| 1 |
S. Ray*,M. Desai, and S. Pyne, Systematic mining of patterns of polysubstance use in a nationwide population survey, Computers in Biology and Medicine, Volume 151, Part A, December 2022, 106175. |
| 2 |
S. Ray*, S. Lall, A. Mukhopadhyay, S. Bandyopadhyay, and A. Schönhuth, Deep variational graph autoencoders for novel host-directed therapy options against COVID-19, Artificial Intelligence in Medicine, Volume 134, December 2022, 1024 |
| 3 |
S. Ray*, S. Lall, and S. Bandyopadhyay, A deep integrated framework for predicting SARS-CoV2–Human protein-protein interaction, IEEE Transactions on Emerging Topics in Computational Intelligence, doi: 10.1109/TETCI.2022.3182354., 2022 |
| 4 |
P. Upadhyay and S. Ray*, A regularized multi-task learning approach for cell type
detection in single RNA sequencing data, Frontiers in Genetics, 13 April 2022,
https://doi.org/10.3389/fgene.2022.78883 |
| 5 |
S. Lall,S. Ray*, and S. Bandyopadhyay, A topology preserving graph convolution
network for clustering of single-cell RNA seq data, PLoS Computational Biology,18(3): e1009600. https://doi.org/10.1371/journal.pcbi.1009600, 2022. |
| 6 |
S. Lall, S. Ray*, S. Bandyopadhyay, LSH-GAN enables in-silico generation of cells
for small sample high dimensional scRNA-seq data., Nat. Communication Biology, 577 (2022). https://doi.org/10.1038/s42003-022-0347 |
| 7 |
S. Lall, A. Ghosh, S. Ray*, S. Bandyopadhyay, sc-REnF: An entropy guided robust
feature selection for clustering of single-cell rna-seq data, Briefings in Bioinformatics,bbab517, https://doi.org/10.1093/bib/bbab517, 2022. |
| 8 |
SMM Hossain, L. Khatun, S. Ray*, and A. Mukhopadhyay, Pan-cancer classification by regularized multi-task learning., Scientific Reports, 11, 24252 (2021) |
| 9 |
S. Lall, S. Ray*, S. Bandyopadhyay, RgCop-A regularized copula based method for
gene selection in single cell rna-seq data, PLoS Computational Biology, 17(10):
e1009464. https://doi.org/10.1371/journal.pcbi.1009464, 2021. |
| 10 |
SM. Hossain, L. Khatun, S. Ray*, A. Mukhopadhyay Identification of key immune regulatory genes in HIV-1 progression, Gene, Volume 792, 5 August 2021,
145735 |
| 11 |
P. Gharani, S. Ray, M. Aruru and S. Pyne Differential Patterns of Social Media
Use Associated with Loneliness and Health Outcomes in Selected Socioeconomic
Groups, J. technol. behav. sci. 2021 (https://doi.org/10.1007/s41347-021-
00208-4) |
| 12 |
M. Hossain, AA. Halsana, L. Khatun, and S. Ray*, and A. Mukhopadhyay Discovering Key Transcriptomic Regulators in Pancreatic Ductal Adenocarcinoma using Dirichlet Process Gaussian Mixture Mode, Scientific Reports (7853 (2021),
https://doi.org/10.1038/s41598-021-87234-7 |
| 13 |
M. Islam, M. Hossain and S. Ray*, “DTI-SNNFRA: Drug-target interaction prediction by shared nearest neighbors and fuzzy-rough approximation" PLoS ONE
https://doi.org/10.1371, February 19, 2021 |
| 14 |
F. Nielsen, G. Marti, S. Ray and S. Pyne, “Clustering patterns connecting COVID-19 dynamics and Human mobility using optimal transport"Sankhya B, February,
2021. |
| 15 |
S. Ray, S.Lall and S.Bandyopadhyay "CODC: A copula based model to identify
differential coexpression", npj System Biology and Applications,6, 2020 |
| 16 |
S. Pyne, S. Ray, R. Gurewitsch , M. Aruru, “Transition from Social Vulnerability to
Resiliency vis-à-vis COVID-19",Statistics and Applications, Vol.18, pp-197-208, 2020 |
| 17 |
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, DOI: 10.1109/TCBB.2019.2923173, 2019 |
| 18 |
S. Ray A. Alberuni, and U.Maulik “Computational prediction of HCV-human protein-protein interaction via topological analysis of HCV infected PPI module", IEEE
Transaction on Nanobioscience, 17:55-61, 2018, |
| 19 |
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. |
| 20 |
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, |
| 21 |
U. Maulik, S. Basu and S. Ray* “Identifying protein complexes in PPI network
using non-cooperative sequential game", Scientific Reports, 7:8410, 2017 |
| 22 |
