Dr. Rajat Kumar De
Professor

Biography

Rajat K. De is a Professor of the Indian Statistical Institute, Kolkata, India. He obtained his Ph.D. degree from the same institute in the year 2000. He was a Distinguished Postdoctoral Fellow of the Whitaker Biomedical Engineering Institute, the Johns Hopkins University, USA, during 2002-2003. He visited the Department of Medicine, the University of California, San Diego, USA in the years 2017 and 2018, with a Fulbright-Nehru Academic and Professional Excellence Fellowship. He has been working in the area of machine learning, bioinformatics, computational biology, and systems biology. Professor De has about 100 research papers published in international journals, conference proceedings and in edited books, and co-edited three books.

Education

• Ph.D. in the area of Computer Science from the Indian Statistical Institute, India, in the year 2000. The thesis is on neuro-fuzzy computing for feature evaluation, classification and rule generation.
• Master of Computer Science and Engineering from Jadavpur University, Kolkata, India, in the year 1993 with 1st class.
• Bachelor of Technology in Computer Science and Engineering from Calcutta University, Kolkata, India, in the year 1990 with 1st class.
• Bachelor of Science (Honors in Physics) from Calcutta University, Kolkata, India, in the year 1987 with 1st class.

Fellowships/Scholarships awarded

• Fulbright-Nehru Academic and Professional Excellence Fellowship (Flex Award) for visiting the Department of Medicine, University of California, San Diego, U.S.A., during February-April 2017 and February-April 2018.
• Distinguished Postdoctoral Fellowship by the Whitaker Biomedical Engineering Institute, the Johns Hopkins University, USA, during June 2002 - June 2003.
• Research Associateship by CSIR to work at the Machine Intelligence Unit, Indian Statistical Institute, Kolkata, during November 1998 - June 1999.
• Dr. K. S. Krishnan Senior Research Fellowship by the Department of Atomic Energy, Government of India, for doctoral work at the Machine Intelligence Unit, Indian Statistical Institute, Kolkata, during October 1993 - October 1998.

List of projects

• Multi-dimensional Research to Enable Systems Medicine: Acceleration Using a Cluster Approach: During January 2017-July 2022, sponsored by the Department of Biotechnology, Government of India (Investigator)
• Three Timescale Modeling of Biochemical Pathways: Integration of Signaling, Gene Regulatory and Metabolic Pathways: During April 2019-March 2022, sponsored by Indian Statistical Institute. (Principal Investigator)
• Understanding the Efficacy of Existing Drug Molecules on COVID-19 and Interactive Pathways: A Deep Learning Model: During July 2020-July 2021, sponsored by SERB, Government of India. (Principal Investigator)
• Modeling host-pathogen interactions: During April 2016-March 2019, sponsored by Indian Statistical Institute. (Principal Investigator)
• Development of computational methods for analyzing biochemical pathways as integrated systems: During April 2013-March 2016, sponsored by Indian Statistical Institute. (Principal Investigator)
• Development of pattern recognition and machine learning tools for solving certain problems in systems biology - II: During April 2010-March 2013, sponsored by Indian Statistical Institute. (Principal Investigator)
• Development of pattern recognition and machine learning tools for solving certain problems in systems biology: During April 2008-March 2010, sponsored by Indian Statistical Institute. (Principal Investigator)
• Computational analysis of biochemical pathways related to gene-activity: During April 2005-March 2008, sponsored by Indian Statistical Institute. (Principal Investigator)
• Hybridization of knowledge-based and case-based reasoning in neuro-fuzzy framework for pattern recognition problems: During April 2000-March 2005, sponsored by Indian Statistical Institute. (Co-Principal investigator)

Teaching acivities

• Teaching the course titled “Neural Networks and Applications” in Master of Technology (Computer Science) since 2003-2004 till date.
• Taught the course titled “Database Management Systems” in Master of Technology (Computer Science) in 2003 and 2004.
• Teaching the course titled “Database Management Systems” in Master of Technology (Quality, Reliability and Operations Research).

