Mukhopadhyay:Publications: Difference between revisions

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==Refereed Publications==
==Refereed Publications==
#Rautengarten C, Ebert B, Ouellet M, Nafisi M, Baidoo EE, Benke P, Stranne M, Mukhopadhyay A, Keasling JD, Sakuragi Y, Scheller HV* Arabidopsis Deficient in Cutin Ferulate Encodes a Transferase Required for Feruloylation of ω-Hydroxy Fatty Acids in Cutin Polyester. ''Plant Physiol.'' '''2012''' [http://www.plantphysiol.org/content/158/2/654.long open access]
===M group pubs===
#Juminaga D, Baidoo EEK, Redding-Johanson AM, Batth TS, Burd H, Mukhopadhyay A, Petzold CJ, Keasling JD: Modular Engineering of L-Tyrosine Production in Escherichia coli. ''Appl Environ Microbiol'' '''2012''' [http://aem.asm.org/cgi/content/abstract/AEM.06017-11v1 open access]
#Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson J, Auer M, Wall JD, Mukhopadhyay A* Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility ''Frontiers in Microbiology'' '''2014''' [http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1&FileId=125058&articleId=62592&Version=1&ContentTypeId=58&FileName=Provisional%20PDF.pdf pdf]
# Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A*. Utilizing a highly responsive gene, ''yhjX'', in ''E. coli'' based production of 1,4-Butanediol ''CES'' '''2013''' [http://www.sciencedirect.com/science/article/pii/S0009250913004673 open access]
#Rajeev L, da Rocha U, Klitgord N, Luning E, Fortney J, Axen S, Shih P, Bouskill N, Bowen B, Kerfeld C, Garcia-Pichel F, Brodie E, Northen T*, Mukhopadhyay A*. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ''ISME J'' '''2013''' [http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201383a.html open access]
#Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A* and Stahl DA. Functional Responses of Methanogenic Archaea to Syntrophic Growth. ''ISME J'' '''2012''' [http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201260a.html open access]
#Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A* Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. ''Genome Biology'' '''2011''' [http://genomebiology.com/2011/12/10/R99/abstract open access]
#Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A* Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. ''Genome Biology'' '''2011''' [http://genomebiology.com/2011/12/10/R99/abstract open access]
#Peralta-Yahya P, Ouellet M, Chan R, Mukhopadhyay A, Keasling J, Lee TS. Identification and microbial production of a terpene-based advanced biofuel. ''Nature Communications'' '''2011''' ([http://www.nature.com/ncomms/journal/v2/n9/full/ncomms1494.html open access])
#Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A*. Engineering microbial biofuel tolerance and export using efflux pumps. ''Mol Syst Biol.'' '''2011'''  ([http://www.nature.com/msb/journal/v7/n1/full/msb201121.html Feature Article])
#Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A*. Engineering microbial biofuel tolerance and export using efflux pumps. ''Mol Syst Biol.'' '''2011'''  ([http://www.nature.com/msb/journal/v7/n1/full/msb201121.html Feature Article])
#Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ*. Targeted proteomics for metabolic pathway optimization: application to terpene production. ''Metab Eng.'' '''2011'''[http://www.sciencedirect.com/science/article/pii/S1096717610001254 (Cover)]
#Ouellet M, Dibble D, et al and Holmes BM*, Mukhopadhyay A. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. ''Green Chemistry'' '''2011''' [http://pubs.rsc.org/en/content/articlelanding/2011/gc/c1gc15327g link] [http://blogs.rsc.org/gc/2011/09/27/top-ten-most-accessed-articles-in-august-2/ Top ten!!!]
#Ouellet M, Dibble D, et al and Holmes BM*, Mukhopadhyay A. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. ''Green Chemistry'' '''2011''' [http://pubs.rsc.org/en/content/articlelanding/2011/gc/c1gc15327g link] [http://blogs.rsc.org/gc/2011/09/27/top-ten-most-accessed-articles-in-august-2/ Top ten!!!]
#M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay* A Model for Improving Microbial Biofuel Production using a Synthetic Feedback Loop. ''Systems and Synthetic Biology.'' '''2010''' [http://www.springerlink.com/content/l702737837673027/fulltext.html link]
#B. J. Rutherford, R. Dahl, R. Price, H. L. Szmidt, P. I. Benke, A. Mukhopadhyay*, and J. D. Keasling. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. '''2010''' [http://aem.asm.org/cgi/content/full/76/6/1935 link]
#M. Ouellet, P. D. Adams, J. D Keasling and A. Mukhopadhyay*. A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology '''2009''' [http://www.biomedcentral.com/1472-6750/9/97 link]
#J.L Fortman#, S. Chhabra#, A. Mukhopadhyay#, H. Chou, T.S. Lee, E. Steen, J.D. Keasling. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol. '''2008''' [http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2808%2900112-1 Cover]
#A. Mukhopadhyay#, A.M. Redding#, B.J. Rutherford, J.D. Keasling. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. '''2008''' [http://www.sciencedirect.com/science/article/pii/S0958166908000566 link]
<br>
===Collaborations===
#Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD et al: Engineering dynamic pathway regulation using stress-response promoters. ''Nat Biotechnol'' '''2013'''.
