Publications
Some of our selected publications since 2007...
In Journals
Ray S., Lall S. and Bandyopadhyay S., "CODC: A copula based model to identify differential coexpression",, npj Systems Biology and Application,A Journal of the Nature Publishing Group, (accepted).
Biswas S., Ray S. and Bandyopadhyay S., "Colored Network Motif Analysis by Dynamic Programming Approach: An Application in Host-Pathogen Interaction Network",, IEEE Transactions on Computational Biology and Bioinformatics.
Chakraborty A. and Bandyopadhyay S., "conLSH: Context based Locality Sensitive Hashing for Mapping of noisy SMRT Reads",, Computational Biology and Chemistryvol. 85, no. 107206, April 2020.
Sinha D., Sinha P., Saha R., "Improved dropClust R Package with Integrative Analysis Support for scRNA-seq Data",, Bioinformatics,vol. 36, iss. 6, pp. 1946-1947, March 2020.
Sharma A. et al., "Mutational Landscape of the BAP1 Locus Reveals an Intrinsic Control to Regulate the miRNA Network and the Binding of Protein Complexes in Uveal Melanoma",, Cancers,vol. 11, vol. 10, art. no. 1600, 2019
Pal M. and Bandyopadhyay S., "ESOEA: Ensemble of Single Objective Evolutionary Algorithms for Many objective Optimization",, Swarm and Evolutionary Computation (Special Issue on Differential Evolution), 2019, vol. 50, art.no. 100511.
Roy P., Chowdhury C., Ghosh D., Bandyopadhyay S., "JUIndoorLoc: A Ubiquitous Framework for Smartphone-Based Indoor Localization Subject to Context and Device Heterogeneity",, Wireless Personal Communications, Springer, vol. 106, pp. 739-762, 2019.
Mallick K. , Bandyopadhyay S., Chakraborty S., "Topo2Vec: A Novel Node Embedding Generation Based on Network Topology for Link Prediction",, IEEE Transactions on Computational Social Systems, vol. 6, no. 6, pp. 1306-1317, 2019.
Bhadra T., Mallik S. and Bandyopadhyay S., "Identification of Multi-View Gene Modules using Mutual Information Based Hypograph Mining",, IEEE Transactions on Systems, Man and Cybernetics: Systems,vol. 49, iss. 6, pp. 1119-1130, June 2019 (10.1109/TSMC.2017.2726553)
Sengupta R., Pal M., Saha S. and Bandyopadhyay S., "NAEMO: Neighborhood-sensitive Archived Evolutionary Many-objective Optimization Algorithm",, Swarm and Evolutionary Computation, vol. 46, pp. 201-218, 2019.
Pal M., Alyafi A. A., Ploix S., Reignier P., "Unmasking the Causal Relationships Latent in the Interplay Between Occupants Actions and Indoor Ambience: A Building Energy Management Outlook",, Applied Energy, Elsevier, vol. 238, pp. 1452-1470, March 2019.
Pal M., Saha S., Bandyopadhyay S., "DECOR: Differential Evolution using Clustering based Objective Reduction for Many-Objective Optimization",, Information Sciences, vol. 423, pp.200-218, 2018.
Sengupta D., Lall S. and Bandyopadhyay S., "Structure Aware Principal Component Analysis for Single Cell RNA-seq Data",, Journal of Computational Biology, vol. 25, no. 12, pp. 1365-1373, 2018.
Sinha D., Kumar A., Kumar H., Bandyopadhyay S. and Sengupta D., "dropClust: Eficient Clustering of Ultra-large scRNA-seq Data",, Nucleic Acids Research, 2018. vol. 46, iss. 6, pp. e36
Sen S., Maulik U., Mallik S. and Bandyopadhyay S., "Detecting TF-MiRNA-Gene Network Based Modules for 5hmC and 5mC Brain Samples: A Intra- and Inter-Species Case-Study Between Human and Rhesus",, BMC Genetics, vol. 19, no. 9, 2018
Mallik S. and Bandyopadhyay S., "Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis",, IEEE Transactions on Computational Biology and Bioinformatics, vol. 15, iss. 2, pp. 673-687, 2018.
Chatterjee P., Roy D., Bhattacharyya M. and Bandyopadhyay S., "Biological Networks in Parkinson's Disease: An Insight into the Epigenetic Mechanisms Associated with this Disease",, BMC Genomics, vol. 18, 721, doi: 10.1186/s12864-017-4098-3, 2017.