Ph. D. thesis supervised

• Dr. Anindya Bhattacharya for his Ph. D. thesis titled “Correlation Clustering of Gene Expression Patterns”,(Co-supervisor: Dr. Nirmalya Chowdhury, Jadavpur University). Ph. D. degree awarded by Jadavpur University, Kolkata, India in 2011.
• Dr. Losiana Nayak for her Ph. D. thesis titled “Computational Methodologies for Modularization of Some Biochemical Pathways: Analysis and Annotation”, Ph. D. degree awarded by University of Calcutta, Kolkata, India in 2013.
• Dr. Anupam Ghosh for his Ph. D. thesis titled “Soft Computing Methodologies for Identification of Some Possible Genes Mediating the Development of a Disease: Analysis of Microarray Gene Expression Profiles”, (Co-supervisor: Dr. Bibhash C. Dhara, Jadavpur University). Ph. D. degree awarded by Jadavpur University, Kolkata, India in 2013.
• Dr. Mouli Das for her Ph. D. thesis titled “Certain Optimization Tasks in Biochemical Pathways”, (Joint Supervisor: Professor Subhasis Mukhopadhyay, University of Calcutta), Ph. D. degree awarded by University of Calcutta, Kolkata, India, in 2014.
• Dr. Namrata Tomar for her Ph. D. thesis titled “Development of In Silico Methods for Analysis of Integrated Biochemical Pathways”,Ph. D. degreeawarded by University of Calcutta, Kolkata, India, in 2015.
• Dr. Somnath Tagore for his Ph. D. thesis titled “Mining Certain Pathways in Metabolomics”, (Co-supervisor: Dr. Nirmalya Chowdhury, Jadavpur University),Ph. D. degree awarded by Jadavpur University, Kolkata, India, in 2015.
• Dr. Sanghita Banerjee for her Ph. D. thesis titled tentatively “Deciphering Molecular Evolution of Unstructured Proteins in Light of Gene Regulation”, Ph.D. degree awarded by University of Calcutta, Kolkata, India, in 2019.
• Dr. Abhijit Dasgupta for his Ph. D. thesis titled “Modeling Control Dynamics of Integrated Biochemical Pathways: A Control Theoretic Approach”,(Co-supervisor: Professor Nirmalya Chowdhury, Jadavpur University), Ph.D. degree awarded by Jadavpur University, Kolkata, India, in 2020.
• Dr. Rishika Sen for her Ph. D. thesis titled “In silico Modelling of Host-pathogen Interactions: Identification of Pathogenic Toxins and the Analysis of Their Effect on the Host Pathways”; Ph.D. degree awarded by the Indian Statistical Institute, Kolkata, India, in 2021.
• Mr. Debraj Ghosh for his Ph. D. thesis titled “Development of Stochastic Simulation Algorithms for Modelling Biochemical Pathways”, Ph.D. (Tech.) degree awarded by the University of Calcutta, Kolkata, India, in 2022.

Ph. D. thesis supervising

• Mr. Prasun Dutta for his Ph. D. thesis titled tentatively “On Some Deep Neural Network Models: Applications in Multi-omics Data Integration”, registered in the Indian Statistical Institute, Kolkata, India (Year of registration: 2019).
• Mr. Ritankar Das for his Ph. D. thesis titled tentatively “Computational Methods for Analysing Different Brain Diseases”, registered in the Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India (Date of registration: August 28, 2019).
• Mr. DibyenduBikash Seal for his Ph. D. thesis titled tentatively “On Multi-omics Data Integration and Single-Cell Data Analysis: Machine Learning based Methodology”, registered in the Department of Computer Science and Engineering, University of Calcutta, Kolkata, India (Date of registration: October 25, 2019).
• Ms. Rituparna Sinha for her Ph. D. thesis titled tentatively “Detection and Analysis of Some Human DNA Alterations: A Root Cause of Cancer”, (Joint Supervisor: Professor Rajat Kumar Pal, University of Calcutta) registered in the Department of Computer Science and Engineering, University of Calcutta, Kolkata, India (Date of registration: December 22, 2020).

Books Published

• A. Ghosh, R. K. De, and S. K. Pal (Eds.), Pattern Recognition and Machine Intelligence, Proc. PReMI’07, Lecture Notes in Computer Science (LNCS), vol. 4815, Springer, Heidelberg, 2007. Download PDF
• R. K. De, D. P. Mandal, and A. Ghsosh (Eds.), Machine Interpretation of Patterns: Image Analysis and Data Mining, World Scientific, Singapore, 2010.
• R. K. De and N. Tomar (Eds.), Immunoinformatics: From Biology to Informatics, second edition, under the Series titled Methods in Molecular Biology, by J. Walker (Series Editor), Humana Press, 2014.

Articles in the area of Bioengineering / Bioinformatics / Computational Biology / Systems Biology

• Year : 2007


• L. Nayak and R. K. De, “An algorithm for modularization of MAPK and Calcium signaling pathways: Comparative analysis among different species”, Journal of Biomedical Informatics, vol. 40, pp. 726-749, 2007. Download PDF
• L. Nayak and R. K. De, “Modularized study of human calcium signaling pathway”, Journal of Biosciences, vol. 32, no. 5, pp. 1009-1017, 2007. Download PDF


• Year : 2008


• A. Bhattacharya and R. K. De, “Divisive correlation clustering algorithm (DCCA) for grouping of genes: Detecting varying patterns in expression profiles”, Bioinformatics, vol. 24, 1359 – 1366, 2008. Download PDF
• R. K. De, M. Das, and S. Mukhopadhyay, “Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways”, BMC Systems Biology, 2:65, 2008. Download PDF
• S. Tagore, V. S. Gomase, and R. K. De, “Pathway modeling: New face of graphical probabilistic analysis”, Journal of Proteomics and Bioinformatics, vol. 1, no. 5, pp. 281-286, 2008. Download PDF


