Faculty career @ IMSc

 

• Direct contact of the bacterial surface induces phase separation in the host phagosome membrane          Jayesh JB, N Aniruddha, Koiri D,  Shaikh J,  Choubey S, Mohammed S                                                                         Preprint, Under review                                                                                                                                                                    

• Real-time visualization reveals Mycobacterium tuberculosis ESAT-6 disrupts phagosome via fibril-mediated vesiculation

       Koiri D, Nandi M,  Hameem A, Aher JB, Meher G, Behura A, Kumar A, Choudhary V, Choubey S,

       Mohammed S, 

       Preprint, Under review 

 

• Decoding the role of DNA sequence on protein-DNA co-condensation

       Singh RK., Swain, P., Ganji, M, Choubey, S Under review

       Preprint, Under review

 

• Temporal regulation of organelle biogenesis

       Dixit, S., N, Aniruddha., Choubey, S.  Under review

       Preprint, Under review

​

• Role of protein–protein interactions on organization and dynamics of a model chromatin

       Swain, P., Choubey, S.,  Vemparala S 

       The Journal of Chemical Physics (2024)

​

• Actin Filament Barbed End Depolymerization by Combined Action of Profilin, Cofilin, and Twinfilin

      Arya, A., Choubey, S., Shekhar S. (2024)

       PRX Life (2024) 

 

• Governing principles of transcriptional logic out of equilibrium

       Dixit, S., Middlekoop, TM., Choubey, S.

       Biophysical Journal  (2024)

 

• Gene regulation meets Bayesian Nonparametrics

       Choubey, S.,

       Nature Computational Science  (2023)

 

• Efficacy of information transmission in cellular communication

       Sarkar, S., Ali, Md. Z., Choubey, S.

       Physical Review Research (2023)

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   Postdoctoral and Graduate Research

 

• Sequence-dependent surface condensation of a pioneer transcription factor on DNA

       Morin, J.*, Wittmann, S.*, Choubey, S.*, Klosin, A., Golfier, S., Hyman, AA., Jülicher, F., Grill, S.

       Nature Physics  (2022)  (*Shared first author)

 

• Tunability enhancement of gene regulatory motifs through competition for regulatory protein resources

       Das, S., Choubey, S.

       Physical Review E (2020)

 

• Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif

       Ali, Md. Z.,Parisutham, V., Choubey, S., Brewster, R.

       eLife (2020)

 

• Probing the mechanisms of transcription elongation using nascent RNA statistics

       *Ali, Md. Z., *Choubey, S., Das, D., Brewster, R.

       Biophysical Journal (2020)

       (*Shared first and corresponding author)

 

• Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications

       Ali, Md. Z., Choubey, S.

       Physical Biology (2019)

 

• Cell-to-cell variability in organelle abundance reveals mechanisms of organelle biogenesis

       Choubey, S., Das, D., Majumdar, S.

       Physical Review E (2019)

 

• Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies

       Bashor, C., Patel, N. Choubey, S., Beyzavi, A., Ali Beyzavi, A., Kondev, J., Collins, J., Khalil, A.,

       Science  (2019)

 

• Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells

       Choubey, S., Kondev, J., Sanchez, A.

       Biophysical Journal

​

• Nascent RNA kinetics: Transient and steady state behavior of models of

       transcription,

       Choubey, S.

       Physical Review E  (2018)

 

• Effect of Transcription Factor Resource Sharing on Gene Expression Noise

       Das, D., Dey, S., Brewster, R., Choubey, S.

       Plos Computational Biology (2017)                    

 

• Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states

      Jang, S.*, Choubey, S.*, Furchtgott, L., Zou, LN., Doyle, A., Menon, V., Loew, E.,  Krostag, AR., Martinez, RA.,              Madisen, L., Levi, BP., Ramanathan, S. 

      eLife (2017)

      (*Shared first author)

 

• Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules

       Choubey, S., Sanchez, A., Kondev, J.

       Plos Computational Biology (2015)

 

• Regulation of noise in gene expression

       Sanchez, A., Choubey, S., Kondev, J.

       Annual Review of Biophysics (2013)

 

• Stochastic models of transcriptional regulation: from single molecules to single cells.

       Sanchez, A*., Choubey, S*., Kondev, J.

       Methods (2013)

       (*Shared first author)