneha A. Deshpande, Srinivasa M. Gopal, Tsjerk A. Wassenaar, C. A. Athale and Durba Sengupta* (2015) Thermodynamic and kinetic characterization of transmembrane helix association. Phys. Chem. Chem. Phys., 17:1390-1398 [abstract]
    26. 2014

  26. C.A. Athale*, Dinarina A., Nedelec F. and Karsenti E. (2014) Collective behavior of minus-ended motors in mitotic microtubule asters gliding towards DNA. Phys. Biol. 11: 016008. [paper][Full text on ArXiv]
    27. 2013

    2012

  27. Mahajan S. & C.A. Athale* (2012) Spatial and Temporal Sensing Limits of Microtubule Polarization in Neuronal Growth Cones by Intracellular Gradients and Forces. Biophys. J. 103(12) 2432-2445, 19 December 2012 [abstract][Full text on ArXiv]
    28. 2011 to 2009

  28. Athale C.A.* & Chaudhari HC (2011) Population Length Variability and Nucleoid Numbers in E. coli. Bioinformatics. 27(21): 2944-2948. [Abstract] [PDF] [Supplementary material]
    Pre-2009 (prior to joining IISER Pune)

  1. Athale CA , Dinarina A, Mora-Coral M, Pugieux C, Nedelec F, Karsenti E.* Regulation of microtubule dynamics by reaction cascades around chromosomes. Science. 2008 Nov 21;322(5905):1243-7.[pdf][supplementary material]S. M. Hurtley, Modeling Subcellular Morphogenesis. Sci. Signal. 1, ec408 (2008).
  2. Zhang L, Athale CA , Deisboeck TS.* Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer. J Theor Biol. 2007 Jan 7;244(1):96-107. Epub 2006 Jul 27.
  3. Athale CA , Deisboeck TS. The effects of EGF-receptor density on multiscale tumor growth patterns. J Theor Biol. 2006 Feb 21;238(4):771-9. Epub 2005 Aug 26. [pdf]
  4. Athale C , Mansury Y, Deisboeck TS. Simulating the impact of a molecular ‘decision-process’ on cellular phenotype and multicellular patterns in brain tumors. J Theor Biol. 2005 Apr 21;233(4):469-81. Epub 2004 Nov 30. Erratum in: J Theor Biol. 2006 Apr 21;239(4):516-7. PMID: 15748909 [pdf]
  5. Volz D., Martin Eigel M., Athale C. , Bastian P., Hermann H., Kappel C., Eils R.: Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells. CMSB (Computational Methods in Systems Biology, Paris selected paper in LNCS 3082 Springer 2005, ISBN 3-540-25375-0) 2004: 161-171. [abstract][pdf partial]
  6. Bacher CP, Reichenzeller M, Athale C , Herrmann H, Eils R.4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin – poor tracks. BMC Cell Biol. 2004 Nov 23;5:45. [pdf]
  7. Athale CA , Christensen MO, Eils R, Boege F, Mielke C.Inferring a system model of subcellular topoisomerase II beta localization dynamics. OMICS. 2004 Summer;8(2):167-75.
  8. Eils R, Athale C. Computational imaging in cell biology. J Cell Biol. 2003 May 12;161(3):477-81. Review. [html]
  1. Neha Khetan and Chaitanya A. Athale (2020) Flocking, Swirling and Spinning Stars in a Cell. Book Chapter in The Art of Theoretical Biology pp 86-87 [link]
  2. Athale C.A. (2011) Modelling the Spatial Pattern Forming Modules in Mitotic Spindle Assembly. In “Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology” (Eds. Werner Dubitzky, Jenny Southgate, Hendrik Fuss).
  3. Athale, C.A. & Deisboeck, T.S. (2007) Simulating the impact of Angiogenesis on multiscale tumor growth dynamics using an agent-based Model. In “Endothelial Biomedicine” (William C. Aird (ed)), Cambridge University Press, New York, NY, 2007, Chapter 193.
  4. Athale, C. , Gebhard, M. and Eils, R. (2002). Examining Spatio-Temporal Dynamics in Cell Nuclei by Image Processing Methods. In “Science, Technology and Education of Microscopy: An Overview”, vol. I (ed. A. MŽndez-Vilas): FORMATEX Microscopy Book Series.
Reports, abstracts and data-sets