• Year : 2009


• R. K. De and A. Ghosh, “Linguistic recognition system for identification of some possible genes mediating the development of lung adenocarcinoma”, Information Fusion (Special Issue on Natural Computing in Bioinformatics), vol. 10, no. 3, pp. 260-269, 2009. Download PDF
• A. Bhattacharya and R. K. De, “Bi-correlation clustering algorithm for determining a set of co-regulated genes”, Bioinformatics, vol. 25, no. 21, pp. 2795-2801, 2009. Download PDF
• R. K. De and A. Ghosh, “Interval based fuzzy systems for identification of important genes from microarray gene expression data: Application to carcinogenic development”, Journal of Biomedical Informatics, vol. 42, pp. 1022-1028, 2009. Download PDF
• S. Sinha, T. S. Vasulu, and R. K. De, “Performance and evaluation of microRNA gene identification tools”, Journal of Proteomics and Bioinformatics, vol.2, no. 8, pp. 336-343, 2009. Download PDF


• Year : 2010


• A. Bhattacharya and R. K. De, “Average correlation clustering algorithm (ACCA) for grouping of co-regulated genes with similar pattern of variation in their expression value”, Journal of Biomedical Informatics, vol. 43, no. 4, pp. 560-568, 2010. Download PDF
• N. Tomar, L. Nayak, and R. K. De, “Comparative analysis of various algorithms in modularizing VEGF signaling pathway: Exploring gradual development over various species”, Journal of Biomedical Science and Engineering, vol. 3, no. 10, pp. 931-942, 2010. Download PDF
• N. Tomar and R. K. De, “Immunoinformatics: An integrated scenario”, Immunology, vol. 131, pp. 153-168, 2010. Download PDF
• M. Das, S. Mukhopadhyay, and R. K. De, “Gradient descent optimization in gene regulatory pathways”, PLoS ONE, vol. 5, no. 9, e12475, 2010. doi:10.1371/journal.pone.0012475 Download PDF


• Year : 2011


• A. Bhattacharya and R. K. De, “A novel noise handling method to improve clustering of gene expression patterns”, BMC Bioinformatics, vol. 12 (Suppl 7):A3, doi:10.1186/1471-2105-12-S7-A3 Download PDF
• S. Tagore and R. K. De, “Detecting breakdown points in metabolic networks”, Computational Biology and Chemistry, vol. 35, pp. 371-380, 2011. Download PDF


• Year : 2012


• A. Bhattacharya, N. Chowdhury, and R. K. De, “Comparative analysis of clustering and biclustering algorithms for grouping of genes: co-function and co-regulation”, Current Bioinformatics, vol. 7, pp. 63-76, 2012. Download PDF
• R. K. De and S. Tagore, “Automated reconstruction of metabolic pathways of Homo sapiens involved in the functioning of GAD1 and GAD2 genes based on structural grammars”, Metabolomics: Open Access, S1:005. doi:10.4172/2153-0769.S1-005 Download PDF
• S. Tagore and R. K. De, “SAGPAR: StructurAl Grammar-based automated PAthway Reconstruction”, Interdisciplinary Sciences: Computational Life Sciences, vol. 4, no. 2, pp. 116-127, 2012. Download PDF
• N. Tomar and R. K. De, “Modeling host-pathogen interactions: H. sapiens as a host and C. difficile as a pathogen”, Journal of Molecular Recognition, vol. 25, pp. 474-485, 2012. Download PDF
• R. K. De and N. Tomar, “Modeling the Optimal CCM pathways under Feedback Inhibition using FBA”, Journal of Bioinformatics and Computational Biology, vol. 10, no. 6 (2012) 1250019, DOI: 10.1142/S0219720012500199 Download PDF


• Year : 2013


• N. Tomar, O. Choudhury, A. Chakrabarty, and R. K. De, “An Integrated pathway systems modeling of Saccharomyces cerevisiae HOG pathway: A Petri net based approach”, Molecular Biology Reports, vol. 40, no. 2, pp. 1103-1125, 2013. Download PDF
• A. Ghosh, B. C. Dhara, and R. K. De, "Comparative analysis of cluster validity indices in identifying some possible genes mediating certain cancers", Molecular Informatics, vol. 32, no. 4, pp. 347-354, 2013. Download PDF
• N. Tomar and R. K. De, "Comparing methods for metabolic network analysis and an application to metabolic engineering", Gene, vol. 521, no. 1, pp. 1-14, 2013. Download PDF
• L. Nayak, H. Tunga, and R. K. De, "Disease comorbidity and the human Wnt signaling pathway: A network-wise Study", OMICS: A Journal of Integrative Biology, vol 17, no. 6, pp. 318-337, 2013. Download PDF
• M. Das, C. A. Murthy, and R. K. De, "An optimization rule for in silico identification of targeted overproduction in metabolic pathways", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 914-926, 2013. Download PDF
• M. Das, C. A. Murthy, and R. K. De, " Second order optimization for the inference of gene regulatory pathways", Statistical Applications in Genetics and Molecular Biology, vol. 13, no. 1, pp. 19-33, 2013. Download PDF
• N. Tomar and R. K. De, "A model of an integrated immune system pathway in Homo sapiens and its interaction with superantigen producing expression regulatory pathway in Staphylococcus aureus: Comparing behavior of pathogen perturbed and unperturbed pathway", PLoS ONE, vol. 8, no. 12, pp. e80918, 2013. Download PDF
• S. Tagore and R. K. De, "Simulating an infection growth model in certain healthy metabolic pathways of Homo sapiens for highlighting their role in type I diabetes mellitus using fire-spread strategy, feedbacks and sensitivities", PLoS ONE, vol. 8, no. 9, pp. e69724, 2013, doi:10.1371/journal.pone.0069724, 2013. Download PDF
• M. Das, S. Mukhopadhyay, and R. K. De, “Development of an engineering method to optimize polyamine metabolic pathways”, Current Bioinformatics, vol. 8, pp. 569-576, 2013. Download PDF


