Laboratory of Systems and Synthetic Microbiology

C Wedd, T Yunusov, A Smith, R Li, G Hardo, M Hunter, R Majed, D Fusco, S Bakshi. Single-cell imaging of the lytic phage life cycle dissects the timing and noise in individual infection steps. bioRxiv, 2024.04. 11.588870 (2024)

 G Hardo, R Li , S Bakshi. Quantitative Microbiology with Microscopy: Effects of Projection and Diffraction. NPJ Imaging 2 (1), 26 (2024)

J Rooney, E Rivera-de-Torre, R Li, K Mclean, DRG Price, AJ Nisbet, AH Laustsen, TP Jenkins, A Hofmann, S Bakshi, A Zarkan, C Cantacessi. Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions. Computational and Structural Biotechnology Journal (2024)

P Bera, W Abdul, S Bakshi, J Mondal. Protein Translation Can Fluidize Bacterial Cytoplasm. bioRxiv, 2024.01. 16.575857 (2024)

B Okumus, JM Pedraza, S Bakshi. Next-generation quantitative and synthetic biology: High-sensitivity, high-accuracy, and digital approaches. Frontiers in Bioengineering and Biotechnology 11 : 1146729 (2023). 

G Hardo, M Noka, S Bakshi. SyMBac: Synthetic Micrographs of Bacteria (SyMBac) allows accurate segmentation of bacterial cells using deep neural networks. BMC biology 20 (1), 1-16 (2022)

C Moschner, C Wedd, S Bakshi. The context matrix: Navigating biological complexity for advanced biodesign. Frontiers in Bioengineering and Biotechnology 10: 954707 (2022). 

S Bakshi, E Leoncini, C Baker, SJ Cañas-Duarte, B Okumus, J Paulsson. Tracking bacterial lineages in complex and dynamic environments with applications to growth control and persistence. Nature Microbiology 6, 783–791 (2021).

S Manuse, Y Shan, S Canas-Duarte, S Bakshi, W Sun, H Mori, J Paulsson, K Lewis. Bacterial Persisters are a stochastically formed subpopulation of low-energy cells. PLOS Biology 19 (4), e3001194 (2021).

G Hardo, S Bakshi, Challenges of analysing stochastic gene expression in bacteria using single-cell time-lapse experiments, Essays in Biochemistry, 65 (1): 67–79 (2021).

DT Riglar, DL Richmond, L Potvin-Trottier, AA Verdegaal, AD Naydich,  S Bakshi, E Leoncini, L G Lyon, J Paulsson, PA Silver. Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator. Nature communications 10 (1), 1-12 (2019).

ND Lord, TM Norman, R Yuan, S Bakshi, R Losick, J Paulsson. Stochastic antagonism between two proteins governs a bacterial cell fate switch. Science 366 (6461), 116-120 (2019).

A Lepore, H Taylor, D Landgraf, B Okumus, S Jaramillo-Riveri, L McLaren, S Bakshi, J Paulsson, ME Karoui. Quantification of very low-abundant proteins in bacteria using the HaloTag and epi-fluorescence microscopy. Scientific reports 9 (1), 1-9 (2019).

B Okumus, CJ Baker, JC Arias-Castro, GC Lai, E Leoncini, S Bakshi, S Luro, D Landgraf, J Paulsson.  Single-cell microscopy of suspension cultures using a microfluidics-assisted cell screening platform. Nature Protocols; 13:170. (2018).

B Okumus, D Landgraf, GC Lai, S Bakshi, JC Arias-Castro, S Yildiz, D Huh, R Fernandez-Lopez, CN Peterson, E Toprak, ME Karoui , J Paulsson. Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Nature communications; 7:12130 (2016).

S Bakshi, H Choi, JC Weisshaar. The spatial biology of transcription and translation in rapidly growing Escherichia coli. Frontiers in Microbiology; 6:636 (2015). 

S Bakshi, H Choi, J Mondal, JC Weisshaar. Time-dependent effects of transcription-and translation-halting drugs on the spatial distributions of the Escherichia coli chromosome and ribosomes. Molecular Microbiology; 94 (4): 871-887 (2014). 

S Bakshi, H Choi, N Rangarajan, KJ Barns, JC Weisshaar. Non-perturbative Imaging of Nuceloid Morphology in Live Bacterial Cells during Antimicrobial Peptide Attack. Applied and Environmental Microbiology; 00989-14 (2014). 

S Bakshi, R Dalrymple, W Li, H Choi, JC Weisshaar. Partitioning of RNA Polymerase Activity in Live E. coli from Analysis of Single-molecule Di.usive Trajectories. Biophysical Journal; 105 (12): 2676-2686 (2013).  Link  (Commentary by Dr. Stefan Klump: New and Notable: A Superresolution Census of RNA Polymerase. Biophysical Journal; 105 (12): 2613–2614 (2013). 

N Rangarajan, S Bakshi, JC Weisshaar. Localized Permeabilization of E. coli Membranes by the Antimicrobial Peptide Cecropin A. Biochemistry;  52 (38):6584-6594 (2013). 

Y-J Eun, D Kiekebusch, M Zhou, S Schlimpert, R Trivedi, S Bakshi, T Wahlig, Z Zhong, M Thanbichler, D Weibel . Divin: A Small Molecule Inhibitor of Bacterial Divisome Assemblys. J. Am. Chem. Soc.; 135, 9768-9776 (2013). 

S Bakshi, A Siryaporn, M Goulian, JC Weisshaar. Superresolution Imaging of Ribosomes and RNA Polymerase in Live Escherichia coli Cells. Molecular Microbiology; 85(1): 21-38 (2012). Link. (Commentary by Dr. Julie Biteen: Extending the tools of single‐molecule fluorescence imaging to problems in microbiology. Molecular Microbiology; 85(1): 1-4 (2012). 

S Bakshi, BP Bratton, JC Weisshaar. Sub-diffraction-limit Study of Kaede Diffusion and Spatial distribution in Live Escherichia coli. Biophysical Journal; 101(10):2535-2544 (2011).