• Amin R. Mazloom, Kalyan Basu, Subhrangsu S. Mandal, Mehran Sorourian and Sajal Das ,”DNA Sites Buried in Nucleosome become Accessible at Room Temperature: A Discrete-Event-Simulation based Modeling Approach”, Accepted for pub.  in the Int.  Symposium on Bioinformatics Research and Applications (ISBRA), 2007.

• Amin. R. Mazloom, Kalyan Basu, and Sajal K. Das,”A Random Walk Modelling Approach for Passive Metabolic Pathways in Gram-Negative Bacteria”, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2006.

• Amin R. Mazloom Kalyan Basu and Sajal K. Das ,“A Random Walk Modeling Approach for Modeling Passive Metabolic pathways in Gram-Negative Bacteria”, poster paper at Dallas Bioinformatics Workshop 2006.

• Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal Das, "iSimBioSys : Am 'In Silico' Discrete Event Simulation Framework for Modeling Biological Systems", poster paper at the proceedings of the IEEE Computational Systems Bioinformatics Conference, CSB 2005, pp.170-171.

• Samik Ghosh, Preetam Ghosh, Kalyan Basu, S. Daefler and S. Das, “iSimBioSys: A Discrete Event Simulation Platform for 'in silico' Study of Biological Systems”, accepted for publication at the IEEE 39th Annual Simulation Symposium, 2006.

• Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal Das, "A Diffusion Model to Estimate Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks" , poster paper at the proceedings of the IEEE Computational Systems Bioinformatics Conference, CSB 2005.

• Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler, "Stochastic Modeling of Cytoplasmic Reactions in Complex Biological Systems", accepted for publication at ICCSA 2006, Scotland.

• Kalyan Basu, Samik Ghosh, Preetam Ghosh and Sajal Das, "Genome scale cell modeling using stochastic discrete event simulation", poster presentation at the  2006 Stochastic Networks Conference, UIUC.

• Samik Ghosh, Preetam Ghosh, Kalyan Basu and Sajal Das, "A Hybrid Simulation Framework for genome scale study of molecular dynamics in Escherichia Coli", accepted for publications at the 7th. International Conference on Systems Biology (ICSB) 2006.

• S. Ghosh, D. Young, K. Gadkar, L. Wennerberg, K. Basu, “Towards Optimal Virtual Patients: An Online Adaptive Control Approach”, accepted for publication at the 29th International Conference of the IEEE Engineering in Medicine and Biology Society, 2007.

• S. Ghosh, P. Ghosh, K. Basu, S. Das, "Modeling the stochastic dynamics of gene expression in single cells: A Birth and Death Markov Chain Analysis”, accepted for publicationat The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2007.

• S.Ghosh, A. R. Mazloom, P. Ghosh, K. Basu, S.K Das, "Stochastic simulation of cellular dynamics: A Discrete Event based Approach", book chapter accepted for review at Springer-Verlag series in "Studies in Computational Intelligence", Applications of Computational Intelligence in Bioinformatics and Biomedicine:Current Trends and Open Problems (vol. 2), 2007. 

• S. Ghosh, P. Ghosh, K. Basu, S. Das, "Capturing the stochasticity in prokaryotic gene expression : A Birth and Death Markov Chain Approach", journal paper under review at IEEE/ACM Transactions in Computational Biology and Bioinformatics, 2007.

•  S. Ghosh, P. Ghosh, K. Basu, S. Das, S. Daefler, "A stochastic discrete event simulation approach to study system level dynamics of biological processes ", second round of revision at the ACM Transactions on Modeling and Computer Simulation (TOMACS), special issue on Successes In Modeling and Simulation Methodologies. 

•   P. Ghosh, S. Ghosh, K. Basu, S.K Das , “A Computationally Fast and Parametric Model to estimate Protein-Ligand Docking time for Stochastic Event based Simulation”, accepted for publication in The Transactions on Computational and Systems Biology, 2007.

•   P. Ghosh, S. Ghosh, K. Basu, S.K Das , "Parametric modeling of protein-DNA binding kinetics: A Discrete Event based Simulation approach", second round of revision at the Elsevier Journal on Discrete Applied Mathematics (DAM), 2007.

•  P. Ghosh, S. Ghosh, K. Basu, S.K Das, "A Markov Model-based Analysis of Stochastic Biochemical Systems", accepted for publication at Computational Systems Bioinformatics Conference, (CSB 07), 2007.

•  P. Ghosh, S. Ghosh, K. Basu, S.K Das, "Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes", IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB '07), pp. 439-446, 2007.

•  S. Ghosh, K.Basu, S. Daefler and S.K Das, “iSimBioSys: A Discrete Event Simulation Platform for 'in silico' Study of  Biological Systems”, proceedings of  the 39th IEEE Annual Simulation on Symposium,pp.204-213, 2006.

• K. Basu, S. Ghosh, P. Ghosh and S.K Das, "Genome scale cell modeling using stochastic discrete event simulation", poster presentation at the 7th Stochastic Networks Conference, UIUC, 2006.

•  S. Ghosh, P. Ghosh, K. Basu and S.K Das, "A Hybrid Simulation Framework for genome scale study  of molecular dynamics in Escherichia Coli", proceedings of the 7th. International Conference on Systems Biology (ICSB) 2006.

•  P. Ghosh, S. Ghosh, K. Basu, S.K Das and S. Daefler, “A Stochastic model to estimate the time taken for Protein-Ligand Docking”, IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB '06), pp. 1-8, 2006. 

Technical Reports

• P. Ghosh, S. Ghosh, K. Basu, S. Das, S. Daefler, "Estimation of the holding Time for Cytoplasmic Reactions in Stochastic Event Based Modeling of Complex Biological Networks", TR CSE-2005-09.

• P. Ghosh, S. Ghosh, K. Basu, S. Das, S. Daefler, "Transient analysis of Diffusion for charged molecules to model the input process in a stochastic event based simulation framework for the PhoPQ signal transduction system ", TR CSE-2005-07.

Modeling the two component PhoPQ system in Salmonella Typhimurium

• V.K. Rangavajhala, S. Daefler, "Modeling the Salmonella PhoPQ two component regulatory system", UTA Master's Thesis.