• Year : 2014


• S. Tagore, N. Chowdhury, and R. K. De, "Analyzing methods for path mining with applications in metabolomics", Gene, vol. 534, no. 2, pp. 125-138, 2014. Download PDF
• A. Ghosh, B. C. Dhara, and R. K. De, “Selection of genes mediating certain cancers, using Neuro-Fuzzy Approach”, Neurocomputing, vol. 133, pp. 122-140, 2014. Download PDF
• A. Ghosh and R. K De, “Development of a fuzzy entropy based method for detecting altered gene-gene interactions in carcinogenic state”, Journal of Intelligent & Fuzzy Systems, vol. 26, no. 6, pp. 2731-2746, 2014. Download PDF
• N. Tomar and R. K. De, "A comprehensive view on metabolic pathway analysis methodologies", Current Bioinformatics, vol. 9, no. 3, pp. 295-305, 2014. Download PDF


• Year : 2015


• A. Bhattacharya, N. Chowdhury, and R. K. De, "Concepts of Relative Sample Outlier (RSO) and Weighted Sample Similarity (WSS) for improving performance of clustering genes: Co-function and co-regulation", International Journal of Data Mining and Bioinformatics, vol. 11, no. 3, pp. 314-330, 2015. Download PDF
• S. Baidya and R. K. De, "A novel locally guided genome reassembling technique using an artificial ant system", Applied Intelligence, vol. 43, no. 2, pp. 397-411, 2015. Download PDF
• S. Tagore and R. K. De, "Evolutionary growth of certain metabolic pathways involved in the functioning of GAD and INS genes in Type 1 Diabetes Mellitus: their architecture and stability", Computers in Biology and Medicine, vol. 61, pp. 19-35, 2015. Download PDF
• R. Sinha, S. Samaddar, and R. K. De, "A convex hull based segmentation approach to detect copy number variations (CNV) using next-generation sequencing data", PLoS One, vol. 10, no. 8: e0135895, 2015. doi:10.1371/journal.pone.0135895 Download PDF
• D. Paul, A. Dasgupta, and R. K. De, "Exploring the altered dynamics of mammalian central carbon metabolic pathway in cancer cells: A classical control theoretic approach", PLoS One, vol. 10, no. 9: e0137728, 2015. doi:10.1371/journal.pone.0137728 Download PDF
• A. Ghosh and R. K. De, "Identification of certain cancer-mediating genes using Gaussian fuzzy cluster validity index", Journal of Biosciences, vol. 40, no. 4, pp. 741-754, 2015. Download PDF


• Year : 2016


• A. Ghosh and R. K. De, "Fuzzy Correlated Association Mining: Selecting altered associations among the genes, and some possible marker genes mediating certain cancers", Applied Soft Computing, vol. 38, pp. 587-605, 2016. Download PDF
• L. Nayak, N. P. Bhattacharyya, and R. K. De, "Wnt signal transduction pathways: modules, development and evolution", BMC Systems Biology, 10.2 (2016): 197 Download PDF
• R. Sen, L. Nayak, and R. K. De, "A review on host-pathogen interactions: Classification and prediction", European Journal of Clinical Microbiology & Infectious Diseases, vol. 35, no. 10, pp. 1581-1599, 2016. Download PDF
• S. Banerjee and R. K. De, "Structural Disorder: A tool for housekeeping proteins performing tissue-specific interactions", Journal of Biomolecular Structure & Dynamics, vol. 34, no. 9, pp. 1930-1945, 2016. Download PDF
• A. Dasgupta, D. Paul, and R. K. De, "A fuzzy logic controller based approach to model the switching mechanism of mammalian central carbon metabolic pathway in normal and cancer cells", Molecular Biosystems, vol. 12, no. 8, pp. 2490-2505, 2016. Download PDF
• N. Tomar and R. K. De, "Modeling and analyzing the effects of crosstalk in a biochemical pathway: A study on human mTOR signaling pathway", Current Bioinformatics, vol. 11, no. 5, pp. 1-12, 2016. Download PDF
• I. Ray, S. K. Mahata, and R. K. De, "Obesity: An immunometabolic perspective", Frontiers in Endocrinology, 7:157, pp. 1-9, 2016. doi: 10.3389/fendo.2016.00157 Download PDF
• L. Nayak, I. Ray, and R. K. De, "Precision medicine with electronic medical records: from the patients and for the patients", Annals of Translational Medicine, vol. 4 (Suppl 1), S61, pp. 1-4, 2016. Download PDF


