Publications

PAPERS

• Tianyu Wu, Zane Thornburg, Kevin Tan, et al. “Visualizing Cell Structures with Minecraft.” The Biophysicist. Published online February 03, 2025. doi: 10.35459/tbp.2024.000275

  Kideog Bae, Muzaffer Özbey, Mark A. Anastasio, Stephen A. Boppart, Edita Aksamitiene. “Label-free mitochondria segmentation for morphological and functional study of mitochondria,” Proceedings Volume PC13318, Dynamics and Fluctuations in Biomedical Photonics XXII; PC1331806 (2025) https://doi.org/10.1117/12.3041285

  Jaehyeon Kim, Yue Tian, Guanhua Qiao, Julinna Abulencia Villarta, Fujia Zhao, Andrew He, Ruo-Jing Ho, Haoran Liu, Rohit Bhargava, Yingjie Zhang; Endoscopic Fourier-transform infrared spectroscopy through a fiber microprobe. Rev. Sci. Instrum. 1 March 2025; 96 (3): 033702. https://doi.org/10.1063/5.0233920

  Ezza Khan, Paola E. Mera. “Cell size regulation in bacteria: a tale of old regulators with new mechanisms,” bioRxiv 2025.02.22.639668; doi: https://doi.org/10.1101/2025.02.22.639668

  Cheyenne S. Mitchell and Dhananjay Dhruva and Zachary P. Burke and David J. Durden and Armine I. Dingilian and Mikael P. Backlund, 2025. “Quantum-inspired super-resolution of fluorescent point-like sources”, https://arxiv.org/abs/2412.16835

  Min Kyung Shinn, Dylan T. Tomares, Vicky Liu, Avnika Pant, Yuanxin Qiu, You Jin Song, Yuna Ayala, Gregory W. Strout, Kiersten M. Ruff, Matthew D. Lew, Kannanganattu V. Prasanth, Rohit V. Pappu. “Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases,” bioRxiv 2025.02.26.640430; doi: https://doi.org/10.1101/2025.02.26.640430.

  Samuel Russell, M. Rickard, T. Pogorelov and M. Gruebele “Enzymes in a human cytoplasm model organize into submetabolon complexes,” Proc. Nat. Acad. Sci., USA.122, e2414206122 (2025). https://doi.org/10.1073/pnas.2414206122

  Biel, F. Rashid, S. Natua, T.-Y. Wang, T.-F. Chou, T. V. P. Nguyen, I. Golding, A. Kalsotra and A. M. Sokac, “Reducing Cofilin dosage makes embryos resilient to heat stress”, bioRxiv 2025.01.02.631102 (2025). DOI: https://doi.org/10.1101/2025.01.02.631102

