Publications

Highlights

(For a full list see below or go to Google Scholar )

 

Full List

Emulsion-based evolution of Escherichia coli for higher growth yield on D-xylose identifies central role of cyclic AMP
Orr J, Zen E, Wang X, Rao CV
Systems Microbiology and Biomanufacturing (2022)

System analysis of Lipomyces starkeyi during growth on various plant-based sugars
Deewan A, Liu JJ, Jagtap SS, Yun EJ, Walukiewicz W, Jin YS, Rao CV
Applied Microbiology and Biotechnology (2022)

Characterization of Opposing Responses to Phenol by Bacillus subtilis Chemoreceptors
Bodhankar G, Tohidifar P, Foust Z, Ordal G, Rao CV
American Society of Microbiology (2022)

Identification and analysis of sugar transporters capable of co-transporting glucose and xylose simultaneously
Kuanyshev N, Deewan A, Jagtap SS, Liu JJ, Selvam B, Chen LQ, Shukla D, Rao CV, Jin YS
Biotechnology Journal (2022)

Integrating transcriptomic and metabolomic analysis of the oleaginous yeast Rhodosporidium toruloides IFO0880 during growth under different carbon sources
Jagtap SS, Deewan A, Liu JJ, Walukiewicz HE, Yun EJ, Jin YS, Rao CV
Applied Microbiology and Biotechnology (2021)

Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide
Tan LR, Liu JJ, Woodruff W, Deewan A, Jagtap SS, Yun EJ, Walukiewicz HE, Jin YS, Rao CV
Applied Genetics and Molecular Biotechnology (2021)

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerol
Jagtap SS, Bedekar AA, Singh V, Jin YS, Rao CV
Biotechnology for Biofuels and Bioproducts (2021)

Two tandem mechanisms control bimodal expression of the flagellar genes in Salmonella enterica
Wang X, Koirala S, Aldridge PD, Rao CV
Journal of Bacteriology (2020)

Metabolic engineering of Parageobacillus thermoglucosidasius for the efficient production of (2R, 3R)-butanediol
Zhou J, Lian J, Rao CV
Applied Microbiology and Biotechnology (2020)

Recent developments in pretreatment technologies on lignocellulosic biomass - Effect of key parameters, technological improvements, and challenges
Bhatia SK, Jagtap SS, Bedekar AA, Bhatia RK, Patel AK, Pant D, Banu JR, Rao CV, Kim YG, Yang YH
Bioresource Technology (2020)

The mechanism of bidirectional pH taxis in Bacillus subtilis
Tohidifar P, Plutz MP, Ordal GW, Rao CV
Journal of Bacteriology (2020)

Characterization of the GH16 and GH17 laminarinases from Vibrio breoganii 1C10
Badur AH, Ammar EM, Yalamanchili G, Hehemann JH, Rao CV
Applied Microbiology and Biotechnology (2020)

Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880
Jagtap SS, Bedekar AA, Liu JJ, Jin YS, Rao CV
Biotechnology for Biofuels (2019)

Synergistic action of SPI-1 gene expression in Salmonella enterica serovar typhimurium through transcriptional crosstalk with the flagellar system
Hamed S, Wang X, Shawky RM, Emara M, Aldridge PD, Rao CV
BMC Microbiology (2019)

Global lysine acetylation in Escherichia coli results from growth conditions that favor acetate fermentation
Schilling B, Basisty N, Christensen DG, Sorensen D, Orr JS, Wolfe AJ, Rao CV
Journal of Bacteriology (2019)

pH selectively regulates citric acid and lipid production in Yarrowia lipolytica W29 during nitrogen-limited growth on glucose
Zhang S, Jagtap SS, Deewan A, Rao CV
Journal of Biotechnology (2019)

Extracellular acidic pH inhibits acetate consumption by decreasing gene transcription of the tricarboxylic acid cycle and the glyoxylate shunt
Orr JS, Christensen DG, Wolfe AJ, Rao CV
Journal of Bacteriology (2019)

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data
Dinh HV, Suthers PF, Chan SHJ, Shen Y, Xiao T, Deewan A, Jagtap SS, Rabinowitz JD, Rao CV, Zhao H, Maranas CD
Metabolic Engineering Communications (2019)

Driving the expression of the Salmonella enterica sv Typhimurium flagellum using flhDC from Escherichia coli results in key regulatory and cellular differences
Albanna A, Sim M, Hoskisson PA, Gillespie C, Rao CV & Aldridge PD
Scientific Reports (2018)

Microbial conversion of xylose into useful bioproducts
Jagtap SS, Rao CV
Applied Microbiology and Biotechnology (2018)

