Publications


Following are some of our selected publications in the domain of Bio-Design Automation.

PhD Thesis
The PhD theses carried out in BDA Compute research group are given below:

  1. Hasan Baig, “Methods and Tools for the Analysis, Verification and Synthesis of Genetic Logic Circuits”.

 

Journal Articles

  1. Hasan Baig and Jan Madsen, “GeneTech – A Technology Mapping Tool for Genetic Logic Circuits”, IEEE Transactions on Biomedical Engineering. (Under review)
  2. Hasan Baig and Jan Madsen, “An Automated Approach to Verify the Logic of Genetic Circuits from Experimental Data”, ACM Journal on Emerging Technologies. (Under review)
  3. Hasan Baig and Jan Madsen, “Simulation Approach for Timing Analysis of Genetic Logic Circuits”, ACS Synthetic Biology, January 19, 2017. [Link] [Video Demo]
  4. Hasan Baig and Jan Madsen, “D-VASim – An Interactive Virtual Laboratory Environment for the Simulation and Analysis of Genetic Circuits”, Bioinformatics, October 06, 2016. doi: 10.1093/bioinformatics/btw592. [Link]

International Conferences and Workshops

  1. Hasan Baig and Jan Madsen, “Taming Living Logic using Formal Methods”, Models, Algorithms, Logics and Tools, LNCS, vol. 10460, pp. 503-515, Springer, Cham, 2017. [Link]
  2. Hasan Baig and Jan Madsen, “A Top-down Approach to Genetic Circuit Synthesis and Optimized Technology Mapping”, 9th International Workshop on Bio Design Automation (IWBDA), 28-29, 2017. [Link]
  3. Hasan Baig and Jan Madsen, “Logic Analysis and Verification of n-input Genetic Logic Circuits”, Design Automation and Test in Europe (DATE), pp. 654-657, 2017. [Link] [Video Demo]
  4. Hasan Baig and Jan Madsen, “Logic and Timing Analysis of Genetic Logic Circuits using D-VASim”, 8th International Workshop on Bio Design Automation (IWBDA) 2016, Newcastle upon Tyne, UK, August 16-18, 2016. [Link]
  5. Hasan Baig and Jan Madsen, “D-VASim: Dynamic Virtual Analyzer and Simulator for Genetic Circuits”, 7th International Workshop on Bio-Design Automation (IWBDA) 2015, Seattle Washington, USA, Aug 19-21, 2015. [Link]

Poster/Demo presentations

  1. Hasan Baig and Jan Madsen, “Timing Analysis of Genetic Logic Circuits using D-VASim”. University Booth at Design Automation and Test in Europe (DATE) 2016, Dresden, Germany, Mar 15-17, 2016. [PDF]
  2. Hasan Baig and Jan Madsen, “Analysis and Verification of Genetic Logic Circuits using D-VASim”, Synthetic and Systems Biology Summer School (SSBSS) 2015, Taormina, Italy, July 5-9, 2015.

Reports published by Industries

  1. D-VASim: A Software Tool to Simulate and Analyze Genetic Logic Circuits, published by National Instruments and can be seen here