Publications

2023 2022 2021 2020 2019 2018 2017 2016 2014 2013 2012 2011 pre-2010


2023


Transcription factor dynamics - One molecule at a time
Annual Reviews of Cell and Developmental Biology 2023

Wagh KS, Stavreva DA, Upadhyaya A and Hager GL

[ARCDB]


Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states
Science Advances 2023

Wagh KS, Stavreva DA, Jensen RAM, Paakinaho V, Fettweis G, Schiltz RL, Wustner D, Mandrup S , Presman DM, Upadhyaya A and Hager GL

[Sci. Adv.]


Three-dimensional structured illumination microscopy with enhanced axial resolution
Nat. Biotechnology 2023

Li X, …, La Rivere P, Upadhyaya A and Shroff H

[Nat. Biotech]



2022


A tug of war between filament treadmilling and myosin induced contractility generates actin rings
eLife 2022

Ni Q, Wagh K, Pathni A, Ni H, Vashisht V, Upadhyaya A and Papoian G

[eLife]


Nanotopography modulates cytoskeletal organization and dynamics during T cell activation
Molecular Biology of the Cell 2022

Wheatley B, Rey-Suarez I, Hourwitz MJ, Kerr S, Shroff H, Fourkas JT, and Upadhyaya A

[MBoC]


Stripe transcription factors provide accessibility to co-binding partners in mammalian genomes
Molecular Cell 2022

Zhao Y,…,Upadhyaya A, Weirauch MT, Hager GL, and Casellas R

[Mol. Cell]


Non-Muscle Myosin II Is Essential for the Negative Regulation of B-Cell Receptor Signaling and B-Cell Activation
Frontiers in Immunology 2022

Seeley-Fallen MK, Lazzaro M, Liu C, Li Q-Z, Upadhyaya A, Zhao X, and Song W

[pdf] [FI]


Cytotoxic T Lymphocyte Activation Signals Modulate Cytoskeletal Dynamics and Mechanical Force Generation
Frontiers in Immunology 2022

Pathni A, Ozcelikkale A, Rey-Suarez I, Li L, Davis S, Rogers N, Xiao Z, and Upadhyaya A

[Frontiers in Immunology]


The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation
Science Advances 2022

Rinaldi L, Fettweis G, Garcia DA,…, Upadhyaya A,… and Hager GL

[Sci. Adv.]



2021


Multiview confocal super-resolution microscopy
Nature 2021

Wu Y, Han X, Su Y, Glidewell, M,…, Rey-Suarez I,…Upadhyaya A,…, La Riviere P and Shroff H

[Nature]


WASp is crucial for the unique architecture of the immunological synapse in germinal center B-cells
Frontiers in Cell and Developmental Biology 2021

Li Y, Bhanja A, Upadhyaya A, Zhao X, and Song W

[pdf] [FCDB]


Phase separation in transcription factor dynamics and chromatin organization
Current Opinion in Structural Biology 2021

Wagh KS, Garcia DA, and Upadhyaya A

[COSB]


Actomyosin dynamics modulate microtubule deformation and growth during T cell activation
Molecular Biology of the Cell 2021

Rey-Suarez I, Rogers N, Kerr S, Shroff H, and Upadhyaya A

[MBoC]


Bidirectional feedback between BCR signaling and actin cytoskeletal dynamics
FEBS Journal 2021

Bhanja A, Rey-Suarez I, and Upadhyaya A


Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes
Nature Methods 2021

Chen J, Sasaki H, Lai H, Su Y, Liu J, Wu Y, Zhovmer A, Combs CA, Rey-Suarez I, Chang H-Y, Huang C-C, Li X, Guo M, Nizambad S, Upadhyaya A, Lee S-J, Lucas LAG, and Shroff H

[Nat. Meth.]


Mechanical regulation of transcription - Recent advances
Trends in Cell Biology 2021

Wagh KS, Ishikawa M, Garica DA, Stavreva DA, Upadhyaya A, and Hager GL

[pdf] [Trends in Cell Biology]


Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model
Nucleic Acids Research 2021

Garica DA, Fettweis GJ, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, and Hager GL

[pdf] [Nucleic Acids Research]


An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors
Molecular Cell 2021

Garica DA, Johnson TA, Presman DM, Fettweis G, Wagh KS, Rinaldo, L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, and Hager GL

[pdf] [Molecular Cell]



2020


WASP family proteins regulate the mobility of the B cell receptor during signaling activation
Nat. Commun. 2020

Rey-Suarez I, Wheatley BA, Koo P, Bhanja A, Shu Z, Mochrie S, Song W, Shroff H and Upadhyaya, A

[pdf] [Nat. Commun.]


