Works matching AU Mahadevan, Radhakrishnan

Results: 64

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.

Published in:

2011

By:

Mahadevan, Radhakrishnan;
Palsson, Bernhard Ø.;
Lovley, Derek R.

Publication type:

Correction Notice

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.

