Publications
A search of PubMed and Google Scholar should give you the latest list of our publications.
Preprints Peer-Reviewed PapersBook ChaptersPopular Writing/ComicsBooksReviews/Opinions
A search of PubMed and Google Scholar should give you the latest list of our publications.
Preprints Peer-Reviewed PapersBook ChaptersPopular Writing/ComicsBooksReviews/Opinions| # | Title | Authors | Citation | First author | Publication | Year | Date | DOI |
|---|---|---|---|---|---|---|---|---|
| Physical Principles of Size and Frequency Scaling of Active Cytoskeletal Spirals | Soni A., Yadav S.A., Athale C.A. | arxiv cond-mat -> arXiv:2508.10114. | Soni Aman | ArXiV | submitted | submitted | 10.48550/arXiv.2508.10114 | |
| Coin-tossing by Kinesin-1 Head and Tail Binding Collectively Drives Microtubule Patterns | Basu J, Singh K, Jannasch A and Athale CA | 2025.08.18.670853 | Basu Jashaswi | BioRXiV | submitted | submitted | 10.1101/2025.08.18.670853 |
| # | Title | Authors | Citation | First author | Publication | Year | Date | DOI |
|---|---|---|---|---|---|---|---|---|
| International multisite
implementation of distributed cell-free protein
biomanufacturing to advance health and research
equity. |
da Silva SJR, Matthews Q, Cazaux S,
Vigar JRJ, Santos BNR, Carvalho DCM, Cranmer LA,
Duplat D, Singh S, Simchi M, Benítez-Bolivar P, de
Lima Cavalcanti TYV, Wu K, Mendes RPG, Kale T,
Divarzak ALL, Bozovicar K, Doucet J, Arce A, Léon C,
Ferrando V, Nguyen J, Ho A, de Lima SC, Bayat P, Guo
Y, Cicek S, Tinafar A, Krokovsky L, Machado LC,
Rayhan A, Iwe IA, Klenov A, de Araujo TPG,
Nascimento JPM, Magalhães JJF, Guevara-Suarez M,
Garcia Canete P, Ayi K, Charania M, Stehelin TE,
Chatfield-Reed K, Paiva MHS, Crandall I, Mazzulli T,
da Luz Wallau G, Silva-Júnior A, Bernal A, Athale
CA, Green AA, Weaver SC, González C, Federici
F, Pena L, Pardee K. |
Sci. Adv. 12, eaeb 7039 |
Severino Jefferson Ribeiro da Silva | Science Advances |
2026 |
29-May-2026 |
10.1126/sciadv.aeb7039 |
|
| Quantification
of Spatial Patterns of Microtubule Transport by
Kinesin-1 Head and Tail |
Jashaswi Basu, Kajal Singh, Anita Jannasch, and Chaitanya A. Athale | Bio-protocol 16(10): e5697. | Jashaswi Basu | BioProtocol |
2026 |
In press |
https://DOI.org/10.21769/BioProtoc.5697 |
|
| Spatial
coin-tossing by kinesin-1 head and tail binding
collectively drives microtubule patterns |
Jashaswi Basu, Kajal Singh, Anita
Jannasch, and Chaitanya A. Athale |
Molecular Biology of the Cell, Vol.