Rapid image deconvolution and multiview fusion for optical microscopy
Nat. Biotech. 2020

Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, Prince V, Waters JC, Annunziata CM, Hafner M, Mohler WA, Chitnis AB, Upadhyaya, A, Usdin TB, Bao Z, Colón-Ramos D, La Riviere P, Liu H, Wu Y, and Shroff H

[Nat. Biotech.]


Bcl10 is associated with actin dynamics at the T cell immune synapse
Cellular Immunology 2020

Wagh KS, Wheatley BA, Traver MK, Hussain I, Schaefer BC and Upadhyaya A

[pdf] [Cellular Immunology]



2019


Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling
PLoS Computational Biology 2019

Chandrasekaran A, Upadhyaya A, and Papoian GA

[PLoS Comp. Biol.]


Transcriptional bursting and co-bursting regulation by steroid hormone release pattern and transcription factor mobility
Molecular Cell 2019

Stavreva DA, Garcia DA, Fettweis G, Pegoraro G,… Upadhyaya A and Hager, GL

[pdf] [Molecular Cell]



2018


Single-shot super-resolution total internal reflection fluorescence microscopy
Nat. Meth. 2018

Guo M, …, Upadhyaya, A, Taraska J, and Shroff H

[Nat. Meth.]


Subcellular topography modulates actin dynamics and signaling in B-cells
Molecular Biology of the Cell 2018

Ketchum CM, Sun X, Suberi A, Fourkas JT, Song W and Upadhyaya A

[pdf] [MBoC]


Biophysical techniques to study B cell activation - single-molecule imaging and force measurements
Methods in Molecular Biology 2018

Rey I, Garcia DA, Wheatley BA, Song W, and Upadhyaya A



2017


Dynamic microtubules regulate cellular contractility during T-cell activation
PNAS 2017

Hui KL and Upadhyaya A

[pdf] [PNAS]


Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy
Nature Communications 2017

Wu Y, Kumar A, Smith C, Ardiel E, Chandris P, Christensen R, Rey-Suarez I, Guo M, Vishwasrao HD, Chen J, Tang J, Upadhyaya A, La Riviere PJ, and Shroff H

[Nat. Commun.]


Mechanosensing in the immune response
Seminars in Cell & Developmental Biology 2017

Upadhyaya, A

[pdf]


Topography on a subcellular scale modulates cellular adhesions and actin stress fiber dynamics in tumor associated fibroblasts
Physical Biology 2017

Azatov M, Sun X, Suberi A, Fourkas JT, and Upadhyaya A

[pdf]



2016


The actin crosslinking protein palladin modulates force generation and mechanosensitivity of tumor associated fibroblasts
Scientific Reports 2016

Azatov M, Goicoechea SM, Otey CA, and Upadhyaya A

[pdf]



2014


Cytoskeletal forces during signaling activation in Jurkat T-cells.
Molecular Biology of the Cell 2014

Hui KL, Balagopalan L, Samelson LE, and Upadhyaya A

[pdf]


The actin cytoskeleton coordinates the signal transduction and antigen processing functions of the B cell antigen receptor
Frontiers in Biology 2014

Liu C, Fallen MK, Miller H, Upadhyaya A, and Song W


Actin-binding protein 1 links B-cell antigen receptors to negative signaling pathways.
Proceedings of the National Academy of Sciences of the United States of America 2014

Seeley-Fallen MK, Liu LJ, Shapiro MR, Onabajo OO, Palaniyandi S, Zhu X, Tan TH, Upadhyaya A, and Song W

[PNAS]


Ligand mobility regulates B cell receptor clustering and signaling activation
Biophysical Journal 2014

Ketchum C, Miller H, Song W, and Upadhyaya A

[pdf]


Adhesion-dependent modulation of actin dynamics in Jurkat T cells
Cytoskeleton 2014

Lam Hui K, Kwak SI, and Upadhyaya A

[pdf]



2013


N-WASP is essential for the negative regulation of B cell receptor signaling
PLoS Biology 2013

Liu C, Bai X, Wu J, Sharma S, Upadhyaya A, Dahlberg CI, Westerberg LS, Snapper SB, Zhao X, and Song W

[PLoS Biol.]


