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 21, 1103-1113 (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