PAPERS

• Deepak K Singh, Zhengmin Cong, You Jin Song, Minxue Liu, Ritu Chaudhary, Dazhen Liu, Yu Wang, Rishabh Prasanth, Rajendra K C, Simon Lizarazo, Miriam Akhnoukh, Omid Gholamalamdari, Anurupa Moitra, Lisa M Jenkins, Rohit Bhargava, Erik R Nelson, Kevin Van Bortle, Supriya G Prasanth, Kannanganattu V Prasanth. “MANCR lncRNA Modulates Cell-Cycle Progression and Metastasis by Cis-Regulation of Nuclear Rho-GEF”, Mol Cell Biol. 2024; 44(9):372-390. doi:10.1080/10985549.2024.2383773
• Fredy Kurniawan, Arindam Chakraborty, Humayra Z. Oishi, Minxue Liu, Mariam K. Arif, David Chen, Rishabh Prasanth, Yo-Chuen Lin, Godwin Olalaye, Kannanganattu V. Prasanth, & Supriya G. Prasanth. “Phosphorylation of Orc6 During Mitosis Regulates DNA Replication and Ribosome Biogenesis.” Molecular and Cellular Biology, 44(7), 289–301. https://doi.org/10.1080/10985549.2024.2356880
• Thu Vu Phuc Nguyen, Yuchen Wu, Tianyou Yao, Jimmy T. Trinh, Lanying Zeng, Yann R. Chemla, Ido Golding. (2024) “Co-infecting phages impede each other’s entry into the cell” Current Biol. 34(13):2841-2853, 2024. https://doi.org/10.1016/j.cub.2024.05.032
• Y. Geng, T. V. P. Nguyen, E. Homaee and I. Golding. “Using bacterial population dynamics to count phages and their lysogens”, Nat Commun 15, 7814 (2024). https://doi.org/10.1038/s41467-024-51913-6
• P. Samuel Russell, M. Rickard, T. Pogorelov and M. Gruebele “Enzymes in a human cytoplasm model organize into submetabolon complexes,” Proc. Nat. Acad. Sci., USA. doi: 10.1073/pnas.2414206122 (2024).
• Ira Golding, Ariel Amir. “Gene expression in growing cells: A biophysical primer,” Reviews of Modern Physics, 2024. https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.96.041001
• Bo Yuan, Shulei Wang. “Microbiome Data Integration via Shared Dictionary Learning,” doi: https://doi.org/10.1101/2024.10.04.616752
• Laura Troyer, Yu-Huan Wang, Shobhna , Seunghyeon Kim, Jeechul Woo, Emad Tajkhorshid, Sangjin Kim (2025) Single-molecule imaging reveals the role of membrane-binding motif and C-terminal domain of RNase E in its localization and diffusion in Escherichia coli eLife 14:RP105062, https://doi.org/10.7554/eLife.105062.1
• You Jin Song, Min Kyung Shinn, Sushant Bangru, Yu Wang, Qinyu Sun, Qinyu Hao, Pankaj Chaturvedi, Susan M. Freier, Pablo Perez-Pinera, Erik R. Nelson, Andrew S. Belmont, Mitchell Guttman, Supriya G. Prasanth, Auinash Kalsotra, Rohit V. Pappu, Kannanganattu V. Prasanth. “Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles,” https://doi.org/10.1101/2024.10.31.62131
• Jaehyeon Kim, Yue Tian, Guanhua Qiao, Julinna Abulencia Villarta, Fujia Zhao, Andrew He, Ruo-Jing Ho, Haoran Liu, Rohit Bhargava, and Yingjie Zhang. “Endoscopic Fourier-transform infrared spectroscopy through a fiber microprobe,” https://arxiv.org/pdf/2409.09151
• Joseph Slivka, Emma Gleave, Devinda P. Wijewardena, John T. Canty, Paul R. Selvin, Andrew P. Carter, Ahmet Yildiz. “Stepping dynamics of dynein characterized by MINFLUX”, bioRxiv 2024.07.16.603667; doi: https://doi.org/10.1101/2024.07.16.603667
• Kritika Mehta, Henry Yentsch, Jungbin Lee, Tianyu Terry Gao, Kai Zhang. “Phosphatidylinositol 3-phosphate mediates Arc capsids secretion through the multivesicular body pathway,” Proceedings of National Academy of Sciences (PNAS),2024, 121 (35) e2322422121. https://www.pnas.org/doi/10.1073/pnas.2322422121
• Qinyu Hao, Minxue Liu, Swapna Vidhur Daulatabad, Saba Gaffari, You Jin Song, Rajneesh Srivastava, Shivang Bhaskar, Anurupa Moitra, Hazel Mangan, Elizabeth Tseng, Rachel B Gilmore, Susan M Frier, Xin Chen, Chengliang Wang, Sui Huang, Stormy Chamberlain, Hong Jin, Jonas Korlach, Brian McStay, Saurabh Sinha, Sarath Chandra Janga, Supriya G Prasanth, Kannanganattu V Prasanth (2024) Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression eLife 13:e80684 https://doi.org/10.7554/eLife.8068
• Teak-Jung Oh, Bryan Gworek, Amna Mehfooz, Kai Zhang, Methods for Gene Delivery and Analysis of Optogenetic Induction of Lytic Cell Death, Current Protocols, 2024, 4, e1023. https://doi.org/10.1002/cpz1.1023
• Kenkel, S. and Bhargava, R. Modeling the Thermoelastic Sample Response for Subdiffraction Infrared Spectroscopic Imaging, Chemical & Biomedical Imaging (2024), https://pubs.acs.org/doi/full/10.1021/cbmi.4c00018
• Teak-Jung Oh, Vishnu Krishnamurthy, Jeong Won Han, Junyao Zhu, Zayn Beg, Amna Mehfooz, Bryan Gworek, David J. Shapiro,Kai Zhang “Spatiotemporal control of inflammatory lytic cell death through optogenetic induction of RIPK3 oligomerization”, Journal of Molecular Biology, 2024,436(13):168628. doi: 10.1016/j.jmb.2024.168628
• Seunghyeon Kim, Yu-Huan Wang, Albur Hassan, Sangjin Kim, Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria, bioRxiv 2024.04.18.588412; doi: https://doi.org/10.1101/2024.04.18.588412
• Yuncong Geng, Thu Vu Phuc Nguyen, Ehsan Homaee, Ido Golding, Using population dynamics to count bacteriophages and their lysogens, bioRxiv 2023.10.06.561271; doi: https://doi.org/10.1101/2023.10.06.561271

