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SYSTEMS AND SYNTHETIC BIOLOGY LABORATORY

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51. Manali Das and Amit Ghosh (2024). Molecular insights into mutation-induced conformational changes in Acetyl CoA Carboxylase for improved activity. International Journal of Biological Macromolecules. [Journal Article]
50. Gourab Bhattacharje, Amit Ghosh, Amit Kumar Das (2023). Deciphering the mannose transfer mechanism of mycobacterial PimE by molecular dynamics simulations. Glycobiology [Journal Article]
49. Ayusmita Ray, Pritam Kundu, and Amit Ghosh (2023). Reconstructionof a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes. ACS synthetic Biology [Journal Article]
48. Bharat Manna, Pinaki Chanda, Supratim Datta and Amit Ghosh (2023). Elucidating the Ionic Liquid-Induced Mixed Inhibition of GH1 β-Glucosidase H0HC94. The Journal of Physical Chemistry B, 127: 8406-8416 [Journal Article]
47. Rokesh Radhakrishnan, Bharat Manna, Amit Ghosh (2023). Molecular insights into dissolution of lignin bunch in ionic liquid-water mixture for enhanced biomass conversion. Renewable Energy, 206: 47-59 [Journal Article]
46. Pritam Kundu, Amit Ghosh (2023). Genome-scale community modeling for deciphering the inter-microbial metabolic interactions in fungus-farming termite gut microbiome. Computers in Biology and Medicine, 154: 106600 [Journal Article]
45.Abhijit Bera, Bharat Manna, Debabrata Ganguly, S.K.P.Amarnath, Samik Nanda, Amit Ghosh, and Santanu Chattopadhyay (2023). Pretreatment of Hevea Latex by Sorbitol: Improving the Efficacy of Silica Dispersion by a Biomimetic Approach. ACS Applied Polymer Materials, 5: 441-451 [Journal Article]
44. Pradipta Patra, B.R. Disha, Pritam Kundu, Manali Das, Amit Ghosh (2023). Recent advances in machine learning applications in metabolic engineering. Biotechnology Advances, 62: 108069 [Journal Article]
43. Pritam Kundu , Suman Mobdal, Amit Ghosh (2022). Bacterial species metabolic interaction network for deciphering the lignocellulolytic system in fungal cultivating termite gut microbiota. BioSystems , 221: 104763 [Journal Article]
42. Satyajit Beura, Pritam Kundu, Amit Kumar Das, Amit Ghosh (2022) Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health. Computers in Biology and Medicine, 149: 105997 [Journal Article]
41. G Bhattacharje, Amit Ghosh, A K Das (2022). In-silico identification of critical residues in the mannose-transfer mechanism of phosphatidyl-myo-inositol mannosyltransferase B'. Biochemical and Biophysical Research Communications, 621: 14-19 [Journal Article]
40. R Chakraborty, G Bhattacharje, J Baral, B Manna, J Mullick, B S Mathapati, P Abraham, Madhumathi J, Y Hasija,  Amit Ghosh , Amit Kumar Das (2022). In-silico screening and in-vitro assay show the antiviral effect of Indomethacin against SARS-CoV-2. Computers in Biology and Medicine, 147: 105788 [Journal Article]
39.Gourab Bhattacharje, Amit Ghosh , Amit Kumar Das (2022). Understanding the Mannose Transfer Mechanism of Mycobacterial Phosphatidyl-myo-inositol Mannosyltransferase A from Molecular Dynamics Simulations. ACS Omega, 7: 19288-19304 [Journal Article]
38.Suman Mondal, Pritam Kundu, Amit Ghosh (2022). Understanding the biomass conversion processes of bovine gut microbiota through community-wide metabolic interaction network. Bioresource Technology Reports, 17: 100989 [Journal Article]