Regulation of metabolism in Escherichia coli during growth on mixtures of the non-glucose sugars - arabinose, lactose, and xylose
Ammar EM, Wang X, Rao CV
Scientific Reports (2018)

Production of D-arabitol from D-xylose by the oleaginous yeast Rhodosporidium toruloides IFO0880
Jagtap SS, Rao CV
Applied Microbiology and Biotechnology (2018)

Ancient regulatory role of lysine acetylation in central metabolism
Nakayasu ES, Burnet MC, Walukiewicz HE, Wilkins CS, Shukla AK, Brooks S, Plutz MJ, Lee BD, Schilling B, Wolfe AJ, Müller S, Kirby JR, Rao CV, Cort JR, Payne SH
mBio (2017)

Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions
Badur AH, Plutz MJ, Yalamanchili G, Jagtap SS, Schweder T, Unfried F, Markert S, Polz MF, Hehemann JH, Rao CV
Journal of Biological Chemistry (2017)

Sparsity of Linear Discrete-Time Optimal Control Problems With l_1 Objectives
Rao CV
IEEE Transactions on Automatic Control (2017)

Increasing growth yield and decreasing acetylation in Escherichia coli by optimizing the carbon-to-magnesium Ratio in peptide-based media
Christensen DG, Orr JS, Rao CV, Wolfe AJ
Applied and Environmental Microbiology (2017)

Growth rate control of flagellar assembly in Escherichia coli strain RP437
Sim M, Koirala S, Picton D, Strahl H, Hoskisson PA, Rao CV, Gillespie CS, Aldridge PD
Scientific reports (2017)

Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation
Zhang S, Ito M, Skerker M, Arkin AP, Rao CV
Applied Microbiology and Biotechnology (2016)

Production of 1-decanol by metabolically engineered Yarrowia lipolytica
Rutter CD, Rao CV
Metabolic Engineering (2016)

Metabolic engineering of a probiotic Saccharomyces boulardii
Liu JJ, Kong II, Zhang GC, Jayakody LN, Kim H, Xia PF, Kwak S, Sung BH, Sohn JH, Walukiewicz HE, Rao CV, Jin YS
Applied and Environmental Microbiology (2016)

Stokes trap for multiplexed particle manipulation and assembly using fluidics
Shenoy A, Rao CV, Schroeder CM
Proceedings of the National Academy of Sciences (2016)

Evolutionary engineering of Geobacillus thermoglucosidasius for improved ethanol production
Zhou J, Wu K, Rao CV
Biotechnology and Bioengineering (2016)

Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria
Cao Y, Ryser MD, Payne S, Li B, Rao CV, You L
Cell (2016)

Development and physiological characterization of cellobiose-consuming Yarrowia lipolytica
Lane S, Zhang S, Wei N, Rao C, Jin YS
Biotechnology and Bioengineering (2015)

Alginate lyases from alginate-degrading Vibrio splendidus 12B01 are endolytic
Badur AH, Jagtap SS, Yalamanchili G, Lee JK, Zhao H, Rao CV
Applied and Environmental Microbiology (2015)

High-throughput sequencing reveals adaptation-induced mutations in pentose-fermenting strains of Zymomonas mobilis
Dunn KL, Rao CV
Biotechnology and Bioengineering (2015)

Engineering Yarrowia lipolytica for production of medium-chain fatty acids
Rutter CD, Zhang S, Rao CV
Applied Microbiology and Biotechnology (2015)

Engineering Rhodosporidium toruloides for increased lipid production
Zhang S, Skerker JM, Rutter CD, Maurer MJ, Arkin AP, Rao CV
Biotechnology and Bioengineering (2015)

Reciprocal regulation of l-Arabinose and d-Xylose Metabolism in Escherichia coli
Koirala S, Wang X, Rao CV
Journal of Bacteriology (2015)

A nutrient-tunable bistable switch controls motility in Salmonella enterica serovar Typhimurium
Koirala S, Mears P, Sim M, Golding I, Chemla YR, Aldridge PD, Rao CV
mBio (2014)

Black and white with some shades of grey - the diverse responses of inducible metabolic pathways in Escherichia coli
Rao CV, Koirala S
Molecular Microbiology (2014)

Interactions among the three adaptation systems of Bacillus subtilis chemotaxis as revealed by an in vitro receptor-kinase assay
Walukiewicz HE, Tohidifar P, Ordal GW, Rao CV
Molecular Microbiology (2014)

Expression of a xylose-specific transporter improves ethanol production by metabolically engineered Zymomonas mobilis
Dunn KL, Rao CV
Applied Microbiology and Biotechnology (2014)

Oscillatory behavior of neutrophils under opposing chemoattractant gradients supports a winner-take-all mechanism
Byrne MB, Kimura Y, Kapoor A, He Y, Mattam KS, Hasan KM, Olson LN, Wang F,Kenis PJ, Rao CV
PLoS One (2014)

