American Journal of Bioinformatics Research

American Journal of Bioinformatics Research publishes all the newest and distinguished research articles, reviews and letters in all areas of bioinformatics and computational biology. Each issue contains a series of timely, in-depth written articles by leaders in the field, covering a wide range of the integration of biology with computer and information science.


Amit Ghosh

Post-doctoral Fellow, Lawrence Berkeley National Laboratory, USA

Research Areas

Metabolic Engineering,Computational Biology,Systems Biology,Structural Biology,Biochemistry

Education

2003-2008Ph.D.Indian Institute of Science, Bangalore, India
2001–2003M.ScIndian Institute of Technology (IIT), Kharagpur, India
1998–2001B.ScIndian Institute of Technology (IIT), Kharagpur, India

Experience

2011¨Cpresent"Postdoctoral Research Associate, Joint BioEnergy Institute (JBEI), Lawrence Berkeley
2009-2011"Postdoctoral Research Associate, Dept of Chemical and Biomolecular Engineering,
2003¨C2008"Graduate research assistantship, Molecular Biophysics Unit, Indian Institute of Science,

Publications: Journals

[1]  Amit Ghosh, K.V. Brinda, and Saraswathi Vishveshwara. 2007 Dynamics of Lysozyme Structure Network: Probing the process of Unfolding. Biophysical Journal, 92(7):2523-2535. [Cover Page Illustration http://www.biophysj.org/content/vol92/issue7 ]
[2]  Amit Ghosh and Saraswathi Vishveshwara. 2007. A study of Communication Pathways in Methionyl tRNA Synthetase by Molecular Dynamics Simulations and Structure Network analysis. Proc. Natl. Acad. Sci. U.S.A. 104(40), 15711-15716.
[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, 7(44), 11398-407.
[4]  Saraswathi Vishveshwara, Amit Ghosh and Priti Hansia. 2009. Intra and Inter molecular communications through Protein Structure Network. Curr Protein Pept Sci. 10(2), 146-160.
[5]  Priti Hansia, Amit Ghosh, 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), 1860-72.
[6]  Moitrayee Bhattacharyya, Amit Ghosh, Priti Hansia, 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), 506-17.
[7]  Amit Ghosh, Reiko Sakaguchi, Liu C, Saraswathi Vishveshwara and Ya-Ming Hou. 2011. Allosteric communication in Cysteinyl tRNA Synthetase: A network of direct and indirect readout. Journal of Biological Chemistry. 286(43), 37721-31
[8]  8. Amit Ghosh, Huimin Zhao, and Nathan Price. 2011. Genome-scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces. PLoS One. 6(11), e27316.
[9]  Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Adam Arkin, Jay D. Keasling. A peptide-based method for 13C metabolic flux analysis in microbial communities. 2014 . PLoS Computational Biology, In Press
[10]  Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Adam Arkin, Jay D. Keasling. A 13C-based method for metabolic flux measurement and prediction in genome-scale models. (Under revision in Molecular Systems Biology)

Publications: Conferences/Workshops/Symposiums

[1]  An abstract entitled “13C Metabolic Flux Analysis for Metabolic Engineered Yeast Strains for Production of Fatty Acids” was accepted at the Conference on Constraint-based Reconstruction and Analysis (COBRA), May 20-23, 2014, Charlottesville, VA, USA.
[2]  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.
[3]  An abstract entitled “A peptide-based method for 13C metabolic flux analysis in microbial communities” was accepted for Oral presentation at the Conference on Predicting Cell Metabolism and Phenotypes, March 4-6, 2013, Menlo Park, California, USA.
[4]  An abstract entitled “A peptide-based method for 13C metabolic flux analysis in microbial communities” was accepted for Oral presentation at the 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.
[6]  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.
[7]  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.
[8]  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-2006, December 18-20, 2006, New Delhi, India.
[9]  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, India.