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
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 Escherichiacoli 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.
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”