37. T Mondal, K Das, P Singh, M Natarajan, B Manna, Amit Ghosh, P Singh, SK Saha, K Dhama, T Dutt, S Bag (2022). Thin films of functionalized carbon nanotubes support long-term maintenance and cardio-neuronal differentiation of canine induced pluripotent stem cells. Nanomedicine: Nanotechnology, Biology and Medicine, 40: 102487 [Journal Article]
36. Rokesh Radhakrishnan, Bharat Manna, Amit Ghosh (2022). Solvent Induced Conformational Changes for the Altered Activity of Laccase: A Molecular Dynamics Study. br Journal of Hazardous Materials, 423: 127123 [Journal Article]
35. Ayusmita Ray, Manoranjan Nayak, Amit Ghosh (2022). A review on co-culturing of microalgae: A greener strategy towards sustainable biofuels production. Science of The Total Environment, 802: 149765 [Journal Article]
34. Shubhasish Goswami, Bharat Manna, Krishnananda Chattopadhyay, Amit Ghosh, Supratim Datta (2021). Role of Conformational Change and Glucose Binding Sites in the Enhanced Glucose Tolerance of Agrobacterium tumefaciens 5A GH1 beta-Glucosidase Mutants. Journal of Physical Chemistry B, 125: 9402-9416 [Journal Article]
33. Rokesh Radhakrishnan, Pradipta Patra, Manali Das, Amit Ghosh (2021). Recent advancements in the Ionic liquid mediated lignin valorization for the production of renewable materials and value-added chemicals. Renewable and Sustainable Energy Reviews, 149: 111368 [Journal Article]
32. Bharat Manna, Amit Ghosh (2021). Understanding the Dissolution of Softwood Lignin in Ionic Liquid and Water Mixed Solvents. International Journal of Biological Macromolecules, 182: 402-412 [Journal Article]
31. Piyush Nanda, Amit Ghosh (2021). Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS Cov2 infection. PLoS Computational Biology, 17(4):e1008860 [Journal Article]
30. Bharat Manna, Amit Ghosh (2021). Understanding the conformational change and inhibition of hyperthermophilic GH10 xylanase in ionic liquid. Journal of Molecular Liquids, 332:115875 [Journal Article]
29. Pradipta Patra, Manali Das, Pritam Kundu, Amit Ghosh (2021). Recent Advances in Systems and Synthetic Biology Approaches for Developing Novel Cell-factories in Non-Conventional Yeasts. Biotechnology Advances, 47: 107695 [Journal Article]
28. Bharat Manna, Amit Ghosh (2021). Molecular Insight into glucose induced conformational change to investigate uncompetitive inhibition of GH1 beta-glucosidase. ACS Sustainable Chemistry & Engineering, 9:1613-1624 [Journal Article]
27. Piyush Nanda, Pradipta Patra, Manali Das, Amit Ghosh (2020). Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri. Scientific Reports, 10: 16314 [Journal Article]
26. Kaustav Gangopadhyay, Bharat Manna, Swarnendu Roy, Sunitha Kumari, Olivia Debnath, Subhankar Chowdhury, Amit Ghosh, Rahul Das (2020). An allosteric hot spot in the tandem-SH2 domain of ZAP-70 regulates T-cell signaling. Biochemical Journal, 477(7): 1287-1308 [Journal Article]
25. Bharat Manna, Amit Ghosh (2020). Structure and dynamics of ionic liquid tolerant hyperthermophilic endoglucanase Cel12A from Rhodothermus marinus. RSC Advances, 10: 7933-7947 [Journal Article]
24. Manali Das, Pradipta Patra, Amit Ghosh (2020). Metabolic engineering for enhancing microbial biosynthesis of advanced biofuels. Renewable and Sustainable Energy Reviews, 119: 109562 [Journal Article]
23. Pritam Kundu, Bharat Manna, Subham Majumder, Amit Ghosh (2019). Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota. Scientific Reports, 9: 1-13 [Journal Article]
