Research Interests

• Bioinformatics, System Biology, Granular Computing, Neural Networks, Soft Computing, Genetic Algorithms and Data mining

Publications                      

·        S. Roy, J. Singh and S. S. Ray “Weighted Combination of Lukasiewicz implication and Fuzzy Jaccard similarity in Hybrid Ensemble Framework (WCLFJHEF) for Gene Selection”, Computers in Biology and Medicine, vol. 170, no. 107981, pp. 1-11, 2024.

·        A. Kundu, J. Harsolia, J. K. Pal and S. S. Ray, S. Agrawal and S. Ghosh “Predicting Drug-Resistant miRNAs in Cancer”, Network Modeling Analysis in Health Informatics and Bioinformatics, vol. 12, no. 6, pp. 1-17, 2023.

·        S. S. Ray, S. Agrawal and S. Ghosh “Decision Theoretic Rough Set-Based Neighborhood for Self-Organizing Map”, SN Computer Science, vol. 2, no. 102, pp. 1-15, 2021.

·        J. K. Pal, S. S. Ray and S. K. Pal “Identifying Drug Resistant miRNAs using Entropy Based Ranking”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 3, pp. 973-984, 2021. Webpage and Software

·        S. S. Ray and S. Misra “Genetic Algorithm for Assigning Weights to Gene Expressions using Functional Annotations”, Computers in Biology and Medicine, vol. 104, pp. 149-162, 2019. Webpage and Software

·        J. K. Pal, S. S. Ray, S. B. Cho and S. K. Pal “Fuzzy-Rough Entropy Measure and Histogram Based Patient Selection for miRNA Ranking in Cancer”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, pp. 659-672, 2018. Webpage and Software

·        S. Misra and S. S. Ray “Finding optimum width of discretization for gene expressions using functional annotations”, Computers in Biology and Medicine, vol. 90, pp. 59-67, 2017. Webpage and Software

·        J. K. Pal, S. S. Ray and S. K. Pal “Fuzzy mutual information based grouping and new fitness function for PSO in selection of miRNAs in cancer”, Computers in Biology and Medicine, vol. 89, pp. 540-548, 2017. Webpage and Software

·        S. S. Ray and S. Misra “A Supervised Weighted Similarity Measure for Gene Expressions using Biological Knowledge”, Gene, vol. 595, no. 2, pp. 150-160, 2016. Webpage and Software

·        D. M. Jr, F. M. Lopes, and S. S. Ray “Inference of Gene Regulatory Networks by Topological Prior Information and Data Integration”, Emerging Research in the Analysis and Modeling of Gene Regulatory Networks, I. V. Ivanov, X. Qian and R. Pal (Eds.), pp. 1-51, IGI Global, Hershey, Pennsylvania, 2016.

·        A. Ganivada, S. S. Ray, and S. K. Pal “Fuzzy Rough Granular Networks for Pattern Analysis”, Pattern Recognition and Big Data, S. K. Pal and A. Pal (Eds.), pp. 487-511, World Scientific, Singapore, 2016.

·        S. S. Ray, A. Ganivada, and S. K. Pal “A Granular Self-Organizing Map for Clustering and Gene Selection in Microarray Data”, IEEE Transactions on Neural Networks and Learning Systems, vol. 27, no. 9, pp. 1890-1906, 2016. Webpage and Software

·        J. K. Pal, S. S. Ray, and S. K. Pal “Identifying Relevant Group of miRNAs in Cancer using Fuzzy Mutual Information”, Medical & Biological Engineering & Computing, vol. 54, issue 4, pp. 701-710, 2016. Webpage and Software

·        S. S. Ray and S. Maiti “Noncoding RNAs and their annotation using metagenomics algorithms”, Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, vol. 5, issue 1, pp. 1-20, 2015.

·        F. M. Lopes, S. S. Ray, R. F. Hashimoto, and R. M. Cesar “Entropic Biological Score: a cell cycle investigation for GRNs inference”, Gene, vol. 541, no. 2, pp. 129-137, 2014.

·        Jayanta K. Pal, Shubhra Sankar Ray, and Sankar K. Pal “A Weighted Threshold for detection of Cancerous miRNA Expressions”, Fundamenta Informaticae, vol. 127, nos. 1-4, pp. 289-305, 2013.

·        Avatharam Ganivada, Shubhra Sankar Ray, and Sankar K. Pal “Fuzzy rough sets, and a granular neural network for unsupervised feature selection”, Neural Networks, vol. 48, pp. 91-108, 2013.

·        Shubhra Sankar Ray and Sankar K. Pal “RNA secondary structure prediction using soft computing”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 1, pp. 2-17, 2013.

·        Shubhra Sankar Ray, Jayanta K. Pal, and Sankar K. Pal “Computational Approaches for Identifying Cancer miRNA Expressions”, Gene Expression, vol. 15, nos. 5-6, pp. 243-253, 2013.

