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List of works by Aindrila Mukhopadhyay

4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement

scientific article

A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae

scientific article

A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium.

scientific article published on 2 December 2016

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

scientific article

A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.

scientific article published on 30 October 2017

A model for improving microbial biofuel production using a synthetic feedback loop

scientific article

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

scientific article (publication date: September 2014)

A rapid and inexpensive labeling method for microarray gene expression analysis

scientific article

A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels

scientific article (publication date: 2012)

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

scientific article published on 29 June 2019

Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC.

scientific article

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

scientific article published on 29 August 2020

Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism.

scientific article published on 28 February 2011

Analysis of theArabidopsisCytosolic Proteome Highlights Subcellular Partitioning of Central Plant Metabolism

article

Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of ω-hydroxy fatty acids in cutin polyester

scientific article published on 8 December 2011

Artificial Biosynthetic Pathway for an Unnatural Terpenoid with an Iridiumcontaining P450

Biocompatible Choline-Based Deep Eutectic Solvents Enable One-Pot Production of Cellulosic Ethanol

Biofuel alternatives to ethanol: pumping the microbial well

scientific article published on 28 May 2008

Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification

article

Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough

scientific article

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

scientific article published on 11 April 2013

Chemoinformatic-guided engineering of polyketide synthases

scientific article published on 15 May 2020

Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots

scientific article published on 12 September 2019

Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens

scientific article published on July 2006

Construction of a novel dual-inducible duet-expression system for gene (over)expression in Pseudomonas putida

scientific article published on 03 June 2020

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

scientific article published on 12 November 2020

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

scientific article published on 29 December 2019

DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems

scientific article

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

scientific article

Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass

article

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust

scientific article

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

scientific article published on 29 June 2021

Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450

scientific article published on 19 January 2021

Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants

scientific article published on 17 January 2017

Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol

scientific article published on 12 July 2016

Engineering Robust Production Microbes for Large-Scale Cultivation

scientific article published on 25 February 2019

Engineering dynamic pathway regulation using stress-response promoters.

scientific article

Engineering glucose metabolism of Escherichia coli under nitrogen starvation

scientific article

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks

scientific article published on 9 June 2017

Engineering microbial biofuel tolerance and export using efflux pumps

scientific article

Engineering to produce the biogasoline isopentenol from plant biomass hydrolysates

article

Enhancing fatty acid production by the expression of the regulatory transcription factor FadR.

scientific article published on 28 September 2012

Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae.

scientific article

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants.

scientific article published on 10 October 2016

Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast.

scientific article

Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility

scientific article

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

scientific article published on 17 March 2009

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

scientific article published on 28 January 2020

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

scientific article

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq

scientific article published on 21 August 2020

Functional genomic study of exogenous n-butanol stress in Escherichia coli

scientific article

Functional responses of methanogenic archaea to syntrophic growth

scientific article

Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

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

scientific article published on 23 October 2020

Genomics Characterization of an Engineered <i>Corynebacterium glutamicum</i> in Bioreactor Cultivation Under Ionic Liquid Stress

scientific article published on 18 November 2021

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

scientific article

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

scientific article

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

scientific article published in October 2010

Identification and microbial production of a terpene-based advanced biofuel

scientific article

Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium

scientific article

Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida

scientific article published on 02 January 2020

Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production

article

Importance of systems biology in engineering microbes for biofuel production

scientific article published on June 2008

Improving membrane protein expression and function using genomic edits

scientific article published on 12 October 2017

Improving microbial biogasoline production in Escherichia coli using tolerance engineering.

scientific article

Improving olefin tolerance and production in E. coli using native and evolved AcrB.

scientific article published on 20 January 2015

Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme

scientific article published on 07 November 2019

Integrating input from multiple signals: the VirA/VirG two-component system of Agrobacterium tumefaciens

scientific article published in November 2004

Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries

scientific article published on 04 May 2017

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

scientific article published on 18 August 2020

Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria

scientific article published on 22 July 2020

Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course

scientific article published on 26 July 2019

Isolation and characterization of novel mutations in the pSC101 origin that increase copy number.

scientific article

Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis

scientific article published on 19 March 2012

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust

scientific article

Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

scientific article published on 8 January 2008

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

article

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

scientific article published on 09 April 2019

Machine learning for metabolic engineering: A review

scientific article published on 19 November 2020

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids

scientific article published on 29 April 2019

Modular engineering of L-tyrosine production in Escherichia coli

scientific article published on 21 October 2011

Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs.

scientific article published on 17 January 2018

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

scientific article published on 17 December 2019

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria

scientific article

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing

scientific article published in 2022

Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli

scientific article published on 06 September 2019

Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough

scientific article

Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry

scientific article published on 17 November 2006

Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins

scientific article

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

scientific article published on 13 December 2018

Production of tetra-methylpyrazine using engineered Corynebacterium glutamicum

scientific article published on 02 December 2019

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

scientific article

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

article

Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery-Relevant Compounds

scientific article published on 26 July 2019

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach

scientific article

Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics.

scientific article published on 23 May 2006

Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein.

scientific article published in January 2010

Synthetic and systems biology for microbial production of commodity chemicals.

scientific article

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

scientific article published on 12 October 2011

Systems and synthetic biology tools for advanced bioproduction hosts

scientific article published on 08 January 2020

Targeted proteomics for metabolic pathway optimization: application to terpene production.

scientific article published on 5 January 2011

Techno-economic analysis and life-cycle greenhouse gas mitigation cost of five routes to bio-jet fuel blendstocks

The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization

scientific article

The Future of Antibiotics: Emerging Technologies and Stewardship

scientific article

The Role of Proteomics in the Development of Cellulosic Biofuels

article

The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis.

scientific article

Tolerance Characterization and Isoprenol Production of Adapted Escherichia coli in the Presence of Ionic Liquids

scholarly article by Shizeng Wang et al published 4 December 2018 in ACS Sustainable Chemistry & Engineering

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals

scientific article published on 26 May 2015

Tools to map target genes of bacterial two-component system response regulators

scientific article published on 24 March 2020

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization.

scientific article published on 22 September 2016

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state

scientific article

Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol

article

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

scientific article published on 10 November 2015

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