DATA SETS

Teak-Jung Oh, Kai Zhang, Gene Expression Omnibus: GSE268650

SOURCE CODES

Abraham, M., Alekseenko, A., Basov, V., Bergh, C., Briand, E., Brown, A., Doijade, M., Fiorin, G., Fleischmann, S., Gorelov, S., Gouaillardet, G., Gray, A., Irrgang, M. E., Jalalypour, F., Jordan, J., Kutzner, C., Lemkul, J. A., Lundborg, M., Merz, P., … Lindahl, E. (2024). GROMACS 2024.1 Source code (2024.1). Zenodo. https://doi.org/10.5281/zenodo.10721181

PATENTS

Awarded

US11860087B2, Rohit Bhargava & Seth Kenkel: Method and apparatus for nanoscale infrared absorption tomography

Pending

63/567,768, Yeh & Bhargava : Mid-infrared optical lens assemblies for confocal laser scanning microscopy

• Ghaemi, Z., Nafiu, O., Tajkhorshid, E. Gruebele, M. and Hu, Jianming. A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions. Sci Rep 13, 21392 (2023). https://doi.org/10.1038/s41598-023-45998-0

• Benjamin R. Gilbert , Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grünewald, John E. Stone, Siewert J. Marrink. and Zaida Luthey-Schulten, (2023) “Dynamics of Chromosome Organization in a Minimal Bacterial Cell”, Frontiers in Cell and Developmental Biology, https://doi.org/10.3389/fcell.2023.1214962
• JA Stevens, F Grünewald, PA van Tilburg, M König, BR Gilbert, TA Brier, Z. R. Thornburg, Z. Luthey-Schulten, S.J. Marrink “Molecular Dynamics Simulations of an Entire Cell”, Frontiers in Chemistry, Doi: 10.3389/fchem.2023.1106495.
• Luthey-Schulten, Z. Thornburg, Z., Gilbert, B. (2022) “Integrating cellular and molecular structures and dynamics into whole cell models” Current Opinion Structural Biology, https://doi.org/10.1016/j.sbi.2022.102392
• Thornburg, Z., Bianchi, D., Brier, T. Gilbert, B., Earnest, T., Melo, M, Safronova, N., Saenz, J., Cook, A. Wise, K. Hutchinson, C., Smith, H., Glass, J. Luthey-Schulten, Z. (2022), “Fundamental Behaviors Emerge from Simulations of a Living Minimal Cell”. Cell, doi:10.1016/j.cell.2021.12.025.
• Luthey-Schulten, Zaida (2021). Integrating experiments, theory, and simulations into whole cell models. Nature Methods, https://doi.org/10.1038/s41592-021-01150-2.
• Gilbert, B,. Thornburg, Z., Lam, V., Rashid, F., Glass J., Villa, E., Dame, R., Luthey-Schulten, Z. (2021). Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps. Frontiers in Molecular Biosciences doi: 10.3389/fmolb.2021.644133.
• Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathofer, U., Vant, J.W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D.E., Stone, J.E., Phillips, J.C., Pogorelov, T.V., Mallus, M., Chipot, C., Luthey-Schulten, Z., Tieleman, D.P., Hunter, C. N., Tajkhorshid, E., Aksimentiev, A., Schulten, K. (2019). Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell, 179(5), 1098–1111. https://doi.org/10.1016/j.cell.2019.10.021
• Breuer, M., Earnest, T. M., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C.A., Smith, H.O., Lapek, J.D., Gonzalez, D.J., Crecy-Lagard, V., Haas, D., Hanson, A.D., Labhsetwar, P., Glass, J.I., Luthey-Schulten, Z. (2019). Essential Metabolism for a Minimal Cell. ELife. https://doi.org/10.7554/eLife.36842.001
• Earnest, T. M., Watanabe, R., Stone, J. E., Mahamid, J., Baumeister, W., Villa, E., & Luthey-Schulten, Z. (2017). Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. J. Phys. Chem. B, 121(15), 3871-3881. https://doi.org/10.1021/acs.jpcb.7b00672
• Hallock, M. J., Stone, J. E., Roberts, E., Fry, C., & Luthey-Schulten, Z. (2014). Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. ParallelComputing, 40(5-6), 86-99. https://doi.org/10.1016/j.parco.2014.03.009