#Kazakov A, Rajeev L, Luning EG, Zane G, Siddartha K, Rodionov D, Dubchak I, Arkin A, Wall J, Mukhopadhyay A, Novichkov P. A new family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria" ''J Bact'' '''2013''' 
#Zhou A, Baidoo E E, He Z, Mukhopadhyay A, Baumohl J, Benke P I, Joachimiak M, Xie M, Song R, Arkin A, Hazen T, Keasling J, Wall J, Stahl D, Zhou J Characterization of NaCl-tolerance in ''Desulfovibrio vulagris'' Hildenborough through experimental evolution ''ISME J'' '''2013'''
#Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling J Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng '''2012'''
#Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, et al. A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels. PLoS ONE '''2012'''
#Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics. '''2012'''
#Eudes A, George A, Mukerjee P, et al, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loque D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. '''2012'''
#Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Mukhopadhyay A,Petzold CJ, Scheller HV, Loque D, Heazlewood JL. Isolation and Proteomic Characterization of the Arabidopsis Golgi Defines Functional and Novel Components Involved in Plant Cell Wall Biosynthesis. Plant Physiol.'''2012'''
#Rautengarten C, Ebert B, Ouellet M, Nafisi M, Baidoo EE, Benke P, Stranne M, Mukhopadhyay A, Keasling JD, Sakuragi Y, Scheller HV* Arabidopsis Deficient in Cutin Ferulate Encodes a Transferase Required for Feruloylation of ω-Hydroxy Fatty Acids in Cutin Polyester. ''Plant Physiol.'' '''2012'''
#Juminaga D, Baidoo EEK, Redding-Johanson AM, Batth TS, Burd H, Mukhopadhyay A, Petzold CJ, Keasling JD: Modular Engineering of L-Tyrosine Production in Escherichia coli. ''Appl Environ Microbiol'' '''2012'''
#Peralta-Yahya P, Ouellet M, Chan R, Mukhopadhyay A, Keasling J, Lee TS*. Identification and microbial production of a terpene-based advanced biofuel. ''Nature Communications'' '''2011'''
#Zhou J*, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. ''Nat Rev Microbiol.'' '''2011''' [http://www.nature.com/nrmicro/journal/v9/n6/abs/nrmicro2575.html link]
#Zhou J*, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. ''Nat Rev Microbiol.'' '''2011''' [http://www.nature.com/nrmicro/journal/v9/n6/abs/nrmicro2575.html link]
#Rautengarten C, Ebert B, Herter T, Petzold CJ, Ishii T, Mukhopadhyay A, Usadel B, Scheller HV*. The Interconversion of UDP-Arabinopyranose and UDP-Arabinofuranose is Indispensable for Plant Development in Arabidopsis. ''Plant Cell.'' '''2011'''  
#Rautengarten C, Ebert B, Herter T, Petzold CJ, Ishii T, Mukhopadhyay A, Usadel B, Scheller HV*. The Interconversion of UDP-Arabinopyranose and UDP-Arabinofuranose is Indispensable for Plant Development in Arabidopsis. ''Plant Cell.'' '''2011'''  
#Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ*. Targeted proteomics for metabolic pathway optimization: application to terpene production. ''Metab Eng.'' '''2011'''[http://www.sciencedirect.com/science/article/pii/S1096717610001254 (Cover)]
#Ito J, Batth TS, Petzold CJ, Redding-Johanson AM, Mukhopadhyay A, Verboom R, Meyer EH, Millar AH, Heazlewood JL*. Analysis of the Arabidopsis Cytosolic Proteome Highlights Subcellular Partitioning of Central Plant Metabolism. ''J Proteome Res.'' '''2010'''
#Ito J, Batth TS, Petzold CJ, Redding-Johanson AM, Mukhopadhyay A, Verboom R, Meyer EH, Millar AH, Heazlewood JL*. Analysis of the Arabidopsis Cytosolic Proteome Highlights Subcellular Partitioning of Central Plant Metabolism. ''J Proteome Res.'' '''2010'''
#A Zhou, Z He, AM Redding-Johanson, A Mukhopadhyay, CL Hemme, MP Joachimiak, F Luo, Y Deng, KS Bender, Q He, JD Keasling, DA Stahl, MW Fields, TC Hazen, AP Arkin, JD Wall, J Zhou. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. ''Environ Microbiol.'' '''2010''' 
#J. Ito, C. J. Petzold, A. Mukhopadhyay, J. Heazlewood The role of proteomics in the development of cellulosic biofuels. Current Proteomics. '''2010'''   
#J. Ito, C. J. Petzold, A. Mukhopadhyay, J. Heazlewood The role of proteomics in the development of cellulosic biofuels. Current Proteomics. '''2010'''   
#M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay* A Model for Improving Microbial Biofuel Production using a Synthetic Feedback Loop. ''Systems and Synthetic Biology.'' '''2010''' [http://www.springerlink.com/content/l702737837673027/fulltext.html link]
#Y. Cong, M. Baker, J. Jakana, D. Woolford, E. Miller, S. Reissmann, R. Kumar, A. Redding-Johanson, T. Batth, A. Mukhopadhyay, S. Ludtke, J. Frydman, W. Chiu. 4.0 Å Resolution Cryo-EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement. ''PNAS.'' '''2010'''  
#Y. Cong, M. Baker, J. Jakana, D. Woolford, E. Miller, S. Reissmann, R. Kumar, A. Redding-Johanson, T. Batth, A. Mukhopadhyay, S. Ludtke, J. Frydman, W. Chiu. 4.0 Å Resolution Cryo-EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement. ''PNAS.'' '''2010'''  
#B. J. Rutherford, R. Dahl, R. Price, H. L. Szmidt, P. I. Benke, A. Mukhopadhyay*, and J. D. Keasling. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. '''2010''' [http://aem.asm.org/cgi/content/full/76/6/1935 link]
<br>
 