·        Avatharam Ganivada, Shubhra Sankar Ray, and Sankar K. Pal “Fuzzy Rough Granular Self-Organizing Map and Fuzzy Rough Entropy”, Theoretical Computer Science, vol. 466, pp. 37-63, 2012.

·        Shubhra Sankar Ray, Sukanya Halder, Stephanie Kaypee, and Dhananajay Bhattacharyya, “HD-RNAS: an automated hierarchical database of RNA structures.”, Frontiers in Genetics, vol. 3, no. 59, doi. 10.3389/fgene.2012.00059, pp. 01-10, 2012.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “A Weighted Power Framework for Integrating Multi-Source Information: Gene Function Prediction in Yeast”, IEEE Transactions on Biomedical Engineering, vol. 59, no. 4, pp. 1162-1168, 2012. This is a curated Paper in Computational Analysis category in Saccharomyces Genome Database.

·        Avatharam Ganivada, Shubhra Sankar Ray, and Sankar K. Pal “Fuzzy Rough Granular Self Organizing Map”, The 6th International Conference on Rough Sets and Knowledge Technology (RSKT'11), pp. 659-666, Oct 9-12, Banff, Canada, 2011.

·        Shubhra Sankar Ray, Sukanya Halder and Dhananjay Bhattacharya, “HD-RNAS: Hierarchical Database of RNA Structures ”, International Conference on Frontiers of Interface Between Statistics and Sciences, pp. 724, December 30, 2009 - January 2, India, 2010.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “Combining Multi-Source Information through Functional Annotation based Weighting: Gene Function Prediction in Yeast”, IEEE Transactions on Biomedical Engineering, vol. 56, no. 2, pp. 229-236, 2009. This is a curated Paper in Computational Analysis category in Saccharomyces Genome Database.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “Gene Ordering in Partitive Clustering using Microarray Expressions”, Journal of Biosciences, vol. 32, no. 5, pp. 1019-1025, 2007 (Special Issue- Bioinformatics: From Molecules to Systems). This is a curated Paper in Computational Analysis and Techniques and Reagents category in Saccharomyces Genome Database.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “Dynamic Range Based Distance Measure for Microarray Expressions and A Fast Gene Ordering Algorithm”, IEEE Transactions on Systems, Man, and Cybernetics, Part-B, vol. 37, no. 3, pp. 742-749, 2007.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “Genetic Operators for Combinatorial Optimization in TSP and Microarray Gene Ordering. ”, Applied Intelligence, vol. 26, no. 3, pp. 183-195, 2007.

·        Sankar K. Pal, Sanghamitra Bandyopadhyay and Shubhra Sankar Ray, “Evolutionary Computation in Bioinformatics: A Review”, IEEE Transactions on Systems, Man, and Cybernetics, Part-C, vol. 36, no. 5, pp. 601-615, 2006.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay, Pabitra Mitra and Sankar K. Pal, “Bioinformatics in Neurocomputing Framework”, IEE Proc. Circuits Devices & Systems, vol. 152, pp. 556-564, 2005. (and CODEC-04, pp. 94, January 1-3, 2004, Kolkata).

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “Predicting Gene Function in Yeast through Adaptive Weighting of Multi-Source Information ”, The Eighth International Conference on Systems Biology, pp. 63, no. H03, October 1-6, Long Beach, California, USA, 2007. Full paper

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “New Distance Measure for Microarray Gene Expressions using Linear Dynamic Range of Photo Multiplier Tube ”, International Conference on Computing: Theory and Applications, IEEE Computer Soceity, pp. 337-341, March 5-7, 2007, Kolkata, India. Slides presented in the conference

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “Gene Ordering in Partitive Clustering using Microarray Expressions”, International Conference on Bioinformatics, INCOB 2006, pp. 33, 18-20 December, New Delhi, 2006.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay, and Sankar K. Pal, “New Genetic Operators for Solving TSP: Application to Microarray Gene Ordering”, First International Conference, PReMI 2005, Lecture Notes in Computer Science, vol. 3776, pp. 617-622, 2005, Springer-Verlag, Berlin, 2005.

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay and Sankar K. Pal, “New Operators of Genetic algorithms for Traveling Salesman Problem”, ICPR-04, vol. 2, pp. 497-500, 23-26 August 2004, Cambridge, UK

·        Shubhra Sankar Ray, Sanghamitra Bandyopadhyay, Pabitra Mitra and Sankar K. Pal, “Bioinformatics in Neurocomputing Framework”, CODEC-04, pp. 94, January 1-3, 2004, Kolkata, India

Softwares

• Softwares for Gene Expression

Education

• Research Associate in BioPhysics Division -- July 2008 to August 2009 Saha Institute of Nuclear Physics, Kolkata.
• Phd in Engineering (Jadavpur University) – November  2008, Kolkata.
• M. Tech (Radiophysics and Electronics) – May  2002, Kolkata.
• M. Sc (Electronic Science) - May 2000 – University of Calcutta .
• B. Sc (Physics Hons.) -- July 1995 to May 1998 – University of Calcutta.
• Resume

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