Banerjee Lab

Preprints

• Cell Geometry Limits Bacterial Metabolic Efficiency
  Cylke A, Banerjee S
  bioRxiv:669779 (2025)
  
• Power-law memory governs bacterial adaptation and learning in fluctuating environments
  Kratz JC, Wang H, Si F, Banerjee S
  bioRxiv:650739 (2025)
  
• Anisotropic Cell Shape and Motion Coordinate Hindbrain Neuropore Morphogenesis
  Perez-Verdugo F, Maniou E, Galea G, Banerjee S
  bioRxiv:624679 (2025)
  
• Proliferation symmetry breaking in growing tissues
  Li X, Datta A, Banerjee S
  bioRxiv:610990 (2024)
  

Peer Reviewed

• Physical traits of supercompetitors in cell competition
  Carpenter LC, Banerjee S
  Journal of the Royal Society Interface 22, 20250638 (2025)
  
• Gene expression cycles drive non-exponential bacterial growth
  Cylke A, Banerjee S
  Phys. Rev. Research 7, 033123 (2025)
  
• Design principles and feedback mechanisms in organelle size control
  Banerjee DS, Banerjee S
  Current Opinion in Cell Biology 95, 102533 (2025)
  
• Catalytic growth in a shared enzyme pool ensures robust control of centrosome size
  Banerjee DS, Banerjee S
  eLife 12, RP92203 (2025)
  
• Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening
  Banerjee DS, Chigumira T, Lackner RM, Kratz JC, Chenoweth DM, Banerjee S, Zhang H
  eLife 13, RP101777 (2024)
  
• Energy allocation theory for bacterial growth control in and out of steady state
  Cylke A, Serbanescu D, Banerjee S
  Proceedings of the Royal Society A 480, 20240219 (2024)
  
• Mechanical and biochemical feedback combine to generate complex contractile oscillations in cytokinesis
  Werner ME, Ray DD, Breen C, Staddon MF, Jug F, Banerjee S, Maddox AS
  Current Biology 34, 3201 (2024)
  Current Biology Dispatch: 'Actomyosin cortex: Inherently oscillatory?'
• Differential growth regulates asymmetric size partitioning in Caulobacter crescentus
  Ng TW, Ojkic N, Serbanescu D, Banerjee S
  Life Sci. Alliance 7, e202402591 (2024)
  
• Excitable dynamics driven by mechanical feedback in biological tissues
  Perez-Verdugo F, Banks S, Banerjee S
  Communications Physics 7, 167 (2024)
  
• Growth-induced collective bending and kinetic trapping of cytoskeletal filaments
  Banerjee DS, Freedman SL, Murrell MP, Banerjee S
  Cytoskeleton 81, 409 (2024)
  Cover image
• Mechanical control of cell proliferation patterns in growing epithelial monolayers
  Carpenter LC, Perez-Verdugo F, Banerjee S
  Biophysical Journal 123, 909 (2024)
  
• Gene Expression Tradeoffs Determine Bacterial Survival and Adaptation to Antibiotic Stress
  Kratz JC, Banerjee S
  PRX Life 2, 013010 (2024)
  
• Tension Remodeling Regulates Topological Transitions in Epithelial Tissues
  Perez-Verdugo F, Banerjee S
  PRX Life 1, 023006 (2023)
  Featured in APS Physics Magazine
• Dynamic proteome trade-offs regulate bacterial cell size and growth in fluctuating nutrient environments
  Kratz JC, Banerjee S
  Communications Biology 6, 486 (2023)
  
• Membrane tension induces F-actin reorganization and flow in a biomimetic model cortex
  Sakamoto R, Banerjee DS, Yadav V, Chen S, Gardel ML, Sykes C, Banerjee S, Murrell MP
  Communications Biology 6, 325 (2023)
  
• Super-exponential growth and stochastic size dynamics in rod-like bacteria
  Cylke A, Banerjee S
  Biophysical Journal 122, 1254 (2023)
  
• Interplay between substrate rigidity and tissue fluidity regulates cell monolayer spreading
  Staddon MF, Murrell MP, Banerjee S
  Soft Matter 18, 7877 (2022)
  Part of themed collection: Soft Matter Emerging Investigators
• Effects of antibiotics on bacterial cell morphology and their physiological origins
  Cylke C, Si F, Banerjee S
  Biochemical Society Transactions 50, 1269 (2022)
  