===M Postdoc and Graduate Research===
#A Zhou, Z He, AM Redding-Johanson, A Mukhopadhyay, CL Hemme, MP Joachimiak, F Luo, Y Deng, KS Bender, Q He, JD Keasling, DA Stahl, MW Fields, TC Hazen, AP Arkin, JD Wall, J Zhou. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. ''Environ Microbiol.'' '''2010'''
#Z. He, A. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, C. L. Hemme, K. Huang, E.J. Alm, M.W. Fields, J. Wall, D. Stahl, T.C Hazen, J.D. Keasling, A. P. Arkin, J. Zhou. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl Environ Microbiol. '''2009'''  
#Z. He, A. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, C. L. Hemme, K. Huang, E.J. Alm, M.W. Fields, J. Wall, D. Stahl, T.C Hazen, J.D. Keasling, A. P. Arkin, J. Zhou. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl Environ Microbiol. '''2009'''  
#M. Ouellet, P. D. Adams, J. D Keasling and A. Mukhopadhyay*. A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology '''2009''' [http://www.biomedcentral.com/1472-6750/9/97 link]
#A. Shaikh, Y. J. Tang, A. Mukhopadhyay, H. García Martín, J. Gin, P. I. Benke, J. D. Keasling. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnology Progress '''2009'''  
#A. Shaikh, Y. J. Tang, A. Mukhopadhyay, H. García Martín, J. Gin, P. I. Benke, J. D. Keasling. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnology Progress '''2009'''  
#D.E Elias, A. Mukhopadhyay#, M. Joachimiak#, A. M. Redding,H-C. B. Yen, M. W. Fields, T. C. Hazen , A. P. Arkin, J. D Keasling, J. D. Wall. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Research '''2009'''  
#D.E Elias, A. Mukhopadhyay#, M. Joachimiak#, A. M. Redding,H-C. B. Yen, M. W. Fields, T. C. Hazen , A. P. Arkin, J. D Keasling, J. D. Wall. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Research '''2009'''  
#S. Borglin, D.C. Joyner, J. S. Jacobsen, A. Mukhopadhyay, T.C. Hazen. Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. J Microbiol Methods. '''2009'''  
#S. Borglin, D.C. Joyner, J. S. Jacobsen, A. Mukhopadhyay, T.C. Hazen. Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. J Microbiol Methods. '''2009'''  
#J.L Fortman#, S. Chhabra#, A. Mukhopadhyay#, H. Chou, T.S. Lee, E. Steen, J.D. Keasling. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol. '''2008''' [http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2808%2900112-1 Cover]
#A. Mukhopadhyay#, A.M. Redding#, B.J. Rutherford, J.D. Keasling. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. '''2008''' [http://www.sciencedirect.com/science/article/pii/S0958166908000566 link]
#S. P. Gaucher#, A. M. Redding#, A. Mukhopadhyay, J. D. Keasling, A. K. Singh. Post-translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins. Journal of Proteomic Research '''2008'''  
#S. P. Gaucher#, A. M. Redding#, A. Mukhopadhyay, J. D. Keasling, A. K. Singh. Post-translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins. Journal of Proteomic Research '''2008'''  
#A. S. Shaikh#, Y. J. Tang#, A. Mukhopadhyay, J. D. Keasling*. Isotopomer Distributions in Amino Acids from a Highly Expressed Protein as a Proxy for Those from Total Protein. Analytical Chem '''2008''' [http://pubs.acs.org/doi/abs/10.1021/ac071445%2B link]
#A. S. Shaikh#, Y. J. Tang#, A. Mukhopadhyay, J. D. Keasling*. Isotopomer Distributions in Amino Acids from a Highly Expressed Protein as a Proxy for Those from Total Protein. Analytical Chem '''2008''' [http://pubs.acs.org/doi/abs/10.1021/ac071445%2B link]
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#A. Mukhopadhyay, R. Gao, D. G. Lynn Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem''' 2004''' [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200300828/abstract link]
#A. Mukhopadhyay, R. Gao, D. G. Lynn Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem''' 2004''' [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200300828/abstract link]
#Y. Wang, A. Mukhopadhyay, V. R. Howitz, A. N. Binns, D. G. Lynn Construction of an efficient expression system for Agrobacterium tumefaciens based on the coliphage T5 promoter. Gene '''2000''' [http://www.sciencedirect.com/science/article/pii/S0378111999005417 link]
#Y. Wang, A. Mukhopadhyay, V. R. Howitz, A. N. Binns, D. G. Lynn Construction of an efficient expression system for Agrobacterium tumefaciens based on the coliphage T5 promoter. Gene '''2000''' [http://www.sciencedirect.com/science/article/pii/S0378111999005417 link]
 
