Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

by Jennifer Chiniquy, Megan E. Garber, Aindrila Mukhopadhyay, Nathan J. Hillson
Published 2020-01-01

Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

by Ankita Kothari, Drishti Soneja, Albert Tang, Hans K. Carlson, Adam M. Deutschbauer, Aindrila Mukhopadhyay
Published 2019-12-01

Correction to: Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae

by Maren Wehrs, Jan-Philip Prahl, Jadie Moon, Yuchen Li, Deepti Tanjore, Jay D. Keasling, Todd Pray, Aindrila Mukhopadhyay
Published 2019-12-01

Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae

by Maren Wehrs, Jan-Philip Prahl, Jadie Moon, Yuchen Li, Deepti Tanjore, Jay D. Keasling, Todd Pray, Aindrila Mukhopadhyay
Published 2018-12-01

A Method to Constrain Genome-Scale Models with 13C Labeling Data.

by Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, Jay D Keasling
Published 2015-09-01

Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria

by Thomas Eng, Thomas Eng, Robin A. Herbert, Robin A. Herbert, Robin A. Herbert, Robin A. Herbert, Uriel Martinez, Uriel Martinez, Brenda Wang, Joseph C. Chen, James B. Brown, James B. Brown, James B. Brown, James B. Brown, James B. Brown, Adam M. Deutschbauer, Adam M. Deutschbauer, Mina J. Bissell, Jenny C. Mortimer, Jenny C. Mortimer, Jenny C. Mortimer, Aindrila Mukhopadhyay, Aindrila Mukhopadhyay, Aindrila Mukhopadhyay
Published 2020-07-01

Production of tetra-methylpyrazine using engineered Corynebacterium glutamicum

by Thomas Eng, Yusuke Sasaki, Robin A. Herbert, Andrew Lau, Jessica Trinh, Yan Chen, Mona Mirsiaghi, Christopher J. Petzold, Aindrila Mukhopadhyay
Published 2020-06-01

A peptide-based method for 13C Metabolic Flux Analysis in microbial communities.

by Amit Ghosh, Jerome Nilmeier, Daniel Weaver, Paul D Adams, Jay D Keasling, Aindrila Mukhopadhyay, Christopher J Petzold, Héctor García Martín
Published 2014-09-01

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.

by Lara Rajeev, Eric G Luning, Grant M Zane, Thomas R Juba, Alexey E Kazakov, Pavel S Novichkov, Judy D Wall, Aindrila Mukhopadhyay
Published 2019-01-01

Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates

by Yusuke Sasaki, Thomas Eng, Robin A. Herbert, Jessica Trinh, Yan Chen, Alberto Rodriguez, John Gladden, Blake A. Simmons, Christopher J. Petzold, Aindrila Mukhopadhyay
Published 2019-02-01

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

by Ankita Kothari, Yu-Wei Wu, John-Marc Chandonia, Marimikel Charrier, Lara Rajeev, Andrea M. Rocha, Dominique C. Joyner, Terry C. Hazen, Steven W. Singer, Aindrila Mukhopadhyay
Published 2019-02-01

Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC

by Thomas Eng, Philipp Demling, Robin A. Herbert, Yan Chen, Veronica Benites, Joel Martin, Anna Lipzen, Edward E. K. Baidoo, Lars M. Blank, Christopher J. Petzold, Aindrila Mukhopadhyay
Published 2018-10-01

Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

by Christopher M. Shymansky, Christopher M. Shymansky, Christopher M. Shymansky, George Wang, George Wang, Edward E. K. Baidoo, Edward E. K. Baidoo, Jennifer Gin, Jennifer Gin, Amanda Reider Apel, Amanda Reider Apel, Aindrila Mukhopadhyay, Aindrila Mukhopadhyay, Héctor García Martín, Héctor García Martín, Héctor García Martín, Héctor García Martín, Jay D. Keasling, Jay D. Keasling, Jay D. Keasling, Jay D. Keasling, Jay D. Keasling
Published 2017-05-01

Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation

by Maren Wehrs, Mitchell G. Thompson, Deepanwita Banerjee, Jan-Philip Prahl, Norma M. Morella, Carolina A. Barcelos, Jadie Moon, Zak Costello, Jay D. Keasling, Patrick M. Shih, Deepti Tanjore, Aindrila Mukhopadhyay
Published 2020-08-01

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

by Luísa Czamanski Nora, Maren Wehrs, Joonhoon Kim, Jan-Fang Cheng, Angela Tarver, Blake A. Simmons, Jon Magnuson, Miranda Harmon-Smith, Rafael Silva-Rocha, John M. Gladden, Aindrila Mukhopadhyay, Jeffrey M. Skerker, James Kirby
Published 2019-06-01

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

by Deepanwita Banerjee, Thomas Eng, Andrew K. Lau, Yusuke Sasaki, Brenda Wang, Yan Chen, Jan-Philip Prahl, Vasanth R. Singan, Robin A. Herbert, Yuzhong Liu, Deepti Tanjore, Christopher J. Petzold, Jay D. Keasling, Aindrila Mukhopadhyay
Published 2020-10-01

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

by Ankita Kothari, Simon Roux, Hanqiao Zhang, Anatori Prieto, Drishti Soneja, John-Marc Chandonia, Sarah Spencer, Xiaoqin Wu, Sara Altenburg, Matthew W. Fields, Adam M. Deutschbauer, Adam P. Arkin, Eric J. Alm, Romy Chakraborty, Aindrila Mukhopadhyay
Published 2021-06-01

Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

by Elsayed T. Mohamed, Allison Z. Werner, Davinia Salvachúa, Christine A. Singer, Kiki Szostkiewicz, Manuel Rafael Jiménez-Díaz, Thomas Eng, Mohammad S. Radi, Blake A. Simmons, Aindrila Mukhopadhyay, Markus J. Herrgård, Steven W. Singer, Gregg T. Beckham, Adam M. Feist
Published 2020-12-01

Development of a native Escherichia coli induction system for ionic liquid tolerance.

by Marijke Frederix, Kimmo Hütter, Jessica Leu, Tanveer S Batth, William J Turner, Thomas L Rüegg, Harvey W Blanch, Blake A Simmons, Paul D Adams, Jay D Keasling, Michael P Thelen, Mary J Dunlop, Christopher J Petzold, Aindrila Mukhopadhyay
Published 2014-01-01

Conversion of poplar biomass into high-energy density tricyclic sesquiterpene jet fuel blendstocks

by Gina M. Geiselman, James Kirby, Alexander Landera, Peter Otoupal, Gabriella Papa, Carolina Barcelos, Eric R. Sundstrom, Lalitendu Das, Harsha D. Magurudeniya, Maren Wehrs, Alberto Rodriguez, Blake A. Simmons, Jon K. Magnuson, Aindrila Mukhopadhyay, Taek Soon Lee, Anthe George, John M. Gladden
Published 2020-11-01