• Cell-Matrix Elastocapillary Interactions Drive Pressure-Based Wetting of Cell Aggregates
  Yousafzai MS, Yadav V, Amiri S, Staddon MF, Tabatabai AP, Errami Y, Jaspard G, Amiri S, Banerjee S, and Murrell MP
  Physical Review X 12, 031027 (2022)
  
• Size regulation of multiple organelles competing for a limiting subunit pool
  Banerjee DS, Banerjee S
  PLoS Computational Biology 18, e1010253 (2022)
  
• Emergence and maintenance of variable-length actin filaments in a limiting pool of building blocks
  Banerjee DS, Banerjee S
  Biophysical Journal 121, 2436 (2022)
  
• Antibiotic resistance via bacterial cell shape-shifting
  Ojkic N, Serbanescu D, Banerjee S
  mBio 13, e00659-22 (2022)
  Editor's Pick
• Force-dependent intercellular adhesion strengthening underlies asymmetric adherens junction contraction
  Cavanaugh K, Staddon MF, Chmiel TA, Harmon RM, Budnar S, Yap AS, Banerjee S, Gardel ML
  Current Biology 32, 1986 (2022)
  
• Pulsatile contractions and pattern formation in excitable actomyosin cortex
  Staddon MF, Munro EM, Banerjee S
  PLoS Computational Biology 18, e1009981 (2022)
  
• Cellular resource allocation strategies for cell size and shape control in bacteria
  Serbanescu D, Ojkic N, Banerjee S
  The FEBS Journal (2021)
  
• Cell-scale biophysical determinants of cell competition in epithelia
  Gradeci D, Bove A, Vallardi G, Lowe AR*, Banerjee S*, Charras G*
  eLife 10, e61011 (2021)
  Current Biology Dispatch: 'Cell competition: Bridging the scales through cell-based modeling'
• Hindbrain neuropore tissue geometry determines asymmetric cell-mediated closure dynamics in mouse embryos
  Maniou E, Staddon MF, Marshall A, Greene A, Copp A, Banerjee S*, Galea G*
  PNAS 118, e2023163118 (2021)
  
• Bacterial cell shape control by nutrient-dependent synthesis of cell division inhibitors
  Ojkic N, Banerjee S
  Biophysical Journal 120, 2079 (2021)
  
• Mechanical feedback promotes bacterial adaptation to antibiotics
  Banerjee S*, Lo K, Ojkic N, Stephens R, Scherer NF*, Dinner AR*
  Nature Physics 17, 403 (2021)
  CMU News|Phys.org|EurekAlert!
• Nutrient-dependent trade-offs between ribosomes and division protein synthesis control bacterial cell size and growth
  Serbanescu D, Ojkic N, Banerjee S
  Cell Reports 32, 108183 (2020)
  
• Size-regulated symmetry breaking in reaction-diffusion models of developmental transitions
  Scoones JC, Banerjee DS, Banerjee S
  Cells 9, 1646 (2020)
  
• Adaptive viscoelasticity of epithelial cell junctions: from models to methods
  Cavanaugh K, Staddon MF, Banerjee S, Gardel ML
  Current Opinion in Genetics & Development 63, 86 (2020)
  
• Cell-type specific mechanical response and myosin dynamics during retinal lens development in Drosophila
  Blackie L, Walther RF, Staddon MF, Banerjee S*, Pichaud F*
  Molecular Biology of the Cell 31, 1355 (2020)
  Cover image
• The Actin Cytoskeleton as an Active Adaptive Material
  Banerjee S, Gardel ML, Schwarz US
  Annual Review of Condensed Matter Physics 11, 421 (2020)
  
