Mukhopadhyay:Publications: Difference between revisions
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==Refereed Publications== | ==Refereed Publications== | ||
===M group pubs=== | ===M group pubs=== | ||
#Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A* Regulation of nitrite stress response in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. ''J Bacteriology.'' '''2015''' | |||
#Mukhopadhyay A* Tolerance engineering in bacteria for the production of advanced biofuels and chemicals ''Trends in Microbiology'' '''2015''' [http://www.sciencedirect.com/science/article/pii/S0966842X1500102X online] | |||
#Chubukov V, Mingardon F, Schackwitz W, Baidoo EEK, Alonso-Gutierrez J, Hu Q, Lee TS, Keasling JD, MukhopadhyayA* Acute limonene toxicity in ''Escherichia coli'' is caused by limonene-hydroperoxide and alleviated by a point mutation in alkyl hydroperoxidase (AhpC) ''AEM'' '''2015''' [http://aem.asm.org/content/early/2015/04/27/AEM.01102-15.abstract online] | |||
#Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A* Improving olefin tolerance and production in E. coli using native and evolved AcrB. ''Biotechnology and Bioengineering''. '''2015''' [http://onlinelibrary.wiley.com/doi/10.1002/bit.25511/pdf online] | |||
#Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS,Leong SSJ, Mukhopadhyay A*. Improving microbial bio-gasoline production in ''Escherichia coli'' using tolerance engineering. ''mBio'' '''2014''' [http://mbio.asm.org/content/5/6/e01932-14 open access] | |||
#Rajeev L, Luning,EG, Altenburg S, Zane GM, Baidoo EE, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A*. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. ''Frontiers in Microbiology 5.'' '''2014''' [http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00382/abstract open access] | |||
#Frederix M, Hutter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch H, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A* Development of a native Escherichia coli induction system for ionic liquid tolerance ''Plos One'' '''2014''' [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101115 online] | #Frederix M, Hutter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch H, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A* Development of a native Escherichia coli induction system for ionic liquid tolerance ''Plos One'' '''2014''' [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101115 online] | ||
#Rajeev, L., Luning, E. G., Mukhopadhyay, A. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems. ''J. Vis. Exp.'' '''2014''' | #Rajeev, L.*, Luning, E. G., Mukhopadhyay, A. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems. ''J. Vis. Exp.'' '''2014''' | ||
#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://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00077/abstract | #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://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00077/abstract open access] | ||
# 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] | # 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] | #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] | ||
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===Collaborations=== | ===Collaborations=== | ||
#Garcıa-Martin∗, Kumar VS, Weaver D, Ghosh A, Chubukov V, Mukhopadhyay A, Arkin AP, Keasling JD. A method to constrain genome-scale models with 13C labeling data. ''PLoS Comput Biol'' '''2015''' | |||
#Rocha UN* , Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR and Brodie EL, Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust ''Front. Microbiol'' '''2015''' | |||
#Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, García-Martín H.A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. ''PLoS Comput Biol'' '''2014''' | |||
#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'''. | #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''' | #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''' | ||
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==Patents== | ==Patents== | ||
#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. [http://www.freepatentsonline.com/y2011/0294183.html online] or Go to Berkeley lab [http://www.lbl.gov/Tech-Transfer/techs/lbnl2845.html Tech Transfer] | #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. [http://www.freepatentsonline.com/y2011/0294183.html online] or Go to Berkeley lab [http://www.lbl.gov/Tech-Transfer/techs/lbnl2845.html Tech Transfer] | ||
#Mukhopadhyay, Aindrila; Mingardon, Florence; Chanal, Angelique. Modified Host Cells Having tolerance to α-Olefins. U.S. Patent Application Ser. No: 61/986,669 30-Apr-2014. | |||
# Mukhopadhyay, Aindrila, Reider-Apel Amanda, Keasling JD, Discovery of a hexose transporter variant in Sachharomyces cerevisiae that allows growth on xylose” U.S. Patent Application Ser. No: 62/192,517 14-July-2015 | |||
==Recent invited talks== | ==Recent invited talks== | ||
#Mukhopadhyay A, Engineering Microbial Solvent Tolerance using efflux pumps, Gordon research Conference, Lucca, Italy April 24-May 1 2015 | |||
#Mukhopadhyay A, Developing new Transcrip1on factors and promoter systems for S. cerevisiae, Joint Genome Institute, User meeting (Synthetic Biology workshop), Walnut Creek, CA, USA, March 25 2015 | |||
#Mukhopadhyay A, Engineering Solvent Tolerant Bacteria: A Systems Biology Guided Effort, Genomic Science Contractors-Grantees Meeting XIII/USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, Washington DC, USA, Feb 22-25 2015 [https://www.orau.gov/gsp2015/agenda.htm link] | |||
#Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Departmental Seminar, Dept of Chemical engineering, IIT, Mumbai, India, Feb 10th 2015 | |||
#Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Indo-US Conference and Workshop in Systems and Synthetic Biology, New Delhi, India, Nov 9-12 2014 [https://icares.wustl.edu/programs/Pages/Indo-US-Workshop-on-Synthetic-and-Systems-Biology.aspx link] | |||
#Mukhopadhyay A, Engineering Microbial Solvent Tolerance, SIMB, St Louise MO, USA, Jul 24th 2014 | |||
#Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Bioenergy and Photosynthesis Seminar, ASU, Tempe, AZ USA Feb 20th 2014 | |||
#Mukhopadhyay A, Dynamic response of biological soil crust to wetting and drying events, 12th Biennial Conference of Science and Management on the Colorado Plateau Northern Arizona University, Flagstaff, Sept 18th 2013 | |||
# 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 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 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 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 |
Revision as of 00:33, 20 September 2015
Refereed PublicationsM group pubs
Collaborations
M Postdoc and Graduate Research
Book Chapters, Invited articles and Reports
Patents
Recent invited talks
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