Actin-mediated feedback loops in B-cell receptor signaling
Immunological Reviews 2013

Song W, Liu C, Seeley-Fallen MK, Miller H, Ketchum C, and Upadhyaya A

[pdf]


The pivotal position of the actin cytoskeleton in the initiation and regulation of B cell receptor activation
Biochimica et Biophysica Acta 2013

Song W, Liu C, and Upadhyaya A

[Biochim. Biophys. Acta.]



2012


Analyzing actin dynamics during the activation of the B cell receptor in live B cells
Biochemical and Biophysical Research Communications 2012

Liu C, Miller H, Sharma S, Beaven A, Upadhyaya A, and Song W

[BBRC]


Morphology and viscoelasticity of actin networks formed with the mutually interacting crosslinkers - palladin and alpha-actinin
PloS One 2012

Grooman B, Fujiwara I, Otey C, and Upadhyaya A

[pdf]


Membrane dynamics correlate with formation of signaling clusters during cell spreading
Biophysical Journal 2012

Lam Hui K, Wang C, Grooman B, Wayt J, and Upadhyaya A

[pdf]


Actin reorganization is required for the formation of polarized B cell receptor signalosomes in response to both soluble and membrane-associated antigens
Journal of Immunology 2012

Liu C, Miller H, Orlowski G, Hang H, Upadhyaya A, and Song W

[J. Immunol.]



2011


A balance of Bruton's tyrosine kinase and SHIP activation regulates B cell receptor cluster formation by controlling actin remodeling
Journal of Immunology 2011

Liu C, Miller H, Hui KL, Grooman B, Bolland S, Upadhyaya A, and Song W

[J. Immunol.]



pre-2010


Power-limited contraction dynamics of Vorticella convallaria - an ultra-fast biological spring
Biophysical Journal 2008

Upadhyaya A, Wong J, Daniels M, van Oudenaarden A, and Mahadevan L

[pdf]


Neutrophil chemorepulsion in defined interleukin-8 gradients in vitro and in vivo
Journal of Leukocyte Biology 2006

Tharp WG, Yadav R, Irimia D, Upadhyaya A et al.

[J. Leukoc. Biol.]


Actin polymerization - forcing flat faces forward
Current Biology 2004

Upadhyaya A and van Oudenaarden A


Tension in tubulovesicular networks of Golgi and endoplasmic reticulum membranes
Biophysical Journal 2004

Upadhyaya A, Sheetz MP

[pdf]


Elastic instability in growing yeast colonies
Biophysical Journal 2004

Nguyen B, Upadhyaya A, van Oudenaarden A, and Brenner MP

[pdf]


Biomimetic systems for studying actin-based motility
Current Biology 2003

Upadhyaya A and van Oudenaarden A

[pdf]


Probing polymerization forces by using actin-propelled lipid vesicles
Proceedings of the National Academy of Sciences 2003

Upadhyaya A, Chabot JR, Andreeva A, Samadani A, van Oudenaarden A

[pdf]


Improving the realism of the cellular Potts model in simulations of biological cells
Physica A. 2003

Ouchi NB, Glazier JA, Rieu JP, Upadhyaya A, and Sawada, Y

[pdf]


A microfabricated array bioreactor for perfused 3D liver culture
Biotechnology and Bioengineering 2002

Powers MJ, Domansky K, Kaazempur-Mofrad MR, Kalezi A, Capitano A, Upadhyaya A, Kurzawski P, Wack KE, Stolz DB, Kamm R, and Griffith LG


Bursts and cavity formation in Hydra cell aggregates - Experiments and simulations
Physica A 2001

Mombach JCM, de Almeida RMC, Thomas, GL, Upadhyaya A, and Glazier JA

[pdf]


Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates
Physica A 2001

Upadhyaya A, Rieu JP, Sawada Y, and Glazier JA

[pdf]


Diffusion and deformations of single Hydra cells in cellular aggregates
Biophysical Journal 2000

Upadhyaya A, Rieu JP, Ouchi NB, Sawada Y, and Glazier JA

[pdf]


First Steps Towards a Comprehensive Model of Tissues, or A Physicist Looks at Development
Dynamical Networks in Physics and Biology, Springer 1997

Upadhyaya A and Glazier JA

[pdf]