Sinha D., Sengupta D. and Bandyopadhyay S., "ParSel: Parallel Selection of Micro-RNAs for Survival Classification in Cancers",, Molecular Informatics, DOI:10.1002/minf.201600141, vol 36, no. 7, 2017 .
Bandyopadhyay S. and Mallick K., "A New Feature Vector Based on Gene Ontology Terms for Protein-Protein Interaction Prediction",, IEEE/ACM Transactions on Computational Biol- ogy and Bioinformatics, doi 10.1109/TCBB.2016.2555304, vol. 14, no. 4, pp. 762-770, 2017.
Bhattacharyya M., Maity S. and Bandyopadhyay S., "Exploring the Missing Links Between Dietary Habits and Diseases",, IEEE Transactions on NanoBioscience, vol. 16, no. 3, pp. 226-238, 2017.
Sengupta D., Bandyopadhyay S. and Sinha D., "A Scoring Scheme for Online Feature Selection: Simulating Model Performance Without Retraining",, IEEE Transactions on Neural Networks and Learning Systems, vol. 28. no. 2. pp. 405-414, Feb 2017.
Joardar S., Chatterjee A., Bandyopadhyay S. and Maulik U., \Multi-size Patch based Collaborative Representation for Palm Dorsa Vein Pattern Recognition by Enhanced Ensemble Learning with Modified Interactive Artificial Bee Colony Algorithm",, Engineering Applications of Artificial Intelligence, Elseviervol. 60, pp. 151-163, 2017.
Bandyopadhyay, S., & Mallik, S., "Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Uterine Tumor", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016
Sengupta, D., Bandyopadhyay, S., & Sinha, D., "A Scoring Scheme for Online Feature Selection: Simulating Model Performance Without Retraining", NEURAL NETWORKS AND LEARNING SYSTEMS, IEEE Transactions (2016) doi: 10.1109/TNNLS.2016.2514270
Bandyopadhyay, S.; Chowdhary, G.; Sengupta, D., "FOCS: Fast Overlapped Community Search,", Knowledge and Data Engineering, IEEE Transactions (2015) doi: 10.1109/TKDE.2015.2445775
UjjwalMaulik, Saurav Mallik, AnirbanMukhopadhyay and Sanghamitra Bandyopadhyay, “Analyzing Gene Expression and Methylation Data Profiles using StatBicRM: Statistical Biclustering-based Rule Mining”, Plos One, 10(4): e0119448 , 2015.
M. Aqil, A. R. Naqvi, S. Mallik, S. Bandyopadhyay, U. Maulik and S. Jameel, “The HIV Nef protein modulates cellular and exosomal miRNA profiles in human monocytic cells”, Journal of Extracellular Vesicles, 3: 23129, 2014.
S. Bandyopadhyay, D. Ghosh, R. Mitra and Z. Zhao, "MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets", Sci. Rep. 5, 8004;doi:10.1038/srep08004.
S. Bandyopadhyay, S. Ray, A. Mukhopadhyay and U. Maulik, "A Review of In Silico Approaches for Analysis and Prediction of HIV-1-Human Protein-Protein Interactions", Brief Bioinform (2014) doi: 10.1093/bib/bbu0412014
M. Aqil, S. Mallik, S. Bandyopadhyay, U. Maulik and S. Jameel, “Transcriptomic analysis of mRNAs in human monocytic cells expressing the HIV-1 Nef protein and their exosomes”, Application of Systems Biology and Bioinformatics Methods in Biochemistry and Biomedicine, BioMed Research International , vol. 2015, article id: 492395, pp. 1-10.
T. Bhadra and S. Bandyopadhyay, "Unsupervised Feature Selection using an Improved version of Differential Evolution ", Expert Systems with Applications, 2014 (accepted).
S. Bandyopadhyay, T. Bhadra, and U.Maulik, "Variable Weighted Maximal Relevance Minimal Redundancy Criterion for Feature Selection using Normalized Mutual Information'', Journal of Multiple-Valued Logic and Soft Computing, 2013 (accepted).