37, No. 3 |
Jashaswi Basu |
Mol. Biol. Cell. |
2026 |
17-Feb-2026 (online) |
https://doi.org/10.1091/mbc.E25-09-0427 |
|
| Mechanics of Escherichia coli cell width homeostasis and bulge dynamics from MreB and septum inhibition | Kale T, Dasgupta R, Inamdar MM, Athale CA. | Mol Biol Cell. 2025 Aug 28:mbcE24120543 |
Kale Tanvi | Mol. Biol. Cell | 2025 | 2025/08/28 | 10.1091/mbc.E24-12-0543 | |
| Classification of first embryonic division stages of multiple Caenorhabditis species by deep learning | Khatri D, Negi P, Athale CA. | NPJ Syst Biol Appl. 2025 Aug 23;11(1):97. doi: 10.1038/s41540-025-00566-2. | Khatri Dhruv | NPJ Syst Biol Appl | 2025 | 2025/08/23 | 10.1038/s41540-025-00566-2 | |
| Translational Enhancer Based Amplification of Toehold Sensors (TacToe) for Improved Sensitivity and Speed of Viral RNA Detection | Kale T, Pednekar R, Cazaux SM, Letelier VF, Vigar JRJ, Federici F, Pardee K, Athale CA. | ACS Synth Biol. 2025 Jun 20;14(6):1920-1930. doi: 10.1021/acssynbio.4c00861. | Kale Tanvi | ACS Synth Biol | 2025 | 2025/05/29 | 10.1021/acssynbio.4c00861 | |
| Physical effects of crowdant size and concentration on collective microtubule polymerization | Basu J, Soni A, Athale CA. | Biophys J. 2025 Mar 4;124(5):789-806. doi: 10.1016/j.bpj.2025.01.020. | Basu Jashaswi | Biophys J | 2025 | 2025/01/31 | 10.1016/j.bpj.2025.01.020 | |
| In vitro evaluation of multi-protein chimeric antigens in effectively clearing the blood stage of Plasmodium falciparum. | Deshmukh B, Khatri D, Kochar SK, Athale C, Karmodiya K. | Vaccine 53:126952. | Deshmukh B. | Vaccine | 2025 | 2025/04/19 | 10.1016/j.vaccine.2025.126952. | |
| Collective effect of Vigna sp. (mung) tubulin GTP hydrolysis rate divergence on microtubule filament assembly | Basu J, Athale CA. | Cytoskeleton (Hoboken). 2025 Apr;82(4):242-259. doi: 10.1002/cm.21923. | Basu Jashaswi | Cytoskeleton (Hoboken) | 2025 | 2024/09/02 | 10.1002/cm.21923 | |
| KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs | Khatri D, Yadav SA, Athale CA. | Bioinformatics. 2024 Sep 2;40(9):btae538. doi: 10.1093/bioinformatics/btae538. | Khatri Dhruv | Bioinformatics | 2024 | 2024/09/03 | 10.1093/bioinformatics/btae538 | |
| Quantification of cell shape, intracellular flows and transport based on DIC object detection and tracking | Kale T, Khatri D, Basu J, Yadav SA, Athale CA. | J Microsc. 2024 Nov;296(2):162-168. doi: 10.1111/jmi.13295. | Kale Tanvi | J Microsc | 2024 | 2024/04/04 | 10.1111/jmi.13295 | |
| Wave-like oscillations of clamped microtubules driven by collective dynein transport | Yadav SA, Khatri D, Soni A, Khetan N, Athale CA. | Biophys J. 2024 Feb 20;123(4):509-524. doi: 10.1016/j.bpj.2024.01.016. | Yadav Shivani A. | Biophys J | 2024 | 2024/01/23 | 10.1016/j.bpj.2024.01.016 | |
| Allometry of Escherichia coli surface area with volume: effect of size variability, filamentation and division dynamics | Kale T, Khatri D, Athale CA. | Phys Biol. 2023 Jun 20;20(4). doi: 10.1088/1478-3975/acdcda. | Kale Tanvi | Phys Biol | 2023 | 2023/06/08 | 10.1088/1478-3975/acdcda | |
