Research

Publications

  • A. Gupta, P. Gautam, K. Wennerberg and T. Aittokallio (2018), A normalized drug response metric improves accuracy and consistency of drug sensitivity quantification in cell-based screening. Nature Communications, under review.
  • J. Tang, P. Gautam, A. Gupta, L. He, S. Timonen, Y. Akimov, A. Szwajda, A. Jaiswal, D. Turei, B.Yadav, M. Kankainen, J. Saarela, J. Saez-Rodriguez, K. Wennerberg and T. Aittokallio (2018), Systematic prediction of selective synergies with a network pharmacology model: the case of combined Aurora B and ZAK inhibition in MDA-MB-231 breast cancer cells. Cell Reports, under review.
  • X. Qiao, Y. Liu, M. L. Prada, H. Haikala, K. Talvinen, A. Gupta, L. Yetukuri, J. W. Pylvanainen, J. Klefstrom, A. Meinander, T. Aittokallio, P. Kronqvist, V. Hietakangas, M. Eilers, and J. Westermarck (2018), Control of MYC-dependent apoptotic threshold by a co-amplified ubiquitin E3 ligase UBR5, Nature Communications, under review.
  • A. Gupta and P. Mendes (2018), An Overview of Network-Based and Network-Free Approaches for Stochastic Simulation of Biochemical Systems. Computation, 6, 9; doi: 10.3390/computation6010009.
  • J. Tang, Z.R. Tanoli, B Ravikumar, Z. Alam, A. Rebane, M. Vaha-Koskela, G. Peddinti, A. J. van Adrichem, J. Wakkinen, A. Jaiswal, E. Karjalainen, P. Gautam, L. He, E. Parri, S. Khan, A. Gupta, M. Ali, L. Yetukuri, A.L. Gustavsson, B. Seashore-Ludlow, A. Hersey, A.R. Leach, J.P. Overington,G. Repasky, K. Wennerberg, and T. Aittokallio (2017), DrugTargetCommons: a community effort to build a consensus knowledge base for drug-target interactions. Cell Chemical Biology, doi: 10.1016/j.chembiol.2017.11.009.
  • R. Neeli-Venkata, A. Gupta, A. Martikainen, N. Goncalves, J. Fonseca, and A. Ribeiro (2016). Robustness of the process of nucleoid exclusion of protein aggregates in Escherichia coli. Journal of Bacteriology, 198(3), doi: 10.1128/JB.00848-15.
  • S. Oliveira, R. Neeli-Venkata, N. Goncalves, J. Santinha, L. Martins, H. Tran, J. Makela, A. Gupta, M. Barandas, A. Hakkinen, J. Lloyd-Price, J. Fonseca, and A. Ribeiro (2015). Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli. Molecular Microbiology, 99(2), doi: 10.1111/mmi.13257.
  • A. Gupta, J. Lloyd-Price, S. M.D. Oliveira, A.B. Muthukrishnan, and A.S. Ribeiro (2014) Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking. Physical Biology, 11(6):066005, doi: 10.1088/1478-3975/11/6/066005..
  • A. Gupta, J. Lloyd-Price, and A.S. Ribeiro (2014) Modelling Polar Retention of Complexes in Escherichia coli. Lecture Notes in Computer Science 8859. DOI: 10.1007/978-3-319-12982-2_17.
  • A. Gupta, J. Lloyd-Price, and A.S. Ribeiro (2014) In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biology. DOI: 10.3233/ISB-140462.
  • A. Gupta, J. Lloyd-Price, M. Kandhavelu, S. M.D. Oliveira, and A.S. Ribeiro (2013) In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli, Biophysical Journal,106(9). DOI: http://dx.doi.org/10.1016/ j.bpj.2014.03.035.
  • J. Lloyd-Price, A. Gupta, and A.S. Ribeiro (2012) SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations, Bioinformatics, DOI: 10.1093/bioinformatics/bts556.
  • M. Kandhavelu, J. Lloyd-Price, A. Gupta, A.B. Muthukrishnan, O. Yli-Harja, and A.S. Ribeiro (2012) Regulation of the in vivo kinetics of the rate limiting steps of the lac/ara-1 promoter.FEBS Letters 586, 3870-3875. DOI:10.1016/j.febslet.2012.09.014.
  • J. Lloyd-Price, A. Gupta, O. Yli-Harja, and A.S. Ribeiro (2012) Robustness and information propagation in attractors of random Boolean networks, PLoS ONE 7(7):e42018. DOI:10.1371/journal.pone.0042018
  • M. Kandhavelu, H. Mannerstrom, A. Gupta, A. Hakkinen, J. Lloyd-Price, O. Yli-Harja, and A.S. Ribeiro (2011) In vivo kinetics of transcription initiation of the larpromoter in Escherichia coli. Evidence for a sequential mechanism with two rate limiting steps. BMC Systems Biology 5:149. DOI:10.1186/1752-0509-5-149

Presentations

  • A. Gupta, P. Mendes. Benchmarking implementations of stochastic simulation of biochemical networks, Center for Cell Analysis & Modeling, UConn Health, Farmington, CT, USA, March 09, 2018.
  • A. Gupta. Drug sensitivity scoring; past, present, and future, Center for Quantitative Medicine, UConn Health, Farmington, CT, USA, January 2, 2018.
  • A. Gupta, P. Gautam, K. Wennerberg, and T. Aittokallio. Improved drug Response Quantification Based on the Elimination of Experimental Variabilities in High-Throughput Cell-Based Screenings. EU-Life Meeting: Principles of Homeostasis, Max Delbruuck Centrum for Molecular Medicine, Berlin May 22-23, 2017.
  • A. Gupta, J. Lloyd-Price, and A. Ribeiro. Modelling polar retention of complexes in Escherichia coli. 12th Conference on Computational Methods in Systems
    Biology, Manchester, UK, November 17-19, 2014.
  • A. Gupta, J. Lloyd-Price, and A. Ribeiro. Modeling partitioning in cell division and subsequent aging in Bacteria. International Conference in Computational Cell Biology, Blacksburg, Virginia, USA, August 14-16, 2013.
  • A. Gupta, J. Lloyd-Price, M. Kandhavelu, S. Oliveira, and A. Ribeiro. Cell division asymmetries in Escherichia coli when in sub-optimal conditions. 10th International Workshop on Computational Systems Biology, Tampere, Finland, June 10-12, 2013.
  • A. Gupta, J. Lloyd-Price, O. Yli-Harja, and A. Ribeiro. Attractor robustness does not restrict information propagation in critical random Boolean networks,. 9th International Workshop on Computational Systems Biology, Ulm, Germany, June 4-6, 2012.

Theses

  • Doctoral Thesis: “Effects of Intracellular and Partitioning Asymmetries in Escherichia coli.”
  • Master’s Thesis: “Stochastic processes as a source of cell to cell diversity and cellular ageing”

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