Mukhopadhyay:Publications: Difference between revisions
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==Refereed Publications== | ==Refereed Publications== | ||
===M | ===M group pubs=== | ||
#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] | ||
#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]) | ||
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#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] | #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] | ||
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===Collaborations=== | ===Collaborations=== | ||
#Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, et al. | #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''' | #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''' | #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''' | ||
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#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''' | ||
<br> | <br> | ||
===M Postdoc and Graduate Research=== | ===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''' | #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''' | ||
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#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
Refereed PublicationsM group pubs
Collaborations
M Postdoc and Graduate Research
Book Chapters, Invited articles and Reports
Patents
Recent invited talks
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