<br>
<br>
==Book Chapters, Invited articles and Reports==
==Book Chapters, Invited articles and Reports==
#Mukhopadhyay A Microbial host engineering: beyond the metabolic pathway '''2012''' Special Issue: New Science of Synthetic and Systems Biology, Science And Culture Journal (Indian Science News Association) ed. Rupak Bhadra.  
#Mukhopadhyay A Microbial host engineering: beyond the metabolic pathway '''2012''' Special Issue: New Science of Synthetic and Systems Biology, [http://www.scienceandculture-isna.org/latestissue.htm Science And Culture Journal] (Indian Science News Association) ed. Rupak Bhadra. [http://www.scienceandculture-isna.org/mar-april2012/05%20Anindrila%20Mukhopadhyay.pdf pdf]
#Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels '''2012''' Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs. ed. Z. Lewis Liu, Springer Berlin / Heidelberg. 22: 209-238 [http://www.springerlink.com/content/r381461g42l3566g/ link]
#Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels '''2012''' Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs. ed. Z. Lewis Liu, Springer Berlin / Heidelberg. 22: 209-238 [http://www.springerlink.com/content/r381461g42l3566g/ link]
#Rutherford, B.J and Mukhopadhyay, A. '''2012''' Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In: Arora, R. (ed) Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK.
#Rutherford, B.J and Mukhopadhyay, A. '''2012''' Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In: Arora, R. (ed) Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK.
#Mukhopadhyay A, Hauser Loren Workflow 4: Signaling, in the DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science. DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop, Feb. 9–10, 2010
#Mukhopadhyay A, Hauser Loren Workflow 4: Signaling, in the DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science. DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop, Feb. 9–10, 2010 [http://www.genomicscience.energy.gov/compbio/kbase_plan/workshop3.pdf pdf]