A tale of two machines - a review of the BLAST meeting, Tucson, AZ, 20-24 January 2013
Glekas GD, Cates JR, Cohen TM, Rao CV, Ordal GW
Molecular Microbiology (2014)

Escherichia coli swimming is robust against variations in flagellar number
Mears PJ, Koirala S, Rao CV, Golding I, Chemla YR
eLife (2014)

Exploiting market fluctuations and price volatility through feedback control
Rao CV
Computers and Chemical Engineering (2013)

Mammalian target of rapamycin and Rictor control neutrophil chemotaxis by regulating Rac/Cdc42 activity and the actin cytoskeleton
He Y, Li D, Cook SL, Yoon MS, Kapoor A, Rao CV, Kenis PJ, Chen J, Wang F
Molecular Biology of the Cell (2013)

The importance of the interaction of CheD with CheC and the chemoreceptors compared to its enzymatic activity during chemotaxis in Bacillus subtilis
Yuan W, Glekas GD, Allen GM, Walukiewicz HE, Rao CV, Ordal GW
PLoS One (2012)

The Bacillus subtilis chemoreceptor McpC senses multiple ligands using two discrete mechanisms
Glekas GD, Mulhern BJ, Kroc A, Duelfer KA, Lei V, Rao CV, Ordal GW
Journal of Biological Chemistry (2012)

Identification and analysis of the putative pentose sugar efflux transporters in Escherichia coli
Koita K, Rao CV
PLoS One (2012)

Elucidation of the multiple roles of CheD in Bacillus subtilis chemotaxis
Glekas GD, Plutz MJ, Walukiewicz HE, Allen GM, Rao CV, Ordal GW
Molecular Microbiology (2012)

Transcriptional cross talk within the mar-sox-rob regulon in Escherichia coli is limited to the rob and marRAB operons
Chubiz LM, Glekas GD, Rao CV
Journal of Bacteriology (2012)

Computational methods in synthetic biology - towards computer-aided part design
Wu K, Rao CV
Current Opinion in Chemical Biology (2012)

Expanding the synthetic biology toolbox - engineering orthogonal regulators of gene expression
Rao CV
Current Opinion in Biotechnology (2012)

The non-receptor tyrosine kinase Lyn controls neutrophil adhesion by recruiting the CrkL-C3G complex and activating Rap1 at the leading edge
He Y, Kapoor A, Cook S, Liu S, Xiang Y, Rao CV, Kenis PJ, Wang F
Journal of Cell Science (2011)

Cellular Stoichiometry of the Chemotaxis proteins in Bacillus subtilis
Cannistraro VJ, Glekas GD, Rao CV, Ordal GW
Journal of Bacteriology (2011)

Role of the mar-sox-rob regulon in regulating outer membrane porin expression
Chubiz L, Rao CV
Journal of Bacteriology (2011)

Continuous control of flagellar gene expression by the σ28–FlgM regulatory circuit in Salmonella enterica
Saini S, Floess E, Aldridge C, Brown J, Aldridge PD, Rao CV
Molecular Microbiology (2011)

Attractant binding induces distinct structural changes to the polar and lateral signaling clusters in Bacillus subtilis chemotaxis
Wu K, Walukiewicz HE, Glekas GD, Ordal GW, Rao CV
Journal of Biological Chemistry (2011)

Site-specific methylation in Bacillus subtilis chemotaxis - The effect of covalent modifications to the chemotaxis receptor McpB
Glekas GD, Cates JR, Cohen TM, Rao CV, Ordal GW
Microbiology (2011)

The interaction dynamics of a negative feedback loop regulates flagellar number in Salmonella enterica serovar Typhimurium
Aldridge C, Poonchareon K, Saini S, Soloyva A, Rao CV, Imada K, Minamino T, Aldridge PD
Molecular Microbiology (2010)

FliZ Induces a Kinetic Switch in Flagellar Gene Expression
Saini S, Koirala S, Floess E, Mears PJ, Chemla YR, Golding I, Aldridge C, Aldridge PD, Rao CV
Journal of Bacteriology (2010)

Role of cross talk in regulating the dynamic expression of the flagellar Salmonella pathogenicity island 1 and type 1 fimbrial genes
Saini S, Slauch JM, Aldridge PD, Rao CV
Journal of Bacteriology (2010)

The role of coupled positive feedback in the expression of the SPI1 type three secretion system in Salmonella
Saini S, Ellermeier JR, Slauch JM, Rao CV
PLoS Pathogens (2010)

Aromatic acid metabolites of Escherichia coli K-12 can induce the marRAB operon
Chubiz LM, Rao CV
Journal of Bacteriology (2010)