| Evolutionary divergence of anaphase spindle mechanics in nematode embryos constrained by antagonistic pulling and viscous forces | Khatri D, Brugière T, Athale CA, Delattre M. | Mol Biol Cell. 2022 May 15;33(6):ar61. doi: 10.1091/mbc.E21-10-0532. | Khatri Dhruv | Mol Biol Cell | 2022 | 2022/03/02 | 10.1091/mbc.E21-10-0532 | |
| Polymerization kinetics of tubulin from mung seedlings modeled as a competition between nucleation and GTP-hydrolysis rates | Jain K, Basu J, Roy M, Yadav J, Patil S, Athale CA. | Cytoskeleton (Hoboken). 2021 Sep;78(9):436-447. doi: 10.1002/cm.21694. | Jain Kunalika | Cytoskeleton (Hoboken) | 2021 | 2022/03/02 | 10.1002/cm.21694 | |
| Self-organized optimal packing of kinesin-5-driven microtubule asters scales with cell size | Khetan N, Pruliere G, Hebras C, Chenevert J, Athale CA. | J Cell Sci. 2021 May 15;134(10):jcs257543. doi: 10.1242/jcs.257543. | Khetan Neha | J Cell Sci | 2021 | 2021/06/03 | 10.1242/jcs.257543 | |
| Collective dynein transport of the nucleus by pulling on astral microtubules during Saccharomyces cerevisiae mitosis | Jain K, Khetan N, Yadav SA, Palani S, Athale CA. | Yeast. 2021 Jun;38(6):352-366. doi: 10.1002/yea.3552. | Jain Kunalika | Yeast | 2021 | 2021/02/06 | 10.1002/yea.3552 | |
| Quantifying Intracellular Particle Flows by DIC Object Tracking | Chaphalkar AR, Jawale YK, Khatri D, Athale CA. | Biophys J. 2021 Feb 2;120(3):393-401. doi: 10.1016/j.bpj.2020.12.013. | Chaphalkar Anushree R. | Biophys J | 2021 | 2020/12/28 | 10.1016/j.bpj.2020.12.013 | |
| Aster swarming by symmetry breaking of cortical dynein transport and coupling kinesins | Khetan N, Athale CA. | Soft Matter. 2020 Sep 30;16(37):8554-8564. doi: 10.1039/d0sm01086c. | Khetan Neha | Soft Matter | 2020 | 2020/08/26 | 10.1039/d0sm01086c | |
| Modeling the tunability of the dual-feedback genetic oscillator |
Joshi YJ, Jawale YK, Athale CA. |
Phys Rev E. 2020 Jan;101(1-1):012417. doi: 10.1103/PhysRevE.101.012417. |
Joshi Yash J |
Phys Rev E |
2020 |
2020/02/20 |
10.1103/PhysRevE.101.012417 |
|
| Collective effects of yeast cytoplasmic dynein based microtubule transport | Jain K , Khetan N , Athale CA | Soft Matter. 2019 Feb 13;15(7):1571-1581. doi: 10.1039/c8sm01434e. | Jain Kunalika | Soft Matter | 2019 | 2019/01/22 | 10.1039/c8sm01434e | |
|
Open Source 3D-printed focussing mechanism for cellphone-based cellular microscopy |
Jawale YK, Rapol U, Athale CA. |
J Microsc. 2019 Feb;273(2):105-114. doi: 10.1111/jmi.12765. Epub 2018 Nov 12. |
Jawale Yash K |
J Microsc |
2019 |
2018/11/13 |
10.1111/jmi.12765 |
|
|
Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association-diffusion models |
Deshpande SA, Pawar AB, Dighe A, Athale CA, Sengupta D. |
Phys Biol. 2017 May 23;14(3):036002. doi: 10.1088/1478-3975/aa6b68. |
Deshpande Sneha A |
Phys Biol |
2017 |
2017/05/24 |
10.1088/1478-3975/aa6b68 |
|
|
Threshold effect of growth rate on population variability of Escherichia coli cell lengths |
Gangan MS, Athale CA. |
R Soc Open Sci. 2017 Feb 22;4(2):160417. doi: 10.1098/rsos.160417. eCollection 2017 Feb. |