• Z. Ghaemi, M.Gruebele, E.Tajkhorshid, “Molecular Mechanism of Capsid Disassembly in Hepatitis B Virus,” Proc. Nat. Acad Sci. USA 118, e2102530118 (2021).
• Z. Ghaemi, J. R. Peterson, M.Gruebele, and Z. Luthey-Schulten, “An In-Silico Human Cell Platform For Spatio-Temporal Modeling,” PLoS Comput. Biol. 16, e1007717 (2020).
• P. Tripathi, B. Mehrafrooz, A.Aksimentiev, S. E. Jackson, M.Gruebele, and M. Wanunu, “An inverted region in the translocation kinetics of a knotted protein,” J. Phys. Chem. Lett., submitted (2023).
• M. Boob, M. Gruebele, and T. Pogorelov “TMAO: protecting proteins from feeling the heat,” Biophys. J. 122, 1414-1422 (2023).
• I. Srivastava,. B. Lew, Y. Wang,. J. Ludwig, S. Bangru, S. Pandit, Z. Wang, S. Blair, M. Gruebele, S. Nie, V. Gruev, “Cell-Membrane Coated Nanoparticles for Tumor Delineation and Qualitative Estimation of Cancer Biomarkers at Single Wavelength Excitation in Murine and Phantom Models,” ACS Nano 8465-8482 (2023).
• P. Tripathi, A. Firouzbakht, M. Gruebele, and M. Wanunu, “Direct observation of single-protein transition state passage during translocation through a nanopore,” J. Phys. Chem. Lett. 13, 5918-5924 (2022).G. Gopan, Z. Ghaemi, C. Davis and M. Gr
• uebele, “Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM,” Nucl. Acids Res. 50, 8193–8206 (2022).
• P. Tripathi, A. Firouzbakht, M. Gruebele, and M. Wanunu, “Threading Proteins at the Speed Limit of Folding,” Proc. Nat. Acad Sci. USA 119, e2202779119 (2022).M. Rickard, H. Luo, A. De Lio, M. Gruebele and T. Pogorelov, “Impact of the cellular environment on ATP conformations,” J. Phys. Chem. Lett.13, 9809-9814 (2022).

• Hsieh, P.-H., Phal, Y., Prasanth, K.V., Bhargava, R. Cell Phase Identification in a Three-Dimensional Engineered Tumor Model by Infrared Spectroscopic Imaging (2023) Analytical Chemistry, 95 (6), pp. 3349-3357. DOI: 10.1021/acs.analchem.2c0455
• Kenkel, S., Gryka, M., Chen, L., Confer, M.P., Rao, A., Robinson, S., Prasanth, K.V., Bhargava, R. Chemical imaging of cellular ultrastructure by null-deflection infrared spectroscopic measurements (2022) Proceedings of the National Academy of Sciences of the United States of America, 119 (47), art. no. e2210516119, . DOI: 10.1073/pnas.2210516119
• Falahkheirkhah, K., Yeh, K., Mittal, S., Pfister, L., Bhargava, R. Deep learning-based protocols to enhance infrared imaging systems (2021) Chemometrics and Intelligent Laboratory Systems, 217, art. no. 104390, . DOI: 10.1016/j.chemolab.2021.104390
• Phal, Y., Yeh, K., Bhargava, R. Concurrent vibrational circular dichroism measurements with infrared spectroscopic imaging (2021) Analytical Chemistry, 93 (3), pp. 1294-1303. https://www.scopus.com/inward/record.uri?eid=2-s2.0- DOI: 10.1021/acs.analchem.0c0032
• Kenkel, S., Mittal, S., Bhargava, R. Closed-loop atomic force microscopy-infrared spectroscopic imaging for nanoscale molecular characterization (2020) Nature Communications, 11 (1), art. no. 3225, . DOI: 10.1038/s41467-020-17043-5

