Link to google scholar page.

Research Articles

*: corresponding author

Research as Head of Laboratory

[33] V. Gligorovski, M. Labagnara, S. J. Rahi*,
Light-directed evolution of dynamic, multi-state, and computational protein functionalities,
preprint: bioRxiv 2024.02.28.582517 (2024), link
[32] M. Koziński, D. Oner, J. Gwizdala, C. Beigelman, P. Fua, A. Koutsokera, A. Casutt, M. De Palma, J.-D. Aubert, H. Bischof, C. von Garnier, S. J. Rahi, M. Urschler, N. Mansouri*,
Harnessing deep learning to detect Bronchiolitis Obliterans Syndrome from chest CT,
preprint: medRxiv 2024.02.07.24302414 (2024), link
[31] M. I. Villalba, V. Gligorovski, S. J. Rahi, R. G. Willaert, S. Kasas*,
A simplified version of rapid susceptibility testing of bacteria and yeasts using optical nanomotion detection,
Frontiers in Microbiology 15, 1328923 (2024), link
[30] C. Jones*, M. Barzegar-Keshteli, A. Gross, G. Obozinski, S. J. Rahi,
A graph-matching approach to tracking neurons in freely-moving C. elegans,
preprint: bioRxiv 2023.11.30.569341 (2023), link
[29] J. Ma, R. Xie, S. Ayyadhury, C. Ge, A. Gupta, R. Gupta, S. Gu, Y. Zhang, G. Lee, J. Kim, W. Lou, H. Li, E. Upschulte, T. Dickscheid, J. G. de Almeida, Y. Wang, L. Han, X. Yang, M. Labagnara, V. Gligorovski, M. Scheder, S. J. Rahi, C. Kempster, A. Pollitt, L. Espinosa, T. Mignot, J. M. Middeke, J.-N. Eckardt, W. Li, Z. Li, X. Cai, B. Bai, N. F. Greenwald, D. Van Valen, E. Weisbart, B. A. Cimini, Z. Li, C. Zuo, O. Brück, G. D. Bader, B. Wang*,
The multimodality cell segmentation challenge: towards universal solutions,
Nature Methods, in press (2024), link
preprint: arXiv 2308.05864 (2023), link
[28] C. F. Park+, M. Barzegar-Keshteli+, K. Korchagina, A. Delrocq, V. Susoy, C. L. Jones, A. D. T. Samuel, S. J. Rahi*,
Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation,
Nature Methods 21, 142-149 (2024), link
preprint: bioRxiv 2022.03.15.484536 (2022), link
[27] V. Gligorovski, A. Sadeghi, S. J. Rahi*,
Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor,
Nature Communications 14, 3810 (2023), link
preprint: bioRxiv 2020.08.16.253310 (2020), link
[26] L. Bürgy, M. Weigert, G. Hatzopoulos, M. Minder, A. Journé, S. J. Rahi, Pierre Gönczy*,
CenFind: A deep-learning pipeline for efficient centriole detection in microscopy datasets,
BMC Bioinformatics, 24, 120 (2023), link
[25] E. Jamshidi, A. Asgary, A. Yazdiyadeh Kharrazi, N. Tavakoli, A. Zali, M. Mehrazi, M. Jamshidi, B. Farrokhi, A. Maher, C. von Garnier, S. J. Rahi*, N. Mansouri*,
Personalized predictions of adverse side effects of the COVID-19 vaccines,
Heliyon 9, e12753 (2023), link
[24] E. Jamshidi, A. Asgary, P. Shafiekhani, Y. Khajeamiri, K. Mohamed, H. Esmaily, S. J. Rahi, N. Mansouri*,
Longevity of immunity following COVID-19 vaccination: A comprehensive review of currently approved vaccines,
Hum. Vacci. Immunother. 18, e2037384 (2022), link
[23] E. Jamshidi+, A. Asgary+, N. Tavakoli+, A. Zali, S. Setareh, H. Esmaily, S. H. Jamaldini, A. Daaee, A. Babajani, M. A. Sendani Kashi, M. Jamshidi, S. J. Rahi*, N. Mansouri*,
Using machine learning to predict mortality for COVID-19 patients on day zero in the ICU,
Frontiers in Digital Health 3, 681608 (2022), link
preprint: medRxiv 2021.02.04.21251131 (2021), link
[22] E. Jamshidi+ , A. Asgary+ , N. Tavakoli+ , A. Zali, F. Dastan, A. Daaee, M. Badakhshan, H. Esmaily, S. H. Jamaldini, S. Safari, E. Bastanhagh, A. Maher, A. Babajani, M. Mehrazi, M. A. Sendani Kashi, M. Jamshidi, M. H. Sendani, S. J. Rahi*, N. Mansouri*,
Symptom prediction and mortality risk calculation for COVID-19 using machine learning,
Frontiers in Artificial Intelligence 4, 673527 (2021), link
preprint: medRxiv 2021.02.04.21251143 (2021), link
[21] A. Sadeghi, R. Dervey, V. Gligorovski, M. Labagnara, S. J. Rahi*,
The optimal checkpoint strategy balancing risk and speed predicts DNA damage checkpoint override times,
Nature Physics, 18, 832-839 (2022), link
preprint: bioRxiv 2020.08.14.251504 (2020), link
[20] N. Dietler+, M. Minder+, V. Gligorovski+, A. M. Economou, D. A. H. L. Joly, A. Sadeghi, C. H. M. Chan, M. Koziński, M. Weigert, A.-F. Bitbol, S. J. Rahi*,
A convolutional neural network segments yeast microscopy images with high accuracy,
Nature Communications 11, 5723 (2020), link
preprint: bioRxiv 2020.05.11.082594 (2020), link
[19] V. Susoy, W. J. Joyce, S. J. Rahi*,
sto-3 is expressed in R4BL/R and R8BL/R, male-specific ray neurons in C. elegans,
microPublication Biology (2019), link