  1. Snehal Kadam, Yash Jawale, Swapnil Bodkhe, Prashant Uniyal, Ira Phadke, Prachiti Moghe, Harsh Gakhare, Siddhesh Zadey, Gayatri Mundhe, Rahul Biradar, Manasi S. Gangan, Neha Khetan and Chaitanya A. Athale (2016) Mycobacterium Revelio: Characterizing and Modeling Genetic Circuit Components towards a Bacterial Detection Tool. iGEM Report. 27, 2016 by PLOS Collections in iGEM 2015 [PLOS]
  2. Chaitanya A. Athale and Eric Karsenti. Patterning of regulatory gradients by reaction-diffusion cascades around chromosomes in Xenopus egg-extracts (Poster) CSHL/WT Computational Cell Biology, Wellcome Trust, Hinxton, Cambridge, UK. 26-30th March 2008
  3. Chaitanya A. Athale, Ana Dinarina, Francois Nedelec and Eric Karsenti. Modeling the Effect of Microtubule Stabilization Gradients on Centrosomal Spindle Assembly (Poster) Computational Cell Biology, Cold Spring Harbour Labs, USA 6-9 Mar 2007
  4. Chaitanya A. Athale. Shaping a Mitotic Aster by Chemical Gradients (Poster) Biolateral Meeting, Paris, 18-19 Jan 2007
  5. Chaitanya A. Athale.Poster, Principles of Self-Organization in Living Matter, EMBL Heidelberg, 2-5 Jun 2006
  6. Chaitanya A. Athale. Poster, 6th European Society of Mathematical and Theoretical Biology Conference, Dresden, 18-22 Jul 2005.
  7. Gangan, Manasi S. and Athale, Chaitanya A. (2018) Data from: Threshold effect of growth rate on population variability of Escherichia coli cell lengths. Dryad https://datadryad.org/stash/dataset/doi:10.5061/dryad.2bs69 This includes all supporting videos and code.
Book reviews

  1. Athale C.A. (2013) Book Review: “Physics of the Human Body” by Richard P. McCall. Curr. Sci., 104(6): 773.
  2. Athale C.A. (2004) Rezenssion: Essential Mathematical Biology , 5/2004, BIOspektrum. (german) [PDF]
Miscellaneous

  1. Meeting report: Raghunathan A. & Athale C.A. (2017) Modelling natural and synthetic biological networks. Current Science 113: 10 October 2017, 113 (07)
  2. Athale C.A. Open Source Synthetic Biology for (not just) Undergraduates. 17-Mar-2016. IndiaBioscience.org
  3. Athale C.A. (2015) Originality in scientific writing: Avoiding the slippery slope of plagiarism. IndiaBioscience.org
  4. Athale C.A. Web report: Cell-simulations portal ,Web report: Monte Carlo cell simulations ,Web report: Software for cell simulation , Genome Biology
  5. Manasi S. Gangan, Athale C. A. Asymmetric Cell Growth and Nucleoid Displacement in Escherichia coli. BioRxiv [doi: https://doi.org/10.1101/682435] 26-June-2019
  6. Athale C.A. Effect of Replication Fork Dynamics on Escherichia coli Cell Size [arXiv:1601.02240] Updated: v4 on 20 May 2019

Book Chapters

Datasets

Popular Science

Talk on Synthetic Biology (कृत्रिम जैव शास्त्र)

Popular article on molecular motors पेश्यांमधले यांत्रिक मोटार – पुढारी

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