• Cournoyer JE, Altman SD, Gao YL, Wallace CL, Zhang D, Lo GH, Haskin NT, Mehta AP. Engineering artificial photosynthetic life-forms through endosymbiosis. Nat Commun. 2022 Apr 26;13(1):2254. doi: 10.1038/s41467-022-29961-7. PMID: 35474066; PMCID: PMC9042829.
• Ornelas MY, Thomas AY, Johnson Rosas LI, Scoville RO, Mehta AP. Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS Synth Biol. 2022 Nov 18;11(11):3759-3771. doi: 10.1021/acssynbio.2c00359. Epub 2022 Nov 4. PMID: 36331143; PMCID: PMC9662071.
• Ornelas MY, Thomas AY, Johnson Rosas LI, Medina GN, Mehta AP. Characterization, Directed Evolution, and Targeting of DNA Virus-Encoded RNA Capping Enzymes Using Phenotypic Yeast Platforms. ACS Chem Biol. 2023 Aug 18;18(8):1808-1820. doi: 10.1021/acschembio.3c00243. Epub 2023 Jul 27. PMID: 37498174.

• S. Dehghani-Ghahnaviyeh, Z. Zhao, E. Tajkhorshid (2022) Lipid-mediated organization of prestin in the outer hair cell membrane and its implications in sound amplification. Nature Communications, 13:6877.
• K. Kapoor*, T. Chen*, and E. Tajkhorshid (2022) Post-Translational Modifications Optimize the Ability of SARS-CoV-2 Spike for Effective Interaction with Host Cell Receptors. PNAS, 119: e2119761119.
• J. Vermaas, C. Mayne, E. Shinn, and E. Tajkhorshid (2022) Assembly and Analysis of Cell-Scale Membrane Envelopes. J. Chem. Inf. Modeling, 62, 602–617. (cover article)
• I. Singaram, A. Sharma, S. Pant, M. Lihan, M.-J. Park, P. Buwaneka, Y. Hu, N. Mahmud, Y.-M. Kim, V. Gevorgyan, I. Khan, E. Tajkhorshid, and W. Cho (2023) Targeting lipid-protein interaction for drug development: Development of a novel resistance-proof Syk inhibitor for acute myeloid leukemia. Nat. Chem. Biol., 19: 239–250.
• D. Yang, Z. Zhao, E. Tajkhorshid, and E. Gouaux (2023) Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. PNAS, 120 (29), e2304602120.
• H. Jeong, S. Clark, A. Goehring, S. Dehghani-Ghahnaviyeh, A. Rasouli, E. Tajkhorshid, and E. Gouaux (2022) Structure of C. elegans TMC-1 complex illuminates auditory mechanosensory transduction. Nature, 610: 796–803.
• A. K. Vasan*, N. Haloi*, R. J. Ulrich, M. E. Metcalf, P. C. Wen, W. W. Metcalf, P. J. Hergenrother, D. Shukla, and E. Tajkhorshid (2022) Role of internal loop dynamics in antibiotic permeability of outer membrane porins. PNAS, 119 (8), e2117009119.
• R. Dastvan, A. Rasouli*, S. Dehghani-Ghahnaviyeh*, S. Gies, and E. Tajkhorshid (2022) Proton-driven alternating access in a spinster transporter, an emerging family of broad-specificity efflux pumps. Nature Communications, 13: 5161.

• Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Wenxuan Zhao, Daniel Verschueren, Aleksei Aksimentiev, Hendrik Dietz, Cees Dekker. ­A nanopore-powered DNA turbine. Nature Nanotechnology, Accepted (2023).
• Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Aleksei Aksimentiev, Min Chen, Meni Wanunu. Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore. Nature Biotechnology 41: 1130–1139 (2023). Cover.
• Kaikai Chen, Adnan Choudhary, Sarah Sandler, Christopher Maffeo, Caterina Ducati, Aleksei Aksimentiev, Ulrich F. Keyser Super-resolution detection of DNA nanostructures using a nanopore. Advanced Materials 35: 2207434 (2023).
• Christopher Maffeo, Lauren Quednau, James Wilson, Aleksei Aksimentiev. DNA double helix, a tiny electromotor. Nature Nanotechnology 18: 238–242 (2023).
• David Winogradoff, Han-YiChou, Christopher Maffeo, Aleksei Aksimentiev. Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex. Nature Communications 13:5138 (2022).
• Henry Brinkerhoff, Albert S. W. Kang, Jingqian Liu, Aleksei Aksimentiev, Cees Dekker. Multiple re-reads of single proteins at single-amino-acid resolution using nanopores. Science 374, 1509-1513 (2021).
• Jejoong Yoo, Sangwoo Park, Christopher Maffeo, Taekjip Ha, and Aleksei Aksimentiev. DNA Sequence and Methylation Prescribe the Inside-Out Conformational Dynamics and Bending Energetics of DNA Minicircles. Nucleic Acids Research 49, 11459–11475 (2021).

• C. Xi, M. E. Kandel, S. He, C. Hu, Y. J. Lee, K. Sullivan, G. Tracey, H.J. Chung, H.J. Kong,M. A. Anastasio, and G. Popescu.Artificial confocal microscopy for deep label-free imaging. Nature Photonics, 2023: 1-9.
• R. Deshpande, A. Avachat, F. J. Brooks, and M.A. Anastasio. Investigating the robustness of a deep learning-based method for quantitative phase retrieval from propagation-based x-ray phase contrast measurements under laboratory conditions. Physics in Medicine & Biology, 2023, 68, no. 8: 085005.
  Kelkar VA, Gotsis DS, Brooks FJ, KC P, Myers KJ, Zeng R, Anastasio M.A. Assessing the ability of generative adversarial networks to learn canonical medical image statistics. IEEE Transactions on Medical Imaging, In Press, 2023.
• C. Hu, S. He, Y.J. Lee, Y. He, E.M. Kong, H. Li, M.A. Anastasio, G. Popescu G: Live-dead assay on unlabeled cells using phase imaging with computational specificity.Nature Communications. 2022 Feb 7;13(1):1-8.

• Carney S.P., Ma W., Whitley K.D., Jia H., Lohman T.M., Luthey-Schulten Z., Chemla Y.R. (2021) “Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase.” Nat Commun. 12(1):7015. doi: 10.1038/s41467-021-27304-6.
• Rhine K., Makurath M.A., Liu J., Skanchy S., Lopez C., Catalan K.F., Ma Y., Fare C.M., Shorter J., Ha T., Chemla Y.R., Myong S. (2020) “ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS.” Mol Cell. 80(4):666-681.e8.
• Ma W., Whitley K.D., Chemla Y.R., Luthey-Schulten Z., Schulten K. (2018) “Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase.” Elife. pii: e34186.
• Comstock M.J., Whitley K.D., Jia H., Sokoloski J., Lohman T.M., Ha T., Chemla Y.R. (2015) “Direct observation of structure-function relationship in a nucleic acid-processing enzyme” Science 348(6232):352-354.
• Arslan S., Khafizov R., Thomas C.D., Chemla Y.R., Ha T. (2015) “Engineering of a superhelicase through conformational control” Science 348(6232):344-347.