• Year : 2017


• S. Banerjee, S. Chakraborty, and R. K. De, "Deciphering the cause of evolutionary variance within intrinsically disordered regions in human proteins", Journal of Biomolecular Structure & Dynamics, vol. 35, no. 2, pp. 233-249, 2017. Download PDF
• D. Ghosh and R. K. De, “In Silico Modeling of Crabtree Effect”, Endocrine Metabolic & Immune Disorders - Drug Targets, vol. 17, no. 3, pp. 182-188, 2017. Download PDF
• D. Ghosh and R. K. De, “Slow update stochastic simulation algorithms for modeling complex biochemical networks”, BioSystems, vol. 162, pp. 135-146, 2017. Download PDF


• Year : 2018


• L. Nayak and R. K. De, “Precision oncology with electronic medical records”, EMJ Innovations, vol. 2.1, pp. 64-72, 2018. Download PDF
• I. Ray, A. Dasgupta, and R. K. De, “Succinate aggravates NAFLD progression to liver cancer on the onset of obesity: An in silico model”, Journal of Bioinformatics and Computational Biology, 2018, doi:10.1142/S0219720018500087 Download PDF
• S. Samaddar, R. Sinha, and R. K. De, “A model for distributed processing and analyses of NGS data under Map-Reduce paradigm”, IEEE/ACM Transactions of Computational Biology and Bioinformatics, vol. 16, no. 3, pp. 827-840, 2018 Download PDF
• L. Nayak, A. Dasgupta, R. Das, K. Ghosh, and R. K. De, “Computational neuroscience and neuroinformatics: Recent progress and resources”, Journal of Biosciences, vol. 43, no. 5, pp. 1037-1054, 2018. Download PDF


• Year : 2019


• S. Mukherjee, D. Ghosh, and R. K. De, “Expected return time to the initial state for biochemical systems with linear cyclic chains: unidirectional and bidirectional reactions”, Sadhana, 44:3, 2019. Download PDF
• R. Sen, L. Nayak, and R. K. De, “PyPredT6: A Python based Prediction Tool for Identification of Type VI Effector Proteins”, Journal of Bioinformatics and Computational Biology, vol. 17, no. 2, 2019. DOI: 10.1142/S0219720019500197. Download PDF
• R. Sen, S. Tagore, and R. K. De, “Cluster Quality based Non-Reductional (CQNR) oversampling technique and Effector Protein Predictor based on 3D structure (EPP3D) of proteins”, Computers in Biology and Medicine, vol. 112, Article 103374, 2019. Download PDF


• Year : 2020


• R. Sen, S. Tagore, and R. K. De, “ASAPP: Architectural similarity-based automated pathway prediction system and its application in host-pathogen interactions”, IEEE/ACM Transactions of Computational Biology and Bioinformatics, vol. 12, no. 2, pp. 506-515, 2020. Download PDF
• A. Dasgupta, G.K. Bandyopadhyay, I. Ray, K. Bandyopadhyay, N. Chowdhury, R. K. De, and S. K. Mahata, “Catestatin improves insulin sensitivity by attenuating endoplasmic reticulum stress: experimental as well as a PID controller based state space model validation”, Computational and Structural Biotechnology Journal, vol. 18, pp. 464-481, 2020. Download PDF
• A. Dasgupta, N. Chowdhury, and R. K. De, “Metabolic Pathway Engineering: Applications and Perspectives”, Computer Methods and Programs in Biomedicine, vol. 192, 105436, 2020. Download PDF
• D. B. Seal, V. Das, S. Goswami, and R. K. De, “Estimating gene expression from DNA methylation and copy number variation: A deep learning regression model for multi-omics integration”, Genomics, vol. 112, no. 4, pp. 2833-2841, 2020. Download PDF
• A. Dasgupta, L. Nayak, R. Das, D. Basu, P. Chandra, and R. K. De, “Pattern and Rule Mining for Identifying Signatures of Epileptic Patients from Clinical EEG data”, Fundamenta Informaticae (Special Issues of Submission of Selected Papers from PReMI 2017), vol. 176, no. 2, pp. 141-166, 2020. Download PDF
• R. Sinha, R. K. Pal and R. K. De, “GenSeg and MR-GenSeg: A novel segmentation algorithm and its parallel MapReduce based approach for identifying genomic regions with copy number variations”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol 19, pp. 443-454, 2022. Download PDF