T. Bhadra, M. Bhattacharyya, L. Feuerbach, T. Lengauer, and S.Bandyopadhyay, "DNA Methylation Patterns Facilitate the Identification of MicroRNA Transcription Start Sites: A Brain-Specific Study'', PLoS ONE, vol. 8, no. 6, pp. e66722, 2013.
U. Maulik, A. Mukhopadhyay, M. Bhattacharyya, L. Kaderali, B. Brors, S. Bandyopadhyay, and R. Eils, "Mining Quasi-Bicliques from HIV-1Human Protein Interaction Network: A Multiobjective Biclustering Approach'',IEEE/ACM Transactions on Computational Biology and Bioinformatics (accepted).,2013.
M. Bhattacharyya and S. Bandyopadhyay, "Studying the differential co-expression of microRNAs reveals significant role of white matter in early Alzheimer's progression'',Molecular BioSystems,(accepted).,2013.
M. Bhattacharyya and S. Bandyopadhyay, "A New Approach for Combining Knowledge from Multiple Co-expression Networks of MicroRNAs'',IEEE Transactions on Biomedical Engineering (accepted)2013.
A. Chakraborty and S. Bandyopadhyay, "FOGSAA: Fast Optimal Global Sequence Alignment Algorithm'',Scientific Reports (Nature Publishing Group) (accepted),2013.
D Sengupta and S. Bandyopadhyay, "Topological patterns in microRNA-gene regulatory network: studies in colorectal and breast cancer'',Mol. BioSyst. 9 (6), 1360-1371.,2013.
D Sengupta, A Pyne, U Maulik, S Bandyopadhyay, "Reformulated Kemeny Optimal Aggregation with Application in Consensus Ranking of microRNA Targets'',IEEE/ACM Transactions on Computational Biology and Bioinformatics (accepted).,2013.
S Bandyopadhyay, D Sengupta and U Maulik, "GRF: A Greedy Rank Fusion Algorithm for Combining MicroRNA Target Orderings'',Molecular informatics,vol 32, issue 8,2013.
S Bandyopadhyay, S Mallik and A Mukhopadhyay, "A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data'',IEEE/ACM Transactions on Computational Biology and Bioinformatics (accepted),2013.
S Bandyopadhyay and K Mallick, "A New Path Based Hybrid Measure for Gene Ontology Similarity'',IEEE/ACM Transactions on Computational Biology and Bioinformatics (accepted),2013.
S Saha, A Ekbal, K Gupta and S Bandyopadhyay, "Gene expression data clustering using a multiobjective symmetry based clustering technique'',Computers in biology and medicine,43 (11), 1965-1977,2013.
S. Bandyopadhyay, T. Bhadra, U. Maulik and P. Mitra, "Integration of Dense Subgraph Finding with Feature Clustering for Unsupervised Feature Selection'',Pattern Recognition Letters, vol. 40, pp. 104-112, 2014
M. Bhattacharyya, M. Das and S. Bandyopadhyay, "miRT: A Database of Transcription Start Sites of Human MicroRNAs'',Genomics, Proteomics and Bioionformatics,2012.
D. Sengupta, U. Maulik and S. Bandyopadhyay, "Weighted Markov Chain Based Aggregation of Bio-molecule Orderings'',IEEE/ACM Transactions on Computational Biology and Bioinformatics,vol. 9, no. 3, pp. 924-933, 2012.
S. Sengupta and S. Bandyopadhyay, "De novo Design of Potential RecA Inhibitors usingMultiObjective Optimization'',IEEE Transactions/ACM on Computational Biology and Bioinformatics,vol. 9, no.4, pp. 1139-1154, 2012.
A. Mukhopadhyay, S. Ray and M. De, "Detecting Protein Complexes in PPI Network: A Gene Ontology-based Multiobjective Evolutionary Approach'',Molecular BioSystems, Royal Society of Chemistry,Vol. 8, No. 11, pp. 3036-3048, 2012.
M. Bhattacharyya, M. Bhattacharyya and S. Bandyopadhyay, "Recent Directions in Compressing Next Generation Sequencing Data'',Current Bioinformatics,vol. 7, no. 1, pp. 2-6, 2012.
M. Bhattacharyya, L. Feuerbach, T. Bhadra, T. Lengauer, and S. Bandyopadhyay, "MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection'',Statistical Applications in Genetics and Molecular Biology,vol. 11, no. 1, art. 6, DOI: 10.2202/1544-6115.1743.2012.