SprB is the molecular link between Salmonella pathogenicity island 1 (SPI1) and SPI4
Saini S, Rao CV
Journal of Bacteriology (2010)

A modular positive feedback-based gene amplifier
Nistala GJ, Wu K, Rao CV, Bhalerao KD
Journal of Biological Engineering (2010)

The role of configuration and coupling in autoregulatory gene circuits
Wu K, Rao CV
Molecular Microbiology (2010)

Regulation of arabinose and xylose metabolism in Escherichia coli
Desai TD, Rao CV
Applied and Environmental Microbiology (2010)

A PAS domain binds asparagine in the chemotaxis receptor McpB in Bacillus subtilis
Glekas GD, Foster RM, Cates JR, Estrella JA, Wawrzyniak MJ, Rao CV, Ordal GW
Journal of Biological Chemistry (2010)

High-resolution, long-term characterization of bacterial motility using optical tweezers
Min TL, Mears PJ, Chubiz LM, Rao CV, Golding I, Chemla YR
Nature Methods (2009)

The molecular basis of excitation and adaptation during chemotactic sensory transduction in bacteria
Rao CV, Ordal GW
Contributions to Microbiology (2009)

Engineering transcription factors with novel DNA-binding specificity using comparative genomics
Desai TA, Rodionov DA, Gelfand MS, Alm EJ, Rao CV
Nucleic Acids Research (2009)

Role of FimW, FimY, and FimZ in regulating the expression of type i fimbriae in Salmonella enterica serovar Typhimurium
Saini S, Pearl JA, Rao CV
Journal of Bacteriology (2009)

Calling heads from tails - the role of mathematical modeling in understanding cell polarization
Onsum MD, Rao CV
Current Opinions in Cell Biology (2009)

The rate of protein secretion dictates the temporal dynamics of flagellar gene expression
Brown JD, Saini S, Aldridge C, Herbert J, Rao CV, Aldridge PD
Molecular Microbiology (2008)

The three adaptation systems of Bacillus subtilis chemotaxis
Rao CV, Glekas GD, Ordal GW
Trends in Microbiology (2008)

Computational design of orthogonal ribosomes
Chubiz LM, Rao CV
Nucleic Acids Research (2008)

FliZ Is a posttranslational activator of FlhD4C2-dependent flagellar gene expression
Saini S, Brown JD, Aldridge PD, Rao CV
Journal of Bacteriology (2008)

The Salmonella SPI1 type three secretion system responds to periplasmic disulfide bond status via the flagellar apparatus and the RcsCDB system
Lin D, Rao CV, Slauch JM
Journal of Bacteriology (2008)

A mathematical model for neutrophil gradient sensing and polarization
Onsum MD, Rao CV
PLoS Computational Biology (2007)

Phosphatase localization in bacterial chemotaxis - divergent mechanisms, convergent principles
Rao CV, Kirby JR, Arkin AP
Physical Biology (2005)

An allosteric model for transmembrane signaling in bacterial chemotaxis
Rao CV, Frenklach M, Arkin AP
Journal of Molecular Biology (2004)

Design and diversity in bacterial chemotaxis - a comparative study in Escherichia coli and Bacillus subtilis
Rao CV, Kirby JR, Arkin AP
PLoS Biology (2004)

Stochastic chemical kinetics and the quasi-steady-state assumption - Application to the Gillespie algorithm
Rao CV, Kirby JR, Arkin AP
Journal of Chemical Physics (2003)

Constrained state estimation for nonlinear discrete-time systems - stability and moving horizon approximations
Rao CV, Rawlings JB, Mayne DQ
IEEE Transactions on Automatic Control (2003)

Control, exploitation and tolerance of intracellular noise
Rao CV, Wolf DM, Arkin AP
Nature (2002)

Constrained process monitoring - A moving horizon approach
Rao CV, Rawlings JB
AIChE Journal (2002)

Control motifs for intracellular regulatory networks
Rao CV, Arkin AP
Annual Reviews in Biomedical Engineering (2001)

Constrained linear state estimation - a moving horizon approach
Rao CV, Rawlings JB, Lee JH
Automatica (2001)

Constrained Model Predictive Control - Stability and optimality
Mayne DQ, Rawlings JB, Rao CV, Scokaert POM
Automatica (2000)

Linear Programming and Model Predictive Control
Rao CV, Rawlings JB
Journal of Process Control (2000)

Steady states and constraints in model predictive control
Rao CV, Rawlings JB
AIChE Journal (1999)

Application of Interior-Point Methods to Model Predictive Control
Rao CV, Wright SJ, Rawlings JB
Journal of Optimization Theory and Applications (1998)