==Patents==
==Patents==
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==Recent invited talks==
==Recent invited talks==
#Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 [https://www.orau.gov/gtl2012/agenda.htm Plenary session]
# Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Energy Biosciences Institute Seminar Series, Berkeley CA, USA Sept 3rd 2013 [https://cc.readytalk.com/cc/playback/Playback.do?id=3jyojd see talk]
#Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 [http://sim.confex.com/sim/2011/webprogram/Paper19968.html Link]
# Mukhopadhyay A Presenting at Science at the Theater event, [http://today.lbl.gov/2013/05/16/lab-researchers-discuss-their-%E2%80%98big-ideas%E2%80%99-at-recent-science-at-the-theater-talk/ Eight Big Ideas], Berkeley Repertory Theater, Berkeley CA USA May 13th 2013
#Mukhopadhyay A. Study of yeast transcription factors as a strategy to discover new parts for cellular and metabolic engineering. Invited Talk, Yeast Synthetic biology Workshop, UC Mission Bay Campus, San Francisco, Oct 16th 2010. [http://vimeo.com/17126215 video]
# Mukhopadhyay A Lecture to ChemE Students (Biofuel production and processing, ChemE 437; Unit Ops II), invited by Prof James Carothers, University of Washington Seattle, USA, Feb 8th 2013
#Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010.  
# Mukhopadhyay A Advances in Host Engineering for the production of Chemicals and Fuels, Bioenergy and Biotechnology Team, Reliance India Limited, Mumbai, India Jan 3rd 2013
#Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Indo-American Frontiers of Engineering Symposium, Jaypee Palace Hotel, Agra, India, March 10-13, 2010 [http://www.naefrontiers.org/Symposia/IAFOE/IA-PastSymposia/2010IAFOE.aspx link]
# Mukhopadhyay A Advances in Host Engineering for production of Chemicals and Fuels, Special Seminar, DBT-ICT Center for Energy Biosciences, Mumbai, India, Dec 31st 2012
#Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Special Departmental Seminar, Department of Chemistry, Indian Institute of Technology, Mumbai, India March 8th, 2010.
# Mukhopadhyay A Signaling and stress in natural and engineered microbes, Departmental Seminar, Washington University at St Louis, Missouri, Sept 21, 2012
# Mukhopadhyay A Society for General Microbiology, Fall Conference, Warwick, UK, Sept 3-5 2012 [http://www.sgm.ac.uk/meetings/past.cfm link]
# Mukhopadhyay A Engineering Solvent Tolerant Microbes for Biofuel production, ITRI forum 2012, Milpitas, CA June 25th 2012
# Mukhopadhyay A Resolving Community and Metabolic Dynamics in Colorado Plateau Biological Soil Crusts, ASMCUE, San Mateo, June 15th 2012 [http://www.asmcue.org/page02c.shtml link]
# Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 [https://www.orau.gov/gtl2012/agenda.htm Plenary session]
# Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 [http://sim.confex.com/sim/2011/webprogram/Paper19968.html Link]
# Mukhopadhyay A. Study of yeast transcription factors as a strategy to discover new parts for cellular and metabolic engineering. Invited Talk, Yeast Synthetic biology Workshop, UC Mission Bay Campus, San Francisco, Oct 16th 2010. [http://vimeo.com/17126215 video]
# Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010.  
# Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Indo-American Frontiers of Engineering Symposium, Jaypee Palace Hotel, Agra, India, March 10-13, 2010 [http://www.naefrontiers.org/Symposia/IAFOE/IA-PastSymposia/2010IAFOE.aspx link]
# Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Special Departmental Seminar, Department of Chemistry, Indian Institute of Technology, Mumbai, India March 8th, 2010.