R. Mitra and S. Bandyopadhyay, "MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method'',PLoS ONE, vol. 6, no. 9, art id. e24583, DOI :10.1371/journal.pone.0024583, 2011.
D. Sengupta and S. Bandyopadhyay, "Participation of MicroRNAs in Human Interactome: Extraction of MicroRNA-MicroRNA Regulations'',Molecular BioSystems,vol. 7, pp. 1966-1973, DOI: 10.1039/C0MB00347F, 2011.
U. Maulik, M. Bhattacharyya, A. Mukhopadhyay and S. Bandyopadhyay, "Identifying the Immunodeficiency Gateway Proteins in Human and their Involvement in MicroRNA Regulation'',MolecularBioSystems, vol. 7, no. 6, pp. 1842-1851, 2011.
S. Bandyopadhyay and M. Bhattacharyya, "A Biologically Inspired Measure for Co-expression Analysis'',IEEE Transactions on Computational Biology and Bioinformatics,vol. 8, no. 4, pp. 929- 942, 2011.
S. Bandyopadhyay and M. Bhattacharyya, "PuTmiR: A database for extracting neighboring transcription factors of human microRNAs'', BMC Bioinformatics, 11:190, 2010.
S. Bandyopadhyay and R. Mitra, U. Maulik and M. Q. Zhang, "Development of the Human Cancer MicroRNA Network'', Silence, 1:6, 2010.
R. Mitra, S. Bandyopadhyay, U. Maulik and M. Q. Zhang, "SFSSClass: An Integrated Approach for miRNA based Tumor Classification'', BMC Bioinformatics, 11(Suppl 1):S22, 2010.
S. Bandyopadhyay and M. Bhattacharyya, "A Novel Method of Studying the Disease Regulatory Activities of MicroRNAs'', Current Bioinformatics, 4(3), pp. 234-241, 2009.
S. Bandyopadhyay and R. Mitra, "TargetMiner: MicroRNA Target Prediction with Systematic Identification Of Tissue Specific Negative Examples'', Bioinformatics, 25(20), pp. 2625-2631, 2009.
S. Bandyopadhyay and M. Bhattacharyya, "Analyzing miRNA co-expression networks to explore TF-miRNA regulation'', BMC Bioinformatics, 10:163, 2009.
S. Bandyopadhyay and R. Mitra, "A Parallel Pairwise Local Sequence Alignment Algorithm'', IEEE Transactions on NanoBioscience, 8(2), pp. 139-146, 2009.
U. Maulik, A. Mukhopadhyay and S. Bandyopadhyay, "Finding Multiple Coherent Biclusters in Microarray Data using Variable String Length Multiobjective Genetic Algorithm'', IEEE Transactions on Information Technology in BioMedicine, (accepted) 2009.
U. Maulik, A. Mukhopadhyay and S. Bandyopadhyay, "Combining Pareto-Optimal Clusters using Supervised Learning for Identifying Co-expressed Genes'', BMC Bioinformatics, 10:27, 2009.
S. S. Ray, S. Bandyopadhyay and S. K. Pal, "Combining Multi-Source Information through Functional Annotation based Weighting: Gene Function Prediction in Yeast'', IEEE Transactions on Biomedical Engineering, 56(2), pp. 229-236, 2009.
S. Bandyopadhyay, U. Maulik and D. Roy, "Gene Identification: Classical and Computational Intelligence Approaches'', IEEE Transactions on Systems, Man and Cybernetics, Part C, 38(1), pp. 55-68, 2008.
S. Bandyopadhyay, A. Mukhopadhyay and U. Maulik, "An Improved Algorithm for Clustering Gene Expression Data'', Bioinformatics, Oxford University Press, 23(21), pp. 2859-2865, 2007.
S. S. Ray, S. Bandyopadhyay, and S. K. Pal, "Genetic Operators for Combinatorial Optimization in TSP and Microarray Gene Ordering'', Applied Intelligence, 26(3), pp. 183-195, 2007.
S. S. Ray, S. Bandyopadhyay, and S. 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, 37(3), pp. 742-749, 2007.
In Book Chapters
M. Bhattacharyya and S. Bandyopadhyay, "Analyzing Topological Properties of Protein-protein Interaction Networks: A Perspective towards Systems Biology'', Computational Intelligence and Pattern Analysis in Biology Informatics, U. Maulik, S. Bandyopadhyay and J. T. L. Wang (Eds.), John Wiley & Sons, Inc., 2010.
