Faculty career @ IMSc

 

                                                                                                                                                              

• Phase separation as a tunable regulator of canonical gene regulatory motifs.                                   Chakraborty P,  Nandi M, Choubey S                                                                                                                                       Preprint, Under review                                                                                                                                                                                                                             

• 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                                                                                                                                                                   

• Membrane Interfacial Potential Governs Surface Condensation and Fibrillation of α-Synuclein in Neurons    Shaikh J, N Aniruddha, Mitra T, Modak AS, Biswas K, Meher G, Aher JB, Kannan NA, Sahu BS, Ghatak S, Choubey S,  Mohammed S                                                                                                                                                       Nature Communications (2026), In press                                                                                                                                                                

• A moments-based approach for inferring mechanisms of transcriptional regulation using nascent RNA data
  Wen K, Liao Y, Wang J, Choubey S, Jiao F                                                                                                                            Biophysical Journal (2026)                                                                                                                                                               

• Sequence-dependent co-condensation of Lsr2 with DNA elucidates the mechanism of genome compaction in Mycobacterium tuberculosis                                                                                                               Satheesh T, Gaur P, Singh RK, Shahu S, Ramakrishnan S, Srivastava M, Neogi S, Choubey S, Ganji M               Nucleic Acids Research (2026)                                                                                                                                                        

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

       Singh RK, Swain P, Ganji M, Choubey S

       Plos Computational Biology (2025)​

 

• A generalized theoretical framework to investigate multicomponent actin dynamics                                   Nandi M, Shekhar S, Choubey S                                                                                                                                             Plos Computational Biology (2025),  

 

• Temporal regulation of organelle biogenesis

       Dixit S, N Aniruddha, Choubey, S.  

       Physical Biology (2025)

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• 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, 

      Cell Reports (2025) ​​

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• An urgent need for longitudinal microbiome profiling coupled with machine learning interventions             Dey P, Choubey S                                                                                                                                                                        Frontiers in Microbiology  (2024)

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• 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)

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

      Arya, A, Choubey, S, Shekhar S 

       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

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• 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)