Revision as of 00:28, 3 March 2014

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Refereed Publications

M group pubs

  1. Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson J, Auer M, Wall JD, Mukhopadhyay A* Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility Frontiers in Microbiology 2014 pdf
  2. Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A*. Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-Butanediol CES 2013 open access
  3. Rajeev L, da Rocha U, Klitgord N, Luning E, Fortney J, Axen S, Shih P, Bouskill N, Bowen B, Kerfeld C, Garcia-Pichel F, Brodie E, Northen T*, Mukhopadhyay A*. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J 2013 open access
  4. Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A* and Stahl DA. Functional Responses of Methanogenic Archaea to Syntrophic Growth. ISME J 2012 open access
  5. Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A* Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biology 2011 open access
  6. Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A*. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol. 2011 (Feature Article)
  7. Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ*. Targeted proteomics for metabolic pathway optimization: application to terpene production. Metab Eng. 2011(Cover)
  8. Ouellet M, Dibble D, et al and Holmes BM*, Mukhopadhyay A. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. Green Chemistry 2011 link Top ten!!!
  9. M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay* A Model for Improving Microbial Biofuel Production using a Synthetic Feedback Loop. Systems and Synthetic Biology. 2010 link
  10. B. J. Rutherford, R. Dahl, R. Price, H. L. Szmidt, P. I. Benke, A. Mukhopadhyay*, and J. D. Keasling. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli. Appl Environ Microbiol. 2010 link
  11. M. Ouellet, P. D. Adams, J. D Keasling and A. Mukhopadhyay*. A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology 2009 link
  12. J.L Fortman#, S. Chhabra#, A. Mukhopadhyay#, H. Chou, T.S. Lee, E. Steen, J.D. Keasling. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol. 2008 Cover
  13. A. Mukhopadhyay#, A.M. Redding#, B.J. Rutherford, J.D. Keasling. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. 2008 link