22. Snigdha Maiti, Bidisha Acharya, Veda Sheersh Boorla, Bharat Manna, Amit Ghosh, Soumya De (2019). Dynamic Studies on Intrinsically Disordered Regions of Two Paralogous Transcription Factors Reveal Rigid Segments with Important Biological Functions. Journal of Molecular Biology, 431: 1353-1369 [Journal Article]
21. Bharat Manna, Amit Ghosh (2019). Dissolution of Cellulose in Ionic Liquid and water mixtures as revealed by Molecular Dynamics Simulations. Journal of Biomolecular Structure and Dynamics, 37: 3987-4005 [Journal Article]
20. Kheerthana Duraivelan, Aditya J. Basak, Amit Ghosh, Dibyendu Samanta (2018). Molecular and structural bases of interaction between extracellular domains of nectin-2 and N-cadherin. Proteins: Structure, Function, and Bioinformatics, 86: 1157-1164 [Journal Article]
19. Muddassir Mohd, Bharat Manna, Priyanka Singh, Surjeet Singh, Rajesh Kumar, Amit Ghosh, Deepak Sharma (2018). Single-molecule force-unfolding of titin I27 reveals correlation between size of surrounding anions and its mechanical stability. Chemical Communications, 54: 9635-9638 [Journal Article]
18. d'Espaux Leo, Amit Ghosh, Weerawat Runguphan, Maren Wehrs, Feng Xu, Oliver Konzock, Ishaan Dev et al (2017). Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metabolic engineering, 42: 115-125 [Journal Article]
17. Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín (2017). The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC bioinformatics, 18: 205 [Journal Article]
16. Amit Ghosh, David Ando, Jennifer Gin, Weerawat Runguphan, Charles Denby, George Wang, Edward EK Baidoo, Chris Shymansky, Jay D. Keasling, Héctor García Martín (2016). 13c metabolic flux analysis for systematic metabolic engineering of S. cerevisiae for overproduction of fatty acids. Frontiers in bioengineering and biotechnology, 4: 76 [Journal Article]
15. Amit Ghosh (2016). Systems and synthetic biology for the microbial production of biofuels. Current Metabolomics, 4: 5-13 [Journal Article]
14. Yurong Yang, Yan Liang, Xiaozhen Han, Tsan-Yu Chiu, Amit Ghosh, Hui Chen, and Ming Tang (2016). The roles of arbuscular mycorrhizal fungi (AMF) in phytoremediation and tree-herb interactions in Pb contaminated soil. Scientific reports, 6: 20469 [Journal Article]
13. Yurong Yang, Xiaozhen Han, Yan Liang, Amit Ghosh, Jie Chen, and Ming Tang (2015). The combined effects of arbuscular mycorrhizal fungi (AMF) and lead (Pb) stress on Pb accumulation, plant growth parameters, photosynthesis, and antioxidant enzymes in Robinia pseudoacacia L. PLoS One, 10: e0145726 [Journal Article]
12. Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, and Jay D. Keasling (2015). A method to constrain genome-scale models with 13C labeling data. PLoS computational biology, 11: e1004363 [Journal Article]
11. Yurong Yang, Yan Liang, Amit Ghosh, Yingying Song, Hui Chen, and Ming Tang (2015). Assessment of arbuscular mycorrhizal fungi status and heavy metal accumulation characteristics of tree species in a lead-zinc mine area: potential applications for phytoremediation. Environmental Science and Pollution Research, 22: 13179-13193 [Journal Article]
10. Yurong Yang, Yingying Song, Henrik V. Scheller, Amit Ghosh, Yihui Ban, Hui Chen, and Ming Tang (2015). Community structure of arbuscular mycorrhizal fungi associated with Robinia pseudoacacia in uncontaminated and heavy metal contaminated soils. Soil Biology and Biochemistry, 86: 146-158 [Journal Article]