• RhoA mediates epithelial cell shape changes via mechanosensitive endocytosis
  Cavanaugh KE, Staddon MF, Munro E, Banerjee S, Gardel ML
  Developmental Cell 52, 152 (2020)
  Dev Cell Preview: 'A Nudge or a Shove: Altering Actomyosin Pulse Profiles In Vivo'
• Single-cell approaches to cell competition: high-throughput imaging, machine learning and simulations
  Gradeci D, Bove A, Charras G, Lowe AR, Banerjee S
  Seminars in Cancer Biology 63, 60-68 (2020)
• Mechanosensitive junction remodelling promotes robust epithelial morphogenesis
  Staddon MF, Cavanaugh KE, Munro EM, Gardel ML, Banerjee S
  Biophysical Journal 117, 1739 (2019)
  Video Highlight
• Filament nucleation tunes mechanical memory in active polymer networks
  Yadav V, Banerjee D, Tabatabai A, Kovar D, Kim T, Banerjee S, Murrell MP
  Advanced Functional Materials 29, 1905243 (2019)
• Surface-to-volume scaling and aspect ratio preservation in rod-shaped bacteria
  Ojkic N, Serbanescu D, Banerjee S
  eLife 8, e47033 (2019)
  
• Tissue fluidity promotes epithelial wound healing
  Tetley RJ, Staddon MF, Heller D, Hoppe A, Banerjee S, Mao Y
  Nature Physics 15,1195 (2019)
  
• Wound healing coordinates actin architectures to regulate mechanical work
  Ajeti V, Tabatabai AP, Fleszar AJ, Staddon MF, Seara DS, Suarez C, Yousafzai MS, Bi D, Kovar DR, Banerjee S, Murrell MP
  Nature Physics 15, 696 (2019)
  Yale News
• Transcription factories in Igk allelic choice and diversity
  Karki S^§, Banerjee S^§, Mclean K, Dinner AR, Clark MR
  Advances in Immunology 141, 33-49 (2019)
• Continuum models of collective cell migration
  Banerjee S, Marchetti MC
  Cell Migrations: Causes and Functions, Adv Exp Med Biol 1146, pp 45-66 (2019)
• Entropy production rate is maximized in non-contractile actomyosin
  Seara DS, Yadav V, Linsmeier I, Tabatabai AP, Oakes PW, Ali Tabei SM, Banerjee S*, Murrell MP*
  Nature Communications 9, 4948 (2018)
  Highlighted in Nature Collection: Active Matter
• Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing
  Staddon MF, Bi D, Tabatabai AP, Ajeti V, Murrell MP, Banerjee S
  PLoS Computational Biology 14(10), e1006502 (2018)
  Featured in PLoS Comput Bio. Highlighted in PLOS Biologue.
• Force localization modes in dynamic epithelial colonies
  Schaumann EN^§, Staddon MF^§, Gardel ML, Banerjee S
  Molecular Biology of the Cell 29, 2835 (2018)
  A Highlights from MBoC selection. Cover Article.
• Nonequilibrium phase diagrams for actomyosin networks
  Freedman SL, Hocky GM, Banerjee S, Dinner AR
  Soft Matter 14, 7740 (2018)
• Regulated capture of Vk gene topologically associating domains by transcription factories
  Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR
  Cell Reports 24, 2443 (2018)
• Filament rigidity and connectivity tune the deformation modes of active biopolymer networks
  Stam S, Freedman SL, Banerjee S, Weirich KL, Dinner AR, Gardel ML
  Proc. Natl. Acad. Sci. USA 114, E10037–E10045 (2017)
  
• Local cellular neighbourhood controls proliferation in cell competition
  Bove A^§, Gradeci D^§, Fujita Y, Banerjee S*, Charras G*, Lowe AR*
  Molecular Biology of the Cell 28, 3215 (2017)
  
• A versatile framework for simulating the dynamic mechanical structure of cytoskeletal networks
  Freedman SL, Banerjee S, Hocky GM, Dinner AR
  Biophysical Journal 113, 448 (2017)
  
• Biphasic growth dynamics control cell division in Caulobacter crescentus
  Banerjee S, Lo K, Daddysman MK, Selewa A, Kuntz T, Dinner AR, Scherer NF
  Nature Microbiology 2, 17116 (2017)
  