• Year : 2021


• A. Dasgupta, A. Bakshi, N. Chowdhury, and R. K. De, “A control theoretic three timescale model for analyzing energy management in mammalian cancer cells”, Computational and Structural Biotechnology Journal, vol. 19, pp. 477-508, 2021. Download PDF
• D. Ghosh and R. K. De, “Block Search Stochastic Simulation Algorithm (BlSSSA): A fast stochastic simulation algorithm for modeling large biochemical networks”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021 (to appear). Download PDF


• Year : 2022


• D. B. Seal, V. Das, and R. K. De, “CASSL: A cell-type annotation method for single cell transcriptomics data using semi-supervised learning”, Applied Intelligence (to appear). Download PDF

Articles in the area of Computer Science

• Year : 1997


• R. K. De, N. R. Pal, and S. K. Pal, “Feature analysis: Neural network and fuzzy set theoretic approaches”, Pattern Recognition, vol. 30, pp. 1579-1590, 1997. Download PDF
• S. Mitra, R. K. De, and S. K. Pal, “Knowledge-based fuzzy MLP for classification and rule generation”, IEEE Transactions on Neural Networks, vol. 8, pp. 1338-1350, 1997. Download PDF


• Year : 1998


• S. K. Pal, J. Basak, and R. K. De, “Fuzzy feature evaluation index and connectionist realization”, Information Sciences, vol. 105, pp. 173-188, 1998. Download PDF
• J. Basak, R. K. De, and S. K. Pal, “Fuzzy feature evaluation index and connectionist realization-II: Theoretical analysis”, Information Sciences, vol. 111, pp. 1-17, 1998. Download PDF
• J. Basak, R. K. De, and S. K. Pal, “Unsupervised feature selection using neuro-fuzzy approach”, Pattern Recognition Letters, vol. 19, pp. 997-1006, 1998. Download PDF


• Year : 1999


• R. K. De, J. Basak, and S. K. Pal, “Neuro-fuzzy feature evaluation with theoretical analysis”, Neural Networks, vol. 12, pp. 1429-1455, 1999. Download PDF


• Year : 2000


• S. K. Pal, R. K. De, and J. Basak, “Unsupervised feature evaluation: A neuro-fuzzy approach”, IEEE Transactions on Neural Networks, vol. 11, pp. 366-376, 2000. Download PDF
• R. K. De and S. K. Pal, “Pattern classification using fuzzy sets and neural nets: A case based approach”, International Journal of Engineering Intelligent Systems, vol. 8, pp. 103-108, 2000. Download PDF


• Year : 2001


• R. K. De and S. K. Pal, “A connectionist model for selection of cases”, Information Sciences, vol. 132, pp. 179-194, 2001. Download PDF


• Year : 2002


• R. K. De, J. Basak, and S. K. Pal, “Unsupervised feature extraction using neuro-fuzzy approach”, Fuzzy Sets and Systems, vol. 126, pp. 277-291, 2002. Download PDF


• Year : 2003


• M. Acharyya, R. K. De, and M. K. Kundu, “Extraction of features using M-band wavelet packet frame and their neuro-fuzzy evaluation for multi-texture segmentation”, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 25, pp. 1639-1644, 2003. Download PDF
• M. Acharyya, R. K. De, and M. K. Kundu, “Segmentation of remotely sensed images using wavelet features and their evaluation in soft computing framework”, IEEE Transactions on Geoscience and Remote Sensing, vol. 41, pp. 2900-2905, 2003. Download PDF


• Year : 2010


• M. K. Pakhira and R. K. De, “Generational PipeLined Genetic Algorithm (PLGA) using Stochastic Selection”, International Journal of Electrical and Electronics Engineering, vol. 4, no. 1, pp. 75-88, 2010. Download PDF

Book Chapters in the area of Bioengineering / Bioinformatics / Computational Biology / Systems Biology

• Year : 2007


• R. K. De, “Reverse engineering gene regulatory networks: Artificial neural network based methodologies”, in Bioinformatics and Statistics in Fisheries Research: Vol.-III, (A. K. Roy and N. Sarangi (eds.)), Central Institute of Freshwater Aquaculture (CIFA), pp. 30-41, 2007. Download PDF


• Year : 2011


• L. Nayak, N. Tomar, and R. K. De, “Computational phylogeneticity of biological pathways: A developmental study of TCA cycle over a set of organisms”, in Recent Trends in Computational Biology and Computational Statistics Applied in Biotechnology and Bioinformatics, A. K. Roy et. al. (Eds.), New India Publishing AGENCY (NIPA) , New Delhi, India, pp. 337-369, 2011. Download PDF


• Year : 2014


• N. Tomar and R. K. De, "A brief outline of immune system", in Immunoinformatics, R. K. De and N. Tomar (Eds.), pp. 3-12, Humana Press, New York, 2014. Download PDF
• N. Tomar and R. K. De, "Crosstalk between metabolic and immune systems", in Immunoinformatics, R. K. De and N. Tomar (Eds.), pp. 13-21, Humana Press, New York, 2014. Download PDF
• N. Tomar and R. K. De, "Immunoinformatics: A brief review", in Immunoinformatics, R. K. De and N. Tomar (Eds.), pp. 23-55, Humana Press, New York, 2014. Download PDF


