Research Interests

During my doctoral program, I developed solutions for several computationally challenging problems from molecular biology in the areas of gene expression, sequence analysis and progression of cancer. With a background in Computer Science, my coursework in machine learning, data mining, statistics and combinatorics enabled me to approach these problems from a computational and analytical point of view.

In the future, my research interest continues to be in different areas of bioinformatics and related fields with computationally challenging problems. Intricate cellular structures of the organisms, precise and stochastic nature of biological events, error in measurements, massive size of data coupled with domain specific idiosyncrasy (such as high dimension of microarray data) render these problems difficult to solve and expensive to compute. As a result, off-the-shelf machine learning and data mining techniques do not always produce satisfactory results. A more efficacious approach is to build the methods that can leverage the information from the relevant biology domains. As a computational biologist, I would like to see myself in the role of building customized models and methods that will minimize this gap between mathematical logic and biological phenomenon.

For a complete account of my research interest please mail me at nirmalya AT cise DOT ufl DOT edu .

Publications

Journal Papers

• Nirmalya Bandyopadhyay, Manas Somaiya, Tamer Kahveci, Sanjay Ranka
  Analyzing Differential Gene Regulation in Two Group Perturbation Experiments
  accepted to BMC Genomics.
• Nirmalya Bandyopadhyay, Tamer Kahveci
  GBA Manager : An online tool for querying low complexity regions in proteins
  Journal of Computational Biology, 17(1):73-7, 2010. (PDF)
• Nirmalya Bandyopadhyay, Sanjay Ranka, Y. Sun, Steve Goodison, Tamer Kahveci
  Pathway based Feature Selection for Cancer Microarray Data
  Journal of Advances in Bioinformatics, Volume 2009 (2009). (PDF)
• Jun Liu, Nirmalya Bandyopadhyay, Sanjay Ranka, Michael Baudis, Tamer Kahveci
  Inferring Progression Models for CGH data
  Bioinformatics, 25:17, pages 2208-2215, 2009. (PDF)

Conference Papers

• Nirmalya Bandyopadhyay, Sanjay Ranka, Tamer Kahveci
  SSLPred: Predicting Synthetic Sickness Lethality
  Pacific Symposium on Biocomputing (PSB), 2012.
• Nirmalya Bandyopadhyay, Manas Somiya, Sanjay Ranka, Tamer Kahveci,
  Identifying Differentially Regulated Genes ,
  IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011. (PDF)
• Nirmalya Bandyopadhyay, Manas Somiya, Sanjay Ranka, Tamer Kahveci,
  Modeling Perturbations using Gene Networks,
  International Conference on Computational Systems Biology (CSB), 2010. (PDF)
  
• Nirmalya Bandyopadhyay, Mark Settles, Tamer Kahveci,
  RepFrag: A Graph based Method for Finding Repeats and Transposons from Fragmented Genomes,
  International Conference On Bioinformatics and Computational Biology (ACM-BCB), 2010. (PDF)
  

Book Chapters

• Bin Song, I. Esra Büyüktahtakin, Nirmalya Bandyopadhyay, Sanjay Ranka and Tamer Kahveci,
  Identifying Enzyme Knockout Strategies on Multiple Enzyme Associations,
  Bioinformatics - Trends and Methodologies, Mahmood A. Mahdavi (Ed.), ISBN: 978-953-307-282-1, InTech 2011. (PDF)
  
• Nirmalya Bandyopadhyay, K. Basu and Prabhat Mishra,
  HMDES, ISDL and Other Contemporary ADLs, Architecture Description Languages: Applications and Methodologies
  Processor Description Languages, Prabhat Mishra and Nikil Dutt, Editors, Morgan Kaufmann Publishers, 2008.

Presentations

• Identifying Differentially Regulated Genes,
  ICCABS, Orlando, FL, February 2011 (talk).(PPT)
• Risky Keywords Detection and Risk Score Program,
  Amazon.com, Seattle, WA, August 2010 (invited talk).
• Modeling Perturbations using Gene Networks,
  CSB, Palo Alto, CA, August 2010 (talk).(PPT)
• RepFrag: A Graph based Method for Finding Repeats and Transposons from Fragmented Genomes,
  ACM-BCB, Niagara Falls, NY, August 2010 (talk).(PPT)

Software

Developed a web server named GBA Manager using HTML and PHP for executing GBA at the backend. GBA is a novel algorithm for identifying low complexity regions in a protein sequence. (Link)

Professional Activities

Have been a reviewer for

• Knowledge and Information Systems (KAIS)
• Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD)
• International Conference on Cotemporary Computing (IC3)
• International Conference on Computational Systems Bioinformatics (CSB)
• Advances in Bioinformatics