Gangan Manasi S |
R Soc Open Sci |
2017 |
2017/04/08 |
10.1098/rsos.160417 |
|
| Automated Multi-Peak Tracking Kymography (AMTraK): A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy |
Chaphalkar AR, Jain K, Gangan MS, Athale CA. |
PLoS One. 2016 Dec 19;11(12):e0167620. doi: 10.1371/journal.pone.0167620. eCollection 2016. |
Chaphalkar Anushree R |
PLoS One |
2016 |
2016/12/20 |
10.1371/journal.pone.0167620 |
|
|
Khetan N, Athale CA. |
PLoS Comput Biol. 2016 Oct 5;12(10):e1005102. doi: 10.1371/journal.pcbi.1005102. eCollection 2016 Oct. |
Khetan Neha |
PLoS Comput Biol |
2016 |
2016/10/06 |
10.1371/journal.pcbi.1005102 |
||
|
What can simulations tell us about GPCRs: Integrating the scales |
Sengupta D, Joshi M, Athale CA, Chattopadhyay A. |
Methods Cell Biol. 2016;132:429-52. doi: 10.1016/bs.mcb.2015.11.007. Epub 2015 Dec 24. |
Sengupta Durba |
Methods Cell Biol |
2016 |
2016/03/02 |
10.1016/bs.mcb.2015.11.007 |
|
|
Thermodynamic and kinetic characterization of transmembrane helix association |
Pawar AB, Deshpande SA, Gopal SM, Wassenaar TA, Athale CA, Sengupta D. |
Phys Chem Chem Phys. 2015 Jan 14;17(2):1390-8. doi: 10.1039/c4cp03732d. Epub 2014 Nov 26. |
Pawar Aiswarya B |
Phys Chem Chem Phys |
2015 |
2014/11/27 |
10.1039/c4cp03732d |
|
|
Collective behavior of minus-ended motors in mitotic microtubule asters gliding toward DNA |
Athale CA, Dinarina A, Nedelec F, Karsenti E. |
Phys Biol. 2014 Feb;11(1):016008. doi: 10.1088/1478-3975/11/1/016008. Epub 2014 Jan 29. |
Athale Chaitanya A |
Phys Biol |
2014 |
2014/01/31 |
10.1088/1478-3975/11/1/016008 |
|
|
Spatial and temporal sensing limits of microtubule polarization in neuronal growth cones by intracellular gradients and forces |
Mahajan S, Athale CA. |
Biophys J. 2012 Dec 19;103(12):2432-45. doi: 10.1016/j.bpj.2012.10.021. Epub 2012 Dec 18. |
Mahajan Saurabh |
Biophys J |
2012 |
2012/12/25 |
10.1016/j.bpj.2012.10.021 |
|
|
Population length variability and nucleoid numbers in Escherichia coli |
Athale CA, Chaudhari H. |
Bioinformatics. 2011 Nov 1;27(21):2944-8. doi: 10.1093/bioinformatics/btr501. Epub 2011 Sep 19. |
Athale Chaitanya A |
Bioinformatics |
2011 |
2011/09/21 |
10.1093/bioinformatics/btr501 |
|
|
Regulation of microtubule dynamics by reaction cascades around chromosomes |
Athale CA, Dinarina A, Mora-Coral M, Pugieux C, Nedelec F, Karsenti E. |
Science. 2008 Nov 21;322(5905):1243-7. doi: 10.1126/science.1161820. Epub 2008 Oct 23. |
Athale Chaitanya A |
Science |
2008 |
2008/10/25 |
10.1126/science.1161820 |
|
|
Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer |
Zhang L, Athale CA, Deisboeck TS. |
J Theor Biol. 2007 Jan 7;244(1):96-107. doi: 10.1016/j.jtbi.2006.06.034. Epub 2006 Jul 27. |
Zhang Le |
J Theor Biol |
2007 |
2006/09/05 |
10.1016/j.jtbi.2006.06.034 |
|
|
The effects of EGF-receptor density on multiscale tumor growth patterns |
Athale CA, Deisboeck TS. |
J Theor Biol. 2006 Feb 21;238(4):771-9. doi: 10.1016/j.jtbi.2005.06.029. Epub 2005 Aug 26. |
Athale Chaitanya A |
J Theor Biol |
2006 |
2005/08/30 |