• Year : 2018


• N. Tomar and R. K. De, “Tools, databases, and applications of Immunoinformatics. In: Wadhwa G., Shanmughavel P., Singh A., Bellare J. (eds), Current trends in Bioinformatics: An Insight, Springer, Singapore, pp. 159-174, 2018. Download PDF

Book Chapters in the area of Computer Science

• Year : 2000


• R. K. De and S. K. Pal, “Case-based systems: A neuro-fuzzy method for selecting cases”, in Soft Computing for Case-based Reasoning, (S. K. Pal, T. S. Dillon, and D. S. Yeung, (eds.)), London:Springer Verlag, pp. 241-257, 2000. Download PDF
• R. K. De, J. Basak, and S. K. Pal, “Neuro-fuzzy model for unsupervised feature extraction with real life applications”, in Neuro-fuzzy Pattern Recognition, (H. Bunke and A. Kandel (eds.)), London:World Scientific, pp. 23-50, 2000. Download PDF


• Year : 2001


• R. K. De and S. K. Pal, “Neuro-fuzzy models for feature selection and classification”, in Pattern Recognition: From Classical to Modern Approaches, (S. K. Pal and A. Pal (eds.)), Singapore:World Scientific, pp. 475-506, 2001. Download PDF

Conference Proceedings in the area of Bioengineering / Bioinformatics / Computational Biology / Systems Biology

• Year : 2006


• R. K. De and A. Bhattacharya, “Identification of over and under expressed genes mediating allergic asthma”, in Proc. IEA/AIE 2006 conference held in Annecy, France, during June 27-30, 2006. Lecture Notes in Computer Science, vol. 4031, pp. 943-952, 2006. Download PDF
• R. K. De and K. Biswas, “Connectionist modeling of dynamic of gene expression and reverse engineering gene regulatory networks”, Proc. 2006 International Joint Conference on Neural Networks, Vancouver, BC, Canada, July 16-21, 2006, pp. 7503-7509. Download PDF
• R. K. De and L. Nayak, “MAPK signaling pathways and their recursive modularization”, in Proc. 15th International Conference on Computing (CIC’06), Mexico City, Mexico, pp. 203-208, November 21-24, 2006, IEEE Press. Download PDF


• Year : 2007


• M. Das, R. K. De, and S. Mukhopadhyay, “Identification of gene regulatory pathways: A regularization method”, Proc. Second International Conference on Pattern Recognition and Machine Intelligence (PReMI’07), Kolkata, India, December 18-22, 2007, Lecture Notes in Computer Science (LNCS) vol. 4815, pp. 425-432. Download PDF


• Year : 2008


• C. A. Murthy, M. Das, R. K. De, and S. Mukhopadhyay, “Determination of optimal metabolic pathways through a new learning algorithm”, Proc. 19th International Conference on Pattern Recognition (ICPR 2008), Tampa, USA, December 8-11, 2008, IEEE Catalog Number: CFP08182 ISBN: 978-1-4244-2175-6 ISSN: 1051-4651. Download PDF


• Year : 2009


• M. Das, R. K. De, and S. Mukhopadhyay, “A constraint based method for optimization in metabolic pathways”, Proc. 3rd International Conference on Pattern Recognition and Machine Intelligence (PReMI’09), December 16-20, 2009, New Delhi, India, Lecture Notes in Computer Science (LNCS) vol. 5909, pp. 193-198. Download PDF


• Year : 2011


• R. K. De and A. Ghosh, “Neuro-fuzzy methodology for selecting genes mediating lung cancer”, Proc. 4th International Conference on Pattern Recognition and Machine Intelligence (PReMI’11), June 26 – 30, 2011, Moscow, Lecture Notes in Computer Science (LNCS) vol. 6744, pp. 388-393. Download PDF
• A. Bhattacharya and R. K. De, “A methodology for handling a new kind of outliers present in gene expression patterns”, Proc. 4th International Conference on Pattern Recognition and Machine Intelligence (PReMI’11), June 26 – 30, 2011, Moscow, Lecture Notes in Computer Science (LNCS) vol. 6744, pp. 394-399. Download PDF
• L. Nayak and R. K. De, “Developmental trend derived from modules of Wnt signaling pathways”, Proc. 4th International Conference on Pattern Recognition and Machine Intelligence (PReMI’11), June 26 – 30, 2011, Moscow, Lecture Notes in Computer Science (LNCS) vol. 6744, pp. 400-405. Download PDF
• A. Ghosh and R. K. De, “A fuzzy entropy based approach for development of Gene Prediction Networks (GPNs): Detecting altered dependency in carcinogenic state”, Proc ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM-BCB 2011), Chicago, IL, USA, August 1-3, 2011, pp. 320-324. Download PDF


