Publications

Journals:

20. S. Lall, A. Ghosh, S. Ray, S. Bandyopadhyay "sc-REnF: An entropy guided robust feature selection for clustering of single-cell rna-seq data", BioRxiv preprint, doi: https://doi.org/10.1101/2020.10.10.334573.

19. S. Ray and A. Schönhuth "MarkerCapsule: Explainable Single Cell Typing using Capsule Networks",BioRxiv preprint, doi: https://doi.org/10.1101/2020.09.22.307512.

18. F. Nielsen, G. Marti, S. Ray and S. Pyne, ``Clustering patterns connecting COVID-19 dynamics and Human mobility using optimal transport" arXiv preprint, arXiv:2007.10677

17. S Ray, S Lall, A Mukhopadhyay, S Bandyopadhyay and A Schönhuth, ``Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs", arXiv preprint arXiv:2007.02338.

16. S. Ray, S.Lall and S.Bandyopadhyay, “CODC: A copula based model to identify differential coexpression”, npj System Biology and Applications,6, 20, (2020).

15. S. Pyne, S. Ray, R. Gurewitsch , M. Aruru, “Transition from Social Vulnerability to Resiliency `vis-`a-vis COVID-19”, Statistics and Applications, Vol.18, pp-197-208, (2020).

14. S.Biswas, S. Ray and S.Bandyopadhyay, “Colored Network Motif Analysis by Dynamic Programming Approach: An Application in Host-Pathogen Interaction Network”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2019.2923173

(2019).

13. S. Ray A. Alberuni, and U.Maulik , “Computational prediction of HCVhuman protein-protein interaction via topological analysis of HCV infected PPI module”, IEEE Transaction on Nanobioscience, 17:55-61 (2018).

12. S. Ray, A.Mukhopdhyay and U. Maulik, “A Review of Computational Approaches for Analysis of Hepatitis C Virus (HCV)-mediated Liver Diseases”, Briefings in Functional Genomics, doi: 10.1093/bfgp/elx040 (2017).

11. SM. Hossain, S. Ray and A. Mukhopadhyay, “A Comprehensive Analysis on Preservation Patterns of Gene Co-Expression Networks during Alzheimer’s Disease Progression”, BMC Bioinformatics, doi: 10.1186/s12859-017-1946-8 (2017).

10. U. Maulik, S. Basu and S. Ray , “Identifying protein complexes in PPI network using noncooperative sequential game”, Scientific Reports, 7:8410 (2017).

9. M. Hossain and S. Ray and A. Mukhopadhyay, “Preservation affinity in consensus modules among stages of HIV-1 Progression”, BMC Bioinformatics, DOI: 10.1186/s12859-017-1590-3. (2017).

8. S.Ray and U. Maulik , “Identifying differentially coexpressed module during HIV disease progression: A multiobjective approach”, Scientific Reports, doi: 10.1038/s41598017-00090- 2 (2017).

7. S. Ray and U. Maulik, “Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13:6:1086-1099 (2016).

6. S. Ray and S. Bandyopadhyay, “A NMF based approach for integrating multiple data sources to predict HIV-1-human PPIs”, BMC Bioinformatics, doi: 10.1186/s12859-016-0952-6 (2016).

5. S. Ray and S. Bandyopadhyay, “Discovering condition specific topological pattern changes in coexpression network: an application to HIV-1 progression”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13:1086 - 1099 (2016).

4. S. Bandyopadhyay, S. Ray, A. Mukhopadhyay and U. Maulik, “‘A Multiobjective Approach for Identifying Protein Complexes and Studying their Association in Multiple Disorders”, Algorithms for Molecular Biology, doi: 10.1186/s13015-015-0056-2 (2015).

3. 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”, Briefings in Bioinformatics, 16:5: 830-851 . (2015).

2. A. Mukhopadhyay, S. Ray and U. Maulik, “Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach”, BMC Bioinformatics, 15:26 (2014).

1. A. Mukhopadhyay, S. Ray and M. De, “Detecting Protein Complexes in PPI Network: A Gene Ontology-based Multiobjective Evolutionary Approach”, Molecular BioSystems, 8:3036-3048 (2013).

Conferences:

14. S. Lall, S. Ray and S. Bandyopadhyay, “Identifying novel SARS-CoV2–human protein interactions using graph embedding”, ISMB-2020, COVID-19 special track, Accepted (2020).

13. SM. Hossain, A. Mukhopadhyay and S. Ray, “Detecting hub genes and key modules in stomach adenocarcinoma using nsNMF based data integration technique”, IEEE 18th International Conference on Information Technology, Accepted (2019).

12. S. Biswas, S.Ray, and S. Bandyopadhyay, ``Analysis on Preservation Characteristics of Modular Structure during HIV-1 Progression using Weighted and Normalized Graphlet Frequency Distribution", IEEE 4th International Conference for Convergence in Technology (I2CT ),2018 (Accepted).

11. D. Bhattachariya, M. Hossain, R. Sultana and S. Ray ``Topological Inquisition into the PPI Networks Associated with Human Diseases through Graphlet Frequency Distribution", 7th International Conference on Pattern Recognition and Machine Intelligence (PReMI 2017), Kolkata, 2017.

10. SM Hossain, S. Ray, TS Tannee and A. Mukhopadhyay Analyzing Prognosis Characteristics of Hepatitis C using a Biclustering Based Approach Number", 7th International Conference on Advances in Computing and Communications (ICACC-2017) vol. 115, pp 282 - 289.

9. SA. Khan and S.Ray Integrating multi-view data: A hypergraph based approach ", First International Conference on Computational Intelligence, Communications, and Business Analytics (CICBA-2017).

8. S. Ray, SM. Hossain and L. Khatun Discovering preservation pattern from co-expression modules in progression of HIV-1 disease: An eigengene based approach", International Conference on Advances in Computing, Communications and Informatics (ICACCI-2016),2016.

7. SM. Hossain, Z. Mahboob, R. Chowdhury, A. Sohel and S. Ray, "Protein complex detection in PPI network by identifying mutually exclusive protein- protein interactions", In 6h International Conference on Advances in Computing and Communications (ICACC-2016)

6. S. Ray, A. Hossain and U.Maulik, “Disease associated protein complex detection: a multiobjective evolutionary approach”, In Proc. MICROCOM-2016, NIT Durgapur.

5. S. Ray , S. Chakraborty, A. Mukhopadhyay "DCoSpect: A Novel Differentially Coexpressed Gene Module Detection Algorithm Using Spectral Clustering", Proceedings of the 4th International Conference on Frontiers in Intelligent Computing: Theory and Applications (FICTA) 2015, NIT Durgapur, 2015.

4. 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 (Accepted).

3. 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 .

2. 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.

1. S. Ray, M. De and A. Mukhopadhyay, "A Multiobjective GO based Approach to Protein Complex Detection", In Proc. 2nd International Conference on Computer, Communication, Control and Information Technology (C3IT-2012),Volume 4, pp. 555–560 (Procedia Technology, Elsevier), Hooghly, West Bengal, India, February 2012.