• Y. Liu, R. S. Zou, S. He, Y. Nihongaki, X. Li, S. Razavi, B. Wu and T. Ha, “Very fast CRISPR on demand”, Science 368, 1265–1269 (2020).
• Y. Wang, W.T. Cottle, H. Wang, X.A. Feng, J. Mallon, M. Gavrilov, S. Bailey and T. Ha, “Genome Oligopaint via Local Denaturing Fluorescence In situ Hybridization”, Molecular Cell 81:1566-1577 (2021).
• A. Basu, D. Bobrovnikov, B. Cieza, J. P. Arcon, Z. Qureshi, M. Orozco and T. Ha, “Deciphering the mechanical code of the genome and epigenome” Nature Struct. Mol. Bio. 29, 1178-1187 (2022).
• R. S. Zou, A. Marin-Gonzalez, Y. Liu, H. B. Liu, L. Shen, R. Dveirin, J.X.J. Luo, R. Kalhor and T. Ha, “Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites” Nature Cell Biology 24, 1433-1444 (2022).
• A. Basu, D.G. Bobrovnikov, Z. Qureshi, T. Kayikcioglu, T.T.M. Ngo, A. Ranjan, S. Eustermann, B. Cieza, M.T. Morgan, M. Hejna, H.T. Rube, K.P. Hopfner, C. Wolberger, J.S. Song and T. Ha, “Measuring DNA mechanics on the genome scale” Nature 589, 462-467 (2021).

• Lundborg M, Narangifard A, Wennberg CL, Lindahl E, Daneholt B, Norlén L. (2018) Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation. J. Struct. Biol. 203(2), 149-161
• Zhuang Y, Noviello CM, Hibbs RE, Howard RJ, Lindahl E (2022) Differential interactions of resting, activated, and desensitized states of α7 nicotinic acetylcholine receptor with lipidic modulators. Proc. Natl. Acad. Sci. USA. 119(43), e2208081119
• Lycksell M, Rovšnik U, Bergh C, Johansen NT, Martel A, Porcar L, Arleth L, Howard RJ, Lindahl E (2021). Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. Proc. Natl. Acad. Sci. USA 118 (37), e2108006118
• Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E (2023). Structure and dynamics of differential ligand binding in the human ρ-type GABA(A) receptor. Neuron 111, 1-15. https://doi.org/10.1016/j.neuron.2023.08.006
• Bergh C, Rovsnik U, Howard RJ. Lindahl E. (2023) Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. eLife, in press.

• de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli C, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck B, Kreshuk A, Mahamid J, Zaugg J (2023). Convolutional networks for supervised mining of molecular patterns within cellular context. Nature Methods 20, 284–294.
• Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung KHH, Poser I, Müller C, Hyman AA, Savitski M, Mahamid J (2022). Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Cell 186, 1877-1894.
• D’Imprima E, Garcia Montero M, Gawrzak S, Ronchi P, Zagoriy I, Schwab Y, Jechlinger M, Mahamid J (2023). Light and electron microscopy continuum resolution imaging of 3D cell cultures.Developmental Cell 58, 616-632.
  Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J (2022). Visualizing translation dynamics at atomic detail in a bacterial cell. Nature 610: 05–211.
• Bose M, Mahamid J, Ephrussi A (2022). Liquid-to-solid phase transition of oskar RNP granules is essential for their function in the Drosophila germline. Cell 185(8):1308-1324.
• Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J (2021). A Modular Platform for Automated Cryo-FIB Workflows.eLife 2021;10:e70506.

• B.R. Gilbert, Z.R. Thornburg, T.A. Brier, J.A. Stevens, F. Grunewald, J.E. Stone, S.J. Marrink, Z.A. Luthey-Schulten. Dynamics of Chromosome Organization in a Minimal Bacterial Cell. Front. Cell Dev. Biol., 2023, online. doi:10.3389/fcell.2023.1214962
• J.A. Stevens, F. Grünewald, P.A.M. van Tilburg, M. König, B.R. Gilbert, T.A. Brier, Z.R. Thornburg, Z. Luthey-Schulten, S.J. Marrink. Molecular dynamics simulation of an entire cell. Frontiers in Chemistry 11, 2023. doi:10.3389/fchem.2023.1106495
• W. Pezeshkian, F. Grünewald, O. Narykov, S. Lu, T.A. Wassenaar, S.J. Marrink, D. Korkin. Molecular architecture of SARS-CoV-2 envelope by integrative modeling. Structure 31 (4), 492-503, 2023. doi:10.1016/j.str.2023.02.006