• Year : 2012


• M. Das, C. A. Murthy, S. Mukhopadhyay, and R. K. De, “A second-order learning algorithm for computing optimal regulatory pathways”, Proc. 1st Indo-Japan Conference on Perception and Machine Intelligence, 12 – 13 January 2012, Kolkata, India, pp. 227 – 234, 2012. Download PDF
• L. Nayak and R. K. De, “Finding better partitions and conserved Modules in WNT signaling pathways”, Proc. 13th International Conference on Bioinformatics and Computation Biology (BIOCOMP’12), Las Vegas, USA, pp. 89-95, July 16-19, 2012. Download PDF


• Year : 2013


• A. Ghosh and R. K. De, “Gaussian Fuzzy Index (GFI) for cluster validation: Identification of high quality biologically enriched clusters of genes and selection of some possible genes mediating lung cancer”, Proc. 5th International Conference on Pattern Recognition and Machine Intelligence (PReMI’13), December 10 – 14, 2013, Kolkata, India, Lecture Notes in Computer Science (LNCS) vol. 8251, pp. 680-687. Download PDF


• Year : 2015


• L. Nayak, N. P. Bhattacharyya, and R. K. De, "A module tree of Wnt signaling pathways", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'2015), Washington DC, USA, pp. 43-48, 2015. Download PDF
• A. Dasgupta, R. Das, L. Nayak, and R. K. De, "Analyzing epileptogenic brain connectivity networks using clinical EEG data", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'2015), Washington DC, USA, pp. 815-821, 2015. Download PDF


• Year : 2016


• S. Baidya and R. K. De, “An optimal genome reassembling technique by Artificial Bees system for small genome sequences”, 2016 Second International Conference on Research in Computational Intelligence and Communication Networks (ICRCICN), Kolkata, pp. 273-278, 2016. doi: 10.1109/ICRCICN.2016. Download PDF


• Year : 2017


• A. Dasgupta, L. Nayak, R. Das, D. Basu, P. Chandra, and R. K. De, “Feature selection and fuzzy rule mining for epileptic patients from clinical EEG data”, Proc. International Conference on Pattern Recognition and Machine Intelligence, Kolkata, Lecture Notes in Computer Science (LNCS) vol. 10597, pp. 87-95, 2017. Download PDF


• Year : 2019


• A. Dasgupta, R. Das, L. Nayak, A. Dutta, and R. K. De. “Two-class in silico categorization of intermediate epileptic EEG data,” Proc. 8th International Conference on Pattern Recognition and Machine Intelligence, December 17-20, 2019, Tezpur, India, pp. 184-192. Download PDF

Conference Proceedings in the area of Computer Science

• Year : 1995


• R. K. De, S. Mitra, and S. K. Pal, “Knowledge-based fuzzy MLP for pattern classification,” in Proc. Sixth International Fuzzy Systems Association World Congress, (Sao Paulo, Brazil), vol. II, pp. 237-240, 1995. Download PDF
• R. K. De, S. Mitra, and S. K. Pal, “Neuro-fuzzy knowledge-based system for rule generation,” in Proc. Indian Conference on Pattern Recognition, Image Processing and Computer Vision (ICPIC'95), (Kharagpur, India), pp. 130-134, 1995. Download PDF


• Year : 1996


• S. K. Pal, J. Basak, and R. K. De, “Feature selection: A neuro-fuzzy approach,” in Proc. International Conference on Neural Networks (ICNN'96), (Washington, DC, U.S.A.), pp. 1197-1202, 1996. Download PDF


• Year : 1998


• J. Basak, R. K. De, and S. K. Pal, “Unsupervised neuro-fuzzy feature selection”, in Proc. 1998 IEEE International Joint Conference on Neural Networks IJCNN'98, (Anchorage, U.S.A.), pp. 18-23, 1998. Download PDF
• R. K. De, J. Basak, and S. K. Pal, “Unsupervised neuro-fuzzy feature extraction”, in Proc. 5th International Conference on Soft Computing IIZUKA'98, (Iizuka, Japan), pp. 577-580, 1998. Download PDF


• Year : 2004


• M. K. Pakhira, R. K. De, S. Bandyopadhyay, and U. Maulik, “Pipelined Processing of Genetic Clustering”, in Proceedings of the International Conference on Intelligence Sensing and Information Processing, (Chennai, India) pp. 25-28, 2004. Download PDF
• M. K. Pakhira and R. K. De, “Function optimization using a pipelined genetic algorithm”, in Proceedings International Conference on Intelligent Sensors, Sensor Networks and Information Processing, (Melbourne, Australia), IEEE Press, pp. 253-258, December 14-17, 2004. Download PDF


• Year : 2005


• M. K. Pakhira and R. K. De, “A hardware pipeline for function optimization using genetic algorithms”, in Proc. Genetic and Evolutionary Computation Conference (GECCO-2005), (Washington D. C., USA), June 25-29, 2005, pp. 949-956. Download PDF