Collaborations

  1. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD et al: Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013.
  2. Kazakov A, Rajeev L, Luning EG, Zane G, Siddartha K, Rodionov D, Dubchak I, Arkin A, Wall J, Mukhopadhyay A, Novichkov P. A new family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria" J Bact 2013
  3. Zhou A, Baidoo E E, He Z, Mukhopadhyay A, Baumohl J, Benke P I, Joachimiak M, Xie M, Song R, Arkin A, Hazen T, Keasling J, Wall J, Stahl D, Zhou J Characterization of NaCl-tolerance in Desulfovibrio vulagris Hildenborough through experimental evolution ISME J 2013
  4. Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling J Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng 2012
  5. Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, et al. A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels. PLoS ONE 2012
  6. Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics. 2012
  7. Eudes A, George A, Mukerjee P, et al, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loque D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. 2012
  8. Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Mukhopadhyay A,Petzold CJ, Scheller HV, Loque D, Heazlewood JL. Isolation and Proteomic Characterization of the Arabidopsis Golgi Defines Functional and Novel Components Involved in Plant Cell Wall Biosynthesis. Plant Physiol.2012
  9. Rautengarten C, Ebert B, Ouellet M, Nafisi M, Baidoo EE, Benke P, Stranne M, Mukhopadhyay A, Keasling JD, Sakuragi Y, Scheller HV* Arabidopsis Deficient in Cutin Ferulate Encodes a Transferase Required for Feruloylation of ω-Hydroxy Fatty Acids in Cutin Polyester. Plant Physiol. 2012
  10. Juminaga D, Baidoo EEK, Redding-Johanson AM, Batth TS, Burd H, Mukhopadhyay A, Petzold CJ, Keasling JD: Modular Engineering of L-Tyrosine Production in Escherichia coli. Appl Environ Microbiol 2012
  11. Peralta-Yahya P, Ouellet M, Chan R, Mukhopadhyay A, Keasling J, Lee TS*. Identification and microbial production of a terpene-based advanced biofuel. Nature Communications 2011
  12. Zhou J*, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol. 2011 link
  13. Rautengarten C, Ebert B, Herter T, Petzold CJ, Ishii T, Mukhopadhyay A, Usadel B, Scheller HV*. The Interconversion of UDP-Arabinopyranose and UDP-Arabinofuranose is Indispensable for Plant Development in Arabidopsis. Plant Cell. 2011
  14. Ito J, Batth TS, Petzold CJ, Redding-Johanson AM, Mukhopadhyay A, Verboom R, Meyer EH, Millar AH, Heazlewood JL*. Analysis of the Arabidopsis Cytosolic Proteome Highlights Subcellular Partitioning of Central Plant Metabolism. J Proteome Res. 2010
  15. J. Ito, C. J. Petzold, A. Mukhopadhyay, J. Heazlewood The role of proteomics in the development of cellulosic biofuels. Current Proteomics. 2010
  16. Y. Cong, M. Baker, J. Jakana, D. Woolford, E. Miller, S. Reissmann, R. Kumar, A. Redding-Johanson, T. Batth, A. Mukhopadhyay, S. Ludtke, J. Frydman, W. Chiu. 4.0 Å Resolution Cryo-EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement. PNAS. 2010


M Postdoc and Graduate Research

  1. A Zhou, Z He, AM Redding-Johanson, A Mukhopadhyay, CL Hemme, MP Joachimiak, F Luo, Y Deng, KS Bender, Q He, JD Keasling, DA Stahl, MW Fields, TC Hazen, AP Arkin, JD Wall, J Zhou. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol. 2010
  2. Z. He, A. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, C. L. Hemme, K. Huang, E.J. Alm, M.W. Fields, J. Wall, D. Stahl, T.C Hazen, J.D. Keasling, A. P. Arkin, J. Zhou. Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation. Appl Environ Microbiol. 2009
  3. A. Shaikh, Y. J. Tang, A. Mukhopadhyay, H. García Martín, J. Gin, P. I. Benke, J. D. Keasling. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein. Biotechnology Progress 2009
  4. D.E Elias, A. Mukhopadhyay#, M. Joachimiak#, A. M. Redding,H-C. B. Yen, M. W. Fields, T. C. Hazen , A. P. Arkin, J. D Keasling, J. D. Wall. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Research 2009
  5. S. Borglin, D.C. Joyner, J. S. Jacobsen, A. Mukhopadhyay, T.C. Hazen. Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. J Microbiol Methods. 2009
  6. S. P. Gaucher#, A. M. Redding#, A. Mukhopadhyay, J. D. Keasling, A. K. Singh. Post-translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins. Journal of Proteomic Research 2008
  7. A. S. Shaikh#, Y. J. Tang#, A. Mukhopadhyay, J. D. Keasling*. Isotopomer Distributions in Amino Acids from a Highly Expressed Protein as a Proxy for Those from Total Protein. Analytical Chem 2008 link
  8. A. Mukhopadhyay, A. M. Redding#, M. P. Joachimiak#, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, D. C. Joyner, V. J. J. Martin, J. D. Wall, Z-K. Yang, J. Zhou, J. D. Keasling Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 2007 link
  9. Y. Tang#, F. Pingitore#, A. Mukhopadhyay#, R. Phan, T. C. Hazen, J. D. Keasling Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. J. Bacteriol. 2007
  10. A. Mukhopadhyay, Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Q. He, H-Y. Holman, K. Huang, R. Huang, D. C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. Wall, J. Wei, Z. Yang, H-C. Yen, J. Zhou, J. D. Keasling Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach J. Bacteriol. 2006 link
  11. A. M. Redding, A. Mukhopadhyay, D. C. Joyner, T. C. Hazen, J. D. Keasling Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics. Brief Funct Genomic Proteomic 2006
  12. R. Gao, A. Mukhopadhyay, F. Fang, D. G. Lynn Constitutive Activation of Two-Component Response Regulators: Characterization of VirG Activation in Agrobacterium tumefaciens. J Bacteriol 2006,
  13. A. Mukhopadhyay, R. Gao, D. G. Lynn Integrating Input from Multiple Signals: The VirA/VirG Two-Component System of Agrobacterium tumefaciens. ChemBioChem 2004 link
  14. Y. Wang, A. Mukhopadhyay, V. R. Howitz, A. N. Binns, D. G. Lynn Construction of an efficient expression system for Agrobacterium tumefaciens based on the coliphage T5 promoter. Gene 2000 link