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., 201 |
| 23 |
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 |
| 24 |
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 |
| 25 |
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. |
| 26 |
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 |
| 27 |
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 Biologydoi: 10.1186/s13015-015-0056-2,
2015. |
| 28 |
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 |
| 29 |
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. |
| 30 |
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. |
| 31 |
M. Aruru, S. Pyne, and S. Ray A computational framework for identifying patterns
of association and transition in addictive substances use over five decades in the US,
APHA’s (American Public Health Association) Annual Meeting and Expo,
2021 |
| 32 |
S. Ray, S Lall, A Mukhopadhyay, S Bandyopadhyay and A Schönhuth, Deep variational graph autoencoders for novel host-directed therapy options against COVID-19, 29th Conference on Intelligent Systems in Molecular Biology ISMB/ECCB
2021, COVID-19 special track. |
| 33 |
SM. Hossain, S. Ray and A. Mukhopadhyay Detecting Overlapping Gene Communities during Stomach Adenocarcinoma: A Discrete NMF-based Integrative Approach,
2020 IEEE International Conference on Advent Trends in Multidisciplinary
Research and Innovation (ICATMRI), p:1-6, 2021 |
| 34 |
• S. Lall, S. Ray and S. Bandyopadhyay, Identifying novel SARS-CoV2–human protein
interactions using graph embedding, 28th Conference on Intelligent Systems in
Molecular Biology (ISMB-2020, COVID-19 special track), 2020 |
| 35 |
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, 2019 |
| 36 |
D. Bhattacharjee, SM. Hossain, R. Sultana and S. Ray Topological Inquisition into
the PPI Networks Associated with Human Diseases Through Graphlet Frequency
Distribution, Pattern Recognition and Machine Intelligence. PReMI 2017,
volume 10597:431-437, 2017 |
| 37 |
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-20170), Vol:215, pp-282-289, 2017 |
| 38 |
SA. Khan and S.RayIntegrating multi-view data: A hypergraph based approach,
First International Conference on Computational Intelligence, Communications, and Business Analytics (CICBA-2017), Vol:776, 347-357, 201 |
| 39 |
S. Ray, SM. Hossain and L. Khatun, Discovering preservation pattern from coexpression modules in progression of HIV-1 disease: An eigengene based approach,
International Conference on Advances in Computing, Communications and
Informatics (ICACCI-2016), DOI: 10.1109/ICACCI.2016.7732146, 2016. |
| 40 |
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),Volume 93, pp-1054-1060, 2016. |
| 41 |
S. Ray, A. Hossain and U.MaulikDisease associated protein complex detection: a
multi-objective evolutionary approach International Conference on Microelectronics, Computing and Communications (MicroCom), DOI: 10.1109/MicroCom.2016.7522420, 2016. |
| 42 |
S. Ray, S. Chakrabarty and A. Mukhopadhyay DCoSpect: a novel differentially
co-expressed gene Module detection algorithm using spectral clustering, 4th International Conference on Frontiers in Intelligent Computing: Theory and
Applications(FICTA), Vol.404,pp:59-77, 2016. |
| 43 |
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 Fourth International Conference
of Emerging Applications of Information Technology,
DOI:10.1109/EAIT.2014.34, 2015 |
| 44 |
S. Ray, S. Bandyopadhyay, A. Mukhopadhyay, U. Maulik Incorporating Fuzzy Semantic Similarity Measure in Detecting Human Protein Complexes in PPI Network:
A Multiobjective Approach, IEEE International Conference on Fuzzy Systems
(FUZZ-IEEE), DOI: 10.1109/FUZZ-IEEE.2013.6622483, 2013. |
| 45 |
S. Ray, A. Mukhopadhyay and U. MaulikPredicting Annotated HIV-1Human PPIs
using a Biclustering Approach to Association Rule Mining, In Proc. Third International Conference on Emerging Applications of Information Technology,
DOI: 10.1109/EAIT.2012.6407854,pp-28-31, 2012 |