9. Amit Ghosh, Jerome Nilmeier, Daniel Weaver, Paul D. Adams, Jay D. Keasling, Aindrila Mukhopadhyay, Christopher J. Petzold, Héctor García Martín (2014). A peptide-based method for 13C metabolic flux analysis in microbial communities. PLoS computational biology, 10(9): e1003827 [Journal Article]
8. Amit Ghosh, Reiko Sakaguchi, Cuiping Liu, Ya-Ming Hou, and Saraswathi Vishveshwara (2011). Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout. Journal of Biological Chemistry, 286: 37721-37731 [Journal Article]
7. Amit Ghosh, Huimin Zhao, and Nathan D. Price (2011). Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS ONE, 6(11): e27316 [Journal Article]
6. Moitrayee Bhattacharyya, Amit Ghosh, Priti Hansia, and Saraswathi Vishveshwara (2010). Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks. Proteins: Structure, Function, and Bioinformatics, 78(3): 506-517 [Journal Article]
5. Saraswathi Vishveshwara, Amit Ghosh, and Priti Hansia (2009). Intra and inter-molecular communications through protein structure network. Current Protein and Peptide Science, 10(2): 146-160 [Journal Article]
4. Priti Hansia, Amit Ghosh, and Saraswathi Vishveshwara (2009). Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. Molecular BioSystems, 5(12): 1860-187 [Journal Article]
3. Amit Ghosh, and Saraswathi Vishveshwara (2008). Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry, 47(44): 11398-11407 [Journal Article]
2. Amit Ghosh, and Saraswathi Vishveshwara (2007). A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis. Proceedings of the National Academy of Sciences USA, 104(40): 15711-15716 [Journal Article]
1. Amit Ghosh, K. V. Brinda, and Saraswathi Vishveshwara (2008). Dynamics of lysozyme structure network: probing the process of unfolding. Biophysical Journal, 92(7): 2523-2535 [Journal Article]

BOOK CHAPTERS

5. Rokesh Radhakrishnan, Bhumika Shridhar, Amit Ghosh (2023). Laccase-mediated Pretreatment of Lignocellulosic Biomass: Current Status and Future Prospects. Enzymes in the Valorization of Waste, 51-83 [Journal Article]
4. Pradipta Patra, Manali Das, Bharat Manna, Amit Ghosh (2023). Overview of the Mechanism of Hydrolytic Enzymes and Their Application in Waste Treatment. Enzymes in the Valorization of Waste, 61-89, [Journal Article]
3. Nima Hajinajaf ,Manali Das, Pradipta Patra, Amit Ghosh , & Arul M. Varman (2022). Recycling of Multiple Organic Solid Wastes into Biogas via Anaerobic Digestion. Biofuels and Biorefineries173-204. [Journal Article]
2. Bharat Manna, Manali Das, Pradipta Patra, Amit Ghosh (2022).Insight into Various Conventional Physical and Chemical Methods for the Pretreatment of Lignocellulosic Biomass. Clean Energy Production Technologies,31-35. [Journal Article]
1. Manali Das, Aditya Sarnaik, Pradipta Patra, Arul M. Varman, Amit Ghosh (2022). Chapter 18 - Biofuel production from renewable feedstocks: Progress through metabolic engineering. Current Developments in Biotechnology and Bioengineering, 417-448. [Journal Article]

CONFERENCE

17. Suman Mondal, Pritam kundu and Amit Ghosh."Community-wide metabolic interaction network for deciphering the plant biomass degradation potential of bovine gut microbiota" BESCON 2022 Conference ; Nov 5th, 2022; IIT Kharagpur & Bose Institute Kolkata, India.
16. Pritam Kundu, Bharat Manna, Subham Majumder, and Amit Ghosh."Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota.". In: Abstracts of the BESCON 2019 Conference ; Oct 18-19, 2019; IIT Madras, Chennai, India.
