Computer Science and Engineering

• Award for Doctoral Thesis
• Award for Master Thesis
• GYTI Appreciation-2018

Journal
• Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India Sarkar P., Banerjee S., Saha S.A., Mitra P., Sarkar S. By Scientific Reports 13 - (2023)
• A sequence space search engine for computational protein design to modulate molecular functionality Malik A., Banerjee A. , Pal A. , Mitra P. By Journal of Biomolecular Structure & Dynamics 41 2937-2946 (2023)
• A novel computational predictive biological approach distinguishes Integrin 1 as a salient biomarker for breast cancer chemoresistance Das S., Kundu M., Hassan A., Parekh A., Jena B.C., Mundre S., Banerjee I., Yetirajam R., Das C.K., Pradhan A.K., Das S.K., Emdad L., Mitra P., Fisher P.B., Mandal M. By Biochimica et Biophysica Acta - Molecular Basis of Disease 1869 - (2023)
• Modularity-based Parallel Protein Design Algorithm with an Implementation using Shared Memory Programming Pal A., Mulumudy R. , Mitra P. By PROTEINS: Structure, Function, and Bioinformatics 90 658-669 (2022)
• Therapeutic targeting of RBPJ, an upstream regulator of ETV6 gene, abrogates ETV6-NTRK3 fusion gene transformations in glioblastoma Biswas A., Rajesh Y. , Das S. , Banerjee I. , Kapoor N. , Mitra P. , Mandal M. By Cancer Letters 544 215811-215825 (2022)
• ProFuMCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell Das B., Mitra P. By Journal of Molecular Modeling 28 167-175 (2022)
• Human Prion Protein: Exploring the Thermodynamic Stability and Structural Dynamics of its Pathogenic Mutants Halder P., Mitra P. By Journal of Biomolecular Structure & Dynamics 40 11274-11290 (2022)
• A computational framework for modeling functional protein-protein interactions Pal A., Pal D. , Mitra P. By PROTEINS: Structure, Function, and Bioinformatics 89 1353-1364 (2021)
• High-performance Whole-cell Simulation Exploiting Modular Cell Biology Principles Das B., Mitra P. By Journal of Chemical Information and Modeling 61 1481-1492 (2021)
• Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins Pal B., Mitra P. By Journal of Molecular Biology 433 167149- (2021)
• An evolutionary profile guided greedy parallel replica-exchange Monte Carlo search algorithm for rapid convergence in protein design Banerjee A., Pal K. , Mitra P. By IEEE/ACM Transactions on Computational Biology and Bioinformatics 18 489-499 (2021)
• Estimating Change in Foldability due to Multi-point Deletions in Protein Structures Banerjee A., Kumar A. , Ghosh K. K., Mitra P. By Journal of Chemical Information and Modeling 60 6679-6690 (2020)
• Estimating the Effect of Single Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein Banerjee A., Mitra P. By Journal of Chemical Information and Modeling 60 3315-3323 (2020)
• ETV6 gene aberrations in non-haematological malignancies: A review highlighting ETV6 associated fusion genes in solid tumors Biswas A., Rajesh Y. , Mitra P. , Mandal M. By Biochimica et Biophysica Acta - Reviews on Cancer 1874 188389- (2020)
• Ebola Virus VP35 protein: modeling of the tetrameric structure and an analysis of its interaction with Human PKR Banerjee A., Mitra P. By Journal of Proteome Research 19 4533-4542 (2020)
• Boosting phosphorylation site prediction with sequence feature-based Machine learning Maiti S., Hassan A. , Mitra P. By PROTEINS: Structure, Function, and Bioinformatics 88 284-291 (2020)
• Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management Rajesh Y., Banerjee A. , Pal I. , Biswas A. , Das S. , Dey K. K., Kapoor N. , Ghosh A. K., Mitra P. , Mandal M. By Biochimica et Biophysica Acta - General Subjects 1863 1196-1209 (2019)
• Changing the Apoptosis Pathway through Evolutionary Protein Design Shultis D., Mitra P. , Huang X. , Johnson J. , Khattak N. A., Gray F. , Piper C. , Czajka J. , Hansen L. , Wan B. , Chinnaswamy K. , Liu L. , Wang M. , Pan J. , Stuckey J. , Cierpicki T. , Borchers C. H., Wang S. , Lei M. , Zhang Y. By Journal of Molecular Biology 431 825-841 (2019)
• Analyzing change in protein stability associated with Single Point Deletions in a newly defined protein structure database Banerjee A., Levy Y. , Mitra P. By Journal of Proteome Research 18 1402-1410 (2019)
• A Network-based Zoning for Parallel Whole-Cell Simulation Das B., Patil A. R., Mitra P. By Bioinformatics 35 88-94 (2019)
• Ebolavirus interferon antagonists - protein interaction perspectives to combat pathogenesis Banerjee A., Pal A. , Pal D. , Mitra P. By Briefings in Functional Genomics 17(6) 392-401 (2018)
• Bacterial flagellar switching: a molecular mechanism directed by the logic of an electric motor Maiti S., Mitra P. By Journal of Molecular Modeling 24 280-289 (2018)
• An evolution-based approach to de novo protein design and case study on Mycobacterium Tuberculosis Mitra P., Shultis D. , Brender J. R., Czajka J. , Marsh D. , Gray F. , Cierpicki T. , Zhang Y. By PLoS Computational Biology 9 e1003298- (2013)