Book Chapters, Invited articles and Reports

  1. Mukhopadhyay A Microbial host engineering: beyond the metabolic pathway 2012 Special Issue: New Science of Synthetic and Systems Biology, Science And Culture Journal (Indian Science News Association) ed. Rupak Bhadra. pdf
  2. Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels 2012 Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs. ed. Z. Lewis Liu, Springer Berlin / Heidelberg. 22: 209-238 link
  3. Rutherford, B.J and Mukhopadhyay, A. 2012 Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In: Arora, R. (ed) Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK.
  4. Mukhopadhyay A, Hauser Loren Workflow 4: Signaling, in the DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science. DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop, Feb. 9–10, 2010 pdf

Patents

  1. Dunlop, Mary J.; Keasling, Jay D.; Mukhopadhyay, Aindrila Modified Host Cells with Efflux Pumps U.S. Patent Application Ser. No: 13/115,925 25-May-2011. online or Go to Berkeley lab Tech Transfer

Recent invited talks

  1. Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Energy Biosciences Institute Seminar Series, Berkeley CA, USA Sept 3rd 2013 see talk
  2. Mukhopadhyay A Presenting at Science at the Theater event, Eight Big Ideas, Berkeley Repertory Theater, Berkeley CA USA May 13th 2013
  3. Mukhopadhyay A Lecture to ChemE Students (Biofuel production and processing, ChemE 437; Unit Ops II), invited by Prof James Carothers, University of Washington Seattle, USA, Feb 8th 2013
  4. Mukhopadhyay A Advances in Host Engineering for the production of Chemicals and Fuels, Bioenergy and Biotechnology Team, Reliance India Limited, Mumbai, India Jan 3rd 2013
  5. Mukhopadhyay A Advances in Host Engineering for production of Chemicals and Fuels, Special Seminar, DBT-ICT Center for Energy Biosciences, Mumbai, India, Dec 31st 2012
  6. Mukhopadhyay A Signaling and stress in natural and engineered microbes, Departmental Seminar, Washington University at St Louis, Missouri, Sept 21, 2012
  7. Mukhopadhyay A Society for General Microbiology, Fall Conference, Warwick, UK, Sept 3-5 2012 link
  8. Mukhopadhyay A Engineering Solvent Tolerant Microbes for Biofuel production, ITRI forum 2012, Milpitas, CA June 25th 2012
  9. Mukhopadhyay A Resolving Community and Metabolic Dynamics in Colorado Plateau Biological Soil Crusts, ASMCUE, San Mateo, June 15th 2012 link
  10. Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 Plenary session
  11. Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 Link
  12. Mukhopadhyay A. Study of yeast transcription factors as a strategy to discover new parts for cellular and metabolic engineering. Invited Talk, Yeast Synthetic biology Workshop, UC Mission Bay Campus, San Francisco, Oct 16th 2010. video
  13. Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010.
  14. Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Indo-American Frontiers of Engineering Symposium, Jaypee Palace Hotel, Agra, India, March 10-13, 2010 link
  15. Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Special Departmental Seminar, Department of Chemistry, Indian Institute of Technology, Mumbai, India March 8th, 2010.
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