10.1016/j.jtbi.2005.06.029 |
|
|
Inferring a system model of subcellular topoisomerase II beta localization dynamics |
Athale CA, Christensen MO, Eils R, Boege F, Mielke C. |
OMICS. 2004 Summer;8(2):167-75. doi: 10.1089/1536231041388339. |
Athale Chaitanya A |
OMICS |
2004 |
2004/07/23 |
10.1089/1536231041388339 |
| # | Authors | Year | Title | Journal | Volume, issue | DOI |
|---|---|---|---|---|---|---|
| Tanvi Kale, Dhruv Khatri, Jashaswi Basu, Shivani A Yadav, C. A. Athale | 2024 | Quantification of cell shape, intracellular flows and transport based on DIC object detection and tracking. | J. Microsc. | Volume 296, Issue 2 Special Issue: Imaging ONEWORLD November 2024 Pages 162-168 | doi:10.1111/jmi.13295 | |
| Eils R. and Athale, C.A. | 2003 | Computational Imaging in Cell Biology. | J. Cell Biol. | 161(3):477-481 | https://doi.org/10.1083/jcb.200302097 |
| # | Authors | Year | Chapter Title | Book title | Editor | Publisher | Link | DOI |
|---|---|---|---|---|---|---|---|---|
| N. Khetan and C. A. Athale | 2020 | Flocking, swirling and spinning stars in a cell. | Art of Theoretical Biology | Franziska Matthäus, Sebastian Matthäus, Sarah Harris, Thomas Hillen | Springer, Cham | https://link.springer.com/chapter/10.1007/978-3-030-33471-0_43 | https://doi.org/10.1007/978-3-030-33471-0_43 | |
| Athale C.A. | 2011 | Modelling the Spatial Pattern Forming Modules in Mitotic Spindle Assembly. | Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology | Werner Dubitzky, Jennifer Southgate, Hendrik Fuß | Springer, New York, NY, USA | https://link.springer.com/book/10.1007/978-1-4419-7964-3 | https://doi.org/10.1007/978-1-4419-7964-3 | |
| Athale C.A. and Deisboeck, T.S. | 2007 | Chapter 193: Simulating the impact of Angiogenesis on multiscale tumor growth dynamics using an agent-based Model. | Endothelial Biomedicine | Cambridge University Press, New York, NY, USA | ||||
| Athale, C., Gebhard, M. and Eils, R. | 2002 | Examining Spatio-Temporal Dynamics in Cell Nuclei by Image Processing Methods. | Science, Technology and Education of Microscopy: An Overview, vol. I | A. Méndez-Vilas (Ed.) | FORMATEX Microscopy Book Series. |
| # | Authors | Year | Book title | Publisher | Link | DOI |
|---|---|---|---|---|---|---|
| Athale C.A. | in prep. | Cellular biophysics: a framework for quantitative cell biology | Taylor and Francis |
| # | Authors | Year | Title | Publisher/Journal | Link |
|---|---|---|---|---|---|
| Tanvi Kale and Chaitanya A. Athale. Illustrator: Madhumita Laddha | 2025 | Balloon Physics: Bacteria v/s Antibiotics | Self | Download and Print (its free!) [PDF], [PNG] | |
| Staff reporter with inputs from C.A. Athale | 2025 | India Science Fest 2025 stall on balloon physics, bacteria and antibiotics | IISER Pune news | India Science Fest | |
| Athale C.A. | 2016 | Open Source Synthetic Biology for (Not Just) Undergraduates | IndiaBioscience | IndiaBioscience Blog | |
| Athale C.A. | 2015 | Originality in scientific writing: Avoiding the slippery slope of plagiarism | India Bioscience | IndiaBioscience Blog |