Research as Independent Fellow

[18] E. V. Nikolaev, S. J. Rahi, E. D. Sontag*,
Subharmonics and chaos in simple periodically forced biomolecular models,
Biophys J. 114, 1232-1240 (2018), link
[17] S. J. Rahi*, J. Larsch, K. Pecani, A. Y. Katsov, N. Mansouri, K. Tsaneva-Atanasova, E. D. Sontag, F. R. Cross,
Oscillatory stimuli differentiate adapting circuit topologies,
Nature Methods 14, 1010-1016 (2017), link
[16] S. J. Rahi*, K. Pecani, A. Ondracka, C. Oikonomou, F. R. Cross,
The CDK-APC/C oscillator predominantly entrains periodic cell-cycle transcription,
Cell 165, 475-487 (2016), link

PhD research

[15] N. Graham*, A. Shpunt, T. Emig, S. J. Rahi, R. L. Jaffe, M. Kardar,
Electromagnetic Casimir Forces of Parabolic Cylinder and Knife-Edge Geometries,
Phys. Rev. D 83, 125007 (2011), link
preprint: arXiv:1103.5942, link
[14] M. F. Maghrebi*, S. J. Rahi, T. Emig, N. Graham, R. L. Jaffe, M. Kardar,
Analytical results on Casimir forces for conductors with edges and tips,
Proc. Natl. Acad. Sci. USA 108, 6867-6871 (2011), link
preprint: arXiv:1010.3223, link
[13] S. Zaheer, S. J. Rahi, T. Emig, R. L. Jaffe,
Casimir potential of a compact object enclosed by a spherical cavity,
Phys. Rev. A 82, 052507 (2010), link
preprint: arXiv:1008.4181, link
[12] S. J. Rahi*, M. Kardar, T. Emig,
Constraints on stable equilibria with fluctuation-induced (Casimir) forces,
Phys. Rev. Lett. 105, 070404 (2010), link
preprint: arXiv:0911.5364, link
[11] N. Graham*, A. Shpunt, T. Emig, S. J. Rahi, R. L. Jaffe, M. Kardar,
Casimir Force at a Knife’s Edge,
Phys. Rev. D 81, 061701(R) (2010), link
preprint: arXiv:0910.4649, link
[10] S. J. Rahi*, S. Zaheer,
Stable Levitation and Alignment of Compact Objects by Casimir Spring Forces,
Phys. Rev. Lett. 104, 070405 (2010), link
preprint: arXiv:0909.4510, link
[9] S. Zaheer*, S. J. Rahi, T. Emig, R. L. Jaffe,
Casimir interactions of an object inside a spherical metal shell,
Phys. Rev. A 81, 030502(R) (2010), link
preprint: arXiv:0908.3270, link
[8] S. J. Rahi*, T. Emig, N. Graham, R. L. Jaffe, M. Kardar,
Scattering Theory Approach to Electrodynamic Casimir Forces,
Phys. Rev. D 80, 085021 (2009), link
preprint: arXiv:0908.2649, link
[7] P. Rodriguez-Lopez, S. J. Rahi, T. Emig,
Three-body Casimir effects and non-monotonic forces,
Phys. Rev. A 80, 022519 (2009), link
preprint: arXiv:0905.0448, link
[6] S. J. Rahi*, M. P. Hertzberg, M. Kardar,
Melting of persistent double-stranded polymers,
Phys. Rev. E 78, 051910 (2008), link
preprint: arXiv:0806.2837, link
[5] S. J. Rahi, P. Virnau*, L. A. Mirny, M. Kardar,
Predicting transcription factor specificity with all-atom models,
Nucleic Acids Res. 36, 6209-6217 (2008), link
preprint: arXiv:0809.4080, link
[4] S. J. Rahi, T. Emig, R. L. Jaffe, M. Kardar*,
Casimir forces between cylinders and plates,
Phys. Rev. A 78, 012104 (2008), link
preprint: arXiv:0805.4241, link
[3] S. J. Rahi, A. W. Rodriguez, T. Emig, R. L. Jaffe, S. G. Johnson, M. Kardar,
Nonmonotonic effects of parallel sidewalls on Casimir forces between cylinders,
Phys. Rev. A 77, 030101(R) (2008), link
preprint: arXiv:0711.1987, link

Undergraduate research

[2] S. J. Rahi, K. Sharp*,
Mapping complicated surfaces onto a sphere,
Int. J. Comput. Geom. Appl. 17, 305-329 (2007), link
[1] W. Gu, S. J. Rahi, V. Helms*,
Solvation free energies and transfer free energies for amino acids from hydrophobic solution to water solution from a very simple residue model,
J. Phys. Chem. B 108, 5806-5814 (2004), link

Book Chapter

S. J. Rahi, T. Emig, R. L. Jaffe,
Geometry and material effects in Casimir physics – Scattering theory,
in Casimir Physics (Lecture Notes in Physics), Eds.: D. Dalvit, P. Milonni, D. Roberts, F. da Rosa (Springer, New York, 2011),
preprint: arXiv:1007.4355, link