• Liquid behavior of cross-linked actin bundles
  Weirich KL, Banerjee S, Dasbiswas K, Witten TA, Vaikuntanathan S, Gardel ML
  Proc. Natl. Acad. Sci. USA 114, 2131 (2017)
• Disordered actomyosin networks are sufficient to produce cooperative and telescopic contractility
  Linsmeier I, Banerjee S, Oakes PW, Jung W, Kim TY, Murrell MP
  Nature Communications 7, 12615 (2016)
  Highlighted in Nature Collection: Active Matter
• Cellular contraction and polarization drive collective cellular motions
  Notbohm J^§, Banerjee S^§, Utuje KJC, Gweon B, Jang H, Park Y, Shin J, Butler JP, Fredberg JJ, Marchetti MC
  Biophysical Journal 110, 2729 (2016)
  
• Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3
  Liang WG, Triandafillou C, Hwang DY, Zulueta MML, Banerjee S, Dinner AR, Hung SC, Tang WJ
  Proc. Natl. Acad. Sci. USA 113, 5000 (2016)
  
• Shape dynamics of growing cell walls
  Banerjee S, Scherer NF, Dinner AR
  Soft Matter 12, 3442 (2016)
  
• Propagating stress waves during epithelial expansion
  Banerjee S*, Utuje KJC, Marchetti MC*
  Physical Review Letters 114, 228101 (2015)
  Featured in Editor's suggestions
• Intergenerational continuity of cell shape dynamics in Caulobacter crescentus
  Wright CS^§, Banerjee S^§, Iyer-Biswas S, Crosson S, Dinner AR, Scherer NF
  Scientific Reports 5, 9155 (2015)
  
• Active Viscoelastic Matter: from bacterial drag reduction to turbulent solids
  Hemmingway EJ, Maitra A, Banerjee S, Marchetti MC, Ramaswamy S, Fielding SM, Cates ME
  Physical Review Letters 114, 098302 (2015)
  
• Geometry regulates traction stresses in adherent cells
  Oakes PW, Banerjee S, Marchetti MC, Gardel ML
  Biophysical Journal 107, 825 (2014)
  Featured in New and Notable
• Optimal shapes and stresses of adherent cells on patterned substrates
  Banerjee S, Sknepnek R, Marchetti MC
  Soft Matter 10, 2424 (2014)
• Polymorphism and bistability in adherent cells
  Banerjee S, Giomi L
  Soft Matter 9, 5251 (2013)
  
• Controlling cell-matrix traction forces by extracellular geometry
  Banerjee S, Marchetti MC
  New Journal of Physics 15, 035015 (2013)
  Featured in Highlights of 2013
• Cadherin-based intercellular adhesions organize epithelial cell-matrix traction forces
  Mertz AF, Che Y, Banerjee S, Goldstein JM, Rosowski KA, Revilla SF, Niessen CM, Marchetti MC, Dufresne ER, Horsley V
  Proc. Natl. Acad. Sci. USA 110, 842 (2013)
  Recommended by F1000Prime
• Contractile stresses in cohesive cell layers on finite-thickness substrates
  Banerjee S, Marchetti MC
  Physical Review Letters 109, 108101 (2012)
  
• Heterogeneous drying stresses in stratum corneum
  German GK, Engl WC, Pashkovski E, Banerjee S, Xu Y, Mertz AF, Hyland C, Dufresne ER
  Biophysical Journal 102, 2424 (2012)
  
• Scaling of traction forces with the size of cohesive cell colonies
  Mertz AF, Banerjee S, Che Y, German GK, Xu Y, Hyland C, Marchetti MC, Horsley V, Dufresne ER
  Physical Review Letters 108, 198101 (2012)
  Featured in Editors' suggestions
• Generic phases of cross-linked active gels: Relaxation, oscillation and contractility
  Banerjee S, Liverpool TB, Marchetti MC
  Europhysics Letters 96, 58004 (2011)
  
• Substrate rigidity deforms and polarizes active gels
  Banerjee S, Marchetti MC
  Europhysics Letters 96, 28003 (2011)
  
• Motor-driven dynamics of cytoskeletal filaments in motility assays
  Banerjee S, Marchetti MC, Müller-Nedebock KK
  Physical Review E 84, 011914 (2011)
  
• Instabilities and oscillations in isotropic active gels
  Banerjee S, Marchetti MC
  Soft Matter 7, 463 (2011)
  

^§equal authorship, *co-corresponding authors