• Surface condensation drives clustering 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, In press
• Tunability enhancement of gene regulatory motifs through competition for regulatory protein resources, Das, S., *Choubey, S.,  (2020)  Physical Review E, 102 (5), 052410
• Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif, Ali, Md. Z.,Parisutham, V., Choubey, S., Brewster, R. (2020) eLife (9):e56517
• Probing the mechanisms of transcription elongation using nascent RNA statistics, *Ali, Md. Z., *Choubey, S., Das, D., Brewster, R. (2020) Biophysical Journal 118(7), 1769-1781
• Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications, Ali, Md. Z., *Choubey, S. (2019) Physical Biology 16(6), 061001
• Cell-to-cell variability in organelle abundance reveals mechanisms of organelle biogenesis, Choubey, S., Das, D., Majumdar, S. (2019) Physical Review E 100(2), 022405
• 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., (2019) Science 364(6440), 593-597
• Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells, Choubey, S., Kondev, J., Sanchez, A. (2018) Biophysical Journal 114 (9), 2072-2082
• Nascent RNA kinetics: Transient and steady state behavior of models of transcription, Choubey, S. (2018) Physical Review E 97(2), 022402
• Effect of Transcription Factor Resource Sharing on Gene Expression Noise, Das, D., Dey, S., Brewster, R., *Choubey, S. (2017) Plos Computational Biology 13(4): e1005491
• 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. (2017) eLife (6):e20487 (*Shared first author)
• Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules, Choubey, S., Sanchez, A., Kondev, J. (2015) Plos Computational Biology 11(11): e1004345
• Regulation of noise in gene expression,  Sanchez, A., *Choubey, S., Kondev, J. (2013) Annual Review of Biophysics 42: (461-491)
• Stochastic models of transcriptional regulation: from single molecules to single cells.,  *Sanchez, A., *Choubey, S., Kondev, J. (2013) Methods 62: 23-25 

         (* Shared first author)