• Erlandson, A., Gade, P., Menikpurage, I.P., Kim, C.Y. and Mera, P.E.(2022) The UvrA-like protein Ecm16 requires ATPase activity to render resistance against echinomycin.Mol Microbiol, 117, 1434-1446. https://www.ncbi.nlm.nih.gov/pubmed/35534931
• Gade, P., Erlandson, A., Ullah, A., Chen, X., Mathews, II, Mera, P.E. and Kim, C.Y. (2023) Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 fromStreptomyces lasalocidi.Sci Rep, 13, 7980. https://www.ncbi.nlm.nih.gov/pubmed/37198233
• Menikpurage, I.P., Puentes-Rodriguez, S.G., Elaksher, R.A. and Mera, P.E.(2023) ParA’s Impact beyond Chromosome Segregation in Caulobacter crescentus. J Bacteriol, 205, e0029622. https://www.ncbi.nlm.nih.gov/pubmed/36692299
• Puentes-Rodriguez, S.G., Norcross, J.D. and Mera, P.E.(2023) To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus. bioRxiv.  https://www.ncbi.nlm.nih.gov/pubmed/37090538 (under revision)

• Shukla, S., Troitskaia, A., Swarna, N., Maity, B.K., Tjioe, M., Bookwalter, C.S., Trybus, K.M., Chemla, Y.R., and Selvin, P.R. (2022). High-throughput force measurement of individual kinesin-1 motors during multi-motor transport. Nanoscale14, 12463–12475. 10.1039/d2nr01701f.

• Vishnu V. Krishnamurthy, Hyojeong Hwang, Jia Fu, Jing Yang*,KaiZhang*,“Optogenetic control of the canonical Wnt signaling pathway during Xenopus laevis embryonic development”,Journal of Molecular Biology, 2021, 433,18,167050. https://doi.org/10.1016/j.jmb.2021.167050
• Savanna S. Skeeters, Ana C. Rosu, Divyanshi, Jing Yang,KaiZhang*“Comparative determination of cytotoxicity of sub-10-nm copper nanoparticles to prokaryotic and eukaryotic cells”, ACS Applied Materials & Interfaces,2020,12, 45, 50203–50211.
• Qin Wang, Huaxun Fan, Feng Li, Savanna R. Sharum, Vishnu Krishnamurthy, Yuanquan Song*,KaiZhang*“Spatiotemporal optogenetic control of neurotrophin signaling accelerates axon regeneration and functional recovery in the peripheral and central nervous system”,eLife,2020, 9: e57395. https://doi.org/10.7554/eLife.57395
• Vishnu V. Krishnamurthy, Jia Fu, Teak-Jung Oh, John Khamo, Jing Yang*,KaiZhang*“A Generalizable Optogenetic Strategy to Regulate Receptor Tyrosine Kinases during Vertebrate Embryonic Development”,Journal of Molecular Biology, 2020, 432, 10, 3149-3158. https://doi.org/10.1016/j.jmb.2020.03.032
• Tyler Camp, Kritika Mehta, Stephen Sligar*,KaiZhang*, “Molecular Orientation Determination in Nanodiscs at the Single-Molecule Level”,Analytical Chemistry, 2019, 92, 2, 2229-2236. https://doi.org/10.1021/acs.analchem.9b04950
• Payel Mondal, Vishnu Krishnamurthy, Savanna Sharum, Neeka Haack, Huiwen Zhou, Jennifer Cheng, Jing Yang, andKaiZhang*“Repurposing protein degradation for optogenetic modulation of protein activities”,ACS Synthetic Biology, 2019. 8, 11, 2585-2592. https://doi.org/10.1021/acssynbio.9b00285
• Indrajit Srivastava, John S. Khamo, Subhendu Pandit, Parinaz Fathi, Xuedong Huang, Anleen Cao, Richard T. Haasch, Shuming Nie,KaiZhang*,Dipanjan Pan* “Influence of Electron Acceptor and Electron Donor on the Photophysical Properties of Carbon Dots: A Comparative Investigation at the Bulk‐State and Single‐Particle Level.Advanced Functional Materials, 2019, 29,1902466. https://doi.org/10.1002/adfm.201902466
• John S. Khamo, Vishnu V. Krishnamurthy, Qixin Chen, Jiajie Diao*, andKaiZhang*, “Optogenetic delineation of receptor tyrosine kinase subcircuits in PC12 cell differentiation“,Cell Chemical Biology, 2019, 26, 400-410. https://doi.org/10.1016/j.chembiol.2018.11.004