• EvoDesign: de novo protein design based on structural and evolutionary profiles Mitra P., Shultis D. , Zhang Y. By Nucleic Acids Research 41 W273-W280 (2013)
• How many protein-protein interaction types exist in nature? Garma L., Mukherjee S. , Mitra P. , Zhang Y. By PLoS One 7 e389- (2012)
• dockYard - a repository to assist modeling of protein-protein docking Mitra P., Pal D. By Journal of Molecular Modeling 17 599-606 (2011)
• Using correlated parameters for improved ranking of protein-protein docking decoys Mitra P., Pal D. By Journal of Computational Chemistry 32 787-796 (2011)
• PRUNE and PROBE two modular web services for protein-protein docking Mitra P., Pal D. By Nucleic Acids Research 39 229-234 (2011)
• Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference Mitra P., Pal D. By Structure 19 304-312 (2011)
• Interface of apoptotic protein complexes has distinct properties Mitra P., Dhar R. , Pal D. By In Silico Biology 9 365-378 (2010)
• New measures for estimating surface complementarity and packing at protein-protein interfaces Mitra P., Pal D. By FEBS Letters 584 1163-1168 (2010)
Others
• Deciphering biological evolution exploiting the topology of Protein Locality Graph Das B., Mitra P. By - (2022)
• Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India Sarkar P., Banerjee S. , Saha S. A., Mitra P. , Sarkar S. By - (2022)
Educational Package
• Algorithms for protein modelling and engineering Mitra P. By - (2021)
Conferences
• Cluster-Based Relative Outlier Under-Sampling Technique Hassan A., Banerjee R. , Mitra P. , Mitra P. By 19th Industrial Conference on Data Mining ICDM 2019 - (2019)
• Protein Design Assisted Residue Conservation and Functional Stability Analysis for Bacterial Chemotaxis Maiti S., Mitra P. By International Conference on Bioinformatics and Systems Biology (BSB 2018) - (2018)
• Integrin 1 regulates doxorubicin resistance in breast cancer via FAK-mediated activation of ERK1 pathway Das S., Jena B. C., Mundre S. , Parekh A. , Rajesh Y. , Mitra P. , Mandal M. By AACR Annual Meeting 2018 4022-4022 (2018)
• Computational method to recognize mutation leading to alterations in protein stability and function Maiti S., Mitra P. By IEEE International Conference on Innovative Technologies in Engineering 2018(ICITE OU) - (2018)
• An evolution-based approach to de novo protein design and remodeling of protein interactions in Mycobacterium tuberculosis genome Mitra P., Shultis D. , Zhang Y. By Modeling of Protein Interactions - (2012)
• Protein-protein docking: simpler approaches for improved prediction Mitra P., Pal D. By International Conference on Mathematical Biology - (2011)
• Efficiently screening monomers of proteins using Naive Bayes classifier Mitra P., Pal D. By Asia Pacific Bioinformatics Conference (APBC 2010) 74- (2010)
• Protein-Protein Interaction in Apoptosis Process Dhar R., Mitra P. , Pal D. By International Conference on Bioinformatics (InCoB 2006) 287- (2006)
• A Two- and Three- Layer Dogleg Channel Routing Algorithm for Minimizing Total Wire Length Ghoshal N., Mitra P. , Pal R. K. By International Conference on Computers and Devices for Communications CNA_0435- (2004)
• A Graph Theoretic Approach to Minimize Total Wire Length in Channel Routing Mitra P., Ghoshal N. , Pal R. K. By IEEE TENCON 2003 414-418 (2003)
• TAH based Total Wire Length Minimization in Two-Layer Channel Routing Mitra P., Ghoshal N. , Chatterji A. , Pal R. K. By National Conference on Emerging Trends in VLSI Design and Testing (NCVDAT-03) 428-437 (2003)
• Total Wire Length Minimization in Channel Routing Mitra P., Ghoshal N. , Pal R. K. By Conference on Horizons of Telecommunication (HOT 2003) 60- (2003)
Symposium
• Computational exploration of critical residues aiding in phosphate sink mechanism related to bacterial chemotaxis Maiti S., Mitra P. By IBSE International Symposium "From Genotype to Phenotype: Computational Approaches to Understand Biological Systems" - (2018)
• Identifying the nature of the interface in protein-protein complexes Mitra P. By International Symposium on Biocomputing 13- (2010)

Principal Investigator

• Joint center for protein interactor discovery and structure
• Predictive docking: Improving the performance by refining protein structures
• Whole cell modeling and simulation in bacterium escherichia coli (SGIGC)
• Designing proteins with enhanced stability by modulating the entropy in the folded state
• Computational Approaches to Study Protein Conformational Disorders
• Development of a CUDA C/C++ based Whole-cell Simulator Package

Co-Principal Investigator

• Designer Therapeutic Elucidation of Novel Small Molecular Inhibitor Targeting ETV6-NTRK3 Associated Gene Fusion in Glioblastoma
• Multimodal and multi-scale imaging for early diagnosis and interventional management of oral pre-cancers and cancer
• Unraveling cancer transformation and progression through biological, electro-mechanical and computational techniques