15. Bharat Manna and Amit Ghosh."Understanding the Stability of Endoglucanase in Ionic Liquid-water Binary Mixtures by Molecular Dynamics Simulation". In: Abstracts of the 43rd Indian Biophysical Society Meeting; March 15-17, 2019; IISER Kolkata, Mohanpur, India.
14. Bharat Manna and Amit Ghosh. Genome scale metabolic network reconstruction of Spirochaeta cellobiosiphila [Abstract]. In: Abstracts of the NGBT conference; Oct 02-04, 2017; Bhubaneswar, Odisha, India: Can J biotech, Volume 1, Special Issue, Page 134. https://doi.org/10.24870/cjb.2017-a120
13. An abstract entitled "Dissolution of Cellulose with Ionic Liquid/Water Mixture: A Molecular Dynamics Study" was accepted and presented as a poster at International Conference on "21st Century Energy Needs - Materials, Systems and Applications", 17th -19th November 2016, IIT Kharagpur, India
12. An abstract entitled "Metabolic engineering of yeast to produce fatty acid derived fuels and chemical" was accepted and presented as a poster at Annual Meeting of the Indian Biophysical Society 2016, 8th -10th Feb 2016, IISc Bangalore, India
11. An abstract entitled "Quantitative Metabolic Systems Biology for systematic metabolic engineering for production of biofuels" was accepted for Oral presentation at Indo-US workshop on "Cell Factories" supported by IUSSTF from 18th - 20th March, 2016 at IIT-Bombay.
10. An abstract entitled 13 C Metabolic Flux Analysis for systematic metabolic engineering of yeast to produce fatty acid derived fuels and chemical was accepted and presented as a poster at 11th International Conference of the metabolomics society, 29th June-2nd July, 2015, San Francisco, CA, USA
9. An abstract entitled " 13 C Metabolic Flux Analysis for Metabolic Engineered Yeast Strains for Production of Fatty Acids" was Presented as a poster at Conference on Constraint-Reconstruction and Analysis(COBRA), May 20-23, 2014, Charlottesville, VA, USA.
8. An abstract entitled "Metabolic Systems Biology for the Microbial Production of Biofuels" was accepted for oral presentation at BIT's 3rd World Congress of Bioenergy (WCBE-2013), April 25-27, 2013' Nanjing, China.
7. An abstract entitled "A peptide-based method for 13 C metabolic flux analysis in microbial communities" was accepted for oral presentation at Conference on Predicting Cell Metabolism and Phenotypes, March 4-6, 2013, Menlo Park, California, USA.
6. An abstract entitled "A peptide-based method for 13 C metabolic flux analysis in microbial communities" was accepted for Oral presentation at Conference on Constraint-based Reconstruction and Analysis (COBRA), Oct 7-9, 2012, Copenhagen, Denmark.
5. An abstract entitled "Integrated Probabilistic Regulatory and Metabolic Network Analysis of Saccharomyces Cerevisiae for Biochemical Production" was accepted for Oral presentation at the AIChE annual meeting 2010, Salt Lake City, Utah, USA.
4. An abstract entitled "In silico and experimental studies of cofactor balance in the engineered pentose sugar utilization pathways in Saccharomyces cerevisiae" was accepted for Oral presentation at the AIChE annual meeting 2009, Nashville, Tennese, USA
3. An abstract entitled "Variation in clique community patterns during allosteric communication in proteins" was accepted and presented as a poster at the 9th International Conference on Systems Biology conference, August 22-27, 2008, Gothenburg Sweden.
2. An abstract entitled "Modeling and molecular dynamics simulation of tRNA bound Methionine tRNA synthetase" was accepted and presented as a poster at the 'International Conference on Bioinformatics-2016' December 18 - 20, 2016. Hotel Ashok. New Delhi
1. An abstract entitled "Dynamics of t-RNA Synthetases" was accepted and presented as a poster at the '21st International t-RNA Workshop from Dec 2-7, 2005 at Indian Institute of Science, Bangalore.