A. Mukhopadhyay, U. Maulik and S. Bandyopadhyay, "Multiobjective Evolutionary Approach to Fuzzy Clustering of Microarray Data'', Analysis of Biological Data: A Soft Computing Approach, World Scientific, pp. 304-328, 2007.
S. Bandyopadhyay, S. Santra, U. Maulik and H. Muehlenbein, "In Silico Design of Ligands Using Properties of Target Active Sites'', Analysis of Biological Data: A Soft Computing Approach, World Scientific, pp. 184-201, 2007.
In Conference Proceedings
D. Ghosh and S. Bandyopadhyay, " A fuzzy citation-kNN algorithm for multiple instance learning", IEEE International Conference on Fuzzy Systems, 2015(accepted)
S.Ray, S.Biswas, A. Mukhopadhyay and S. Bandyopadhyay, "Detecting Perturbation in Co-expression Modules Associated with Different Stages of HIV-1 Progression: A Multi-objective Evolutionary Approach", In Proc. EAIT-2014, Fourth International Conference on Emerging Applications of Information Technology , Kolkata, India, December 19 - 21, 2014.
Saurav Mallik, Ujjwal Maulik, Anirban Mukhopadhyay and Sanghamitra Bandyopadhyay, “Association Rule Extraction from Genome-wide DNA Methylation and Gene Expression Data: A Biclustering-based Technique'', National Seminar on ”Soft Computing : A Panorama of Possibilities” (SCAPP 2013), ISBN: 978-81-31703-83-6, Bhubaneswar, June 1-2, 2013.
Saurav Mallik, Anirban Mukhopadhyay, Ujjwal Maulik and Sanghamitra Bandyopadhyay, “Integrated Analysis of Gene Expression and Genome-wide DNA Methylation for Tumor Prediction: An Association Rule Mining-based Approach'', Proc. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), IEEE Symposium Series on Computational Intelligence - SSCI 2013, Singapore, pp. 120-127, April 16, 2013
Angana Chakraborty, Sanghamitra Bandyopadhyay, "Clustering of Web Sessions by FOGSAA"'', Recent Advances in Intelligent Computational Systems, IEEE RAICS, 2013.
S. Ray, A. Mukhopadhyay and U. Maulik,"Predicting Annotated HIV-1–Human PPIs using a Biclustering Approach to Association Rule Mining'', In Proc. EAIT-2012, pp. 28-31, Kolkata, India, November 2012.
S. Ray, S. Bandyopadhyay, A. Mukhopadhyay, U. Maulik,,"Incorporating Fuzzy Semantic Similarity Measure in Detecting Human Protein Complexes in PPI Network: A Multiobjective Approach'',In Proc. FuzzIEEE-2013, Hyderabad, India, July 2013.
R. Mitra and S. Bandyopadhyay, "Improvement of MicroRNA Target Prediction Using An Enhanced Feature Set: A Machine Learning Approach'', Proceedings of the IEEE International Advance Computing Conference (IACC), Patiala, India, 2009.
M. Bhattacharyya and S. Bandyopadhyay, "Integration of Co-expression Networks for Gene Clustering'', Proceedings of the 7th International Conference on Advances in Pattern Recognition (ICAPR), Kolkata, India, pp. 355-358, 2009.
U. Maulik, A. Mukhopadhyay, S. Bandyopadhyay, X. Zhang and M. Zhang, "Multiobjective Fuzzy Biclustering in Microarray Data: Method and a New Performance Measure'', World Congress on Computational Intelligence (WCCI), , pp. -, 2008.
R. Mitra and S. Bandyopadhyay, "Improved Classification of Poorly Differentiated Tumors: An Advanced Analytical Approach'', Proceedings of Second National Conference on Recent Trends in Information Systems (ReTIS), Kolkata, India, pp. 46-51, 2008.
X. Wang, S. Bandyopadhyay, Z. Xuan, X. Zhao, M. Q. Zhang and X. Zhang, "Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA'', Proceedings of the 6th Annual International Conference on Computational Systems Bioinformatics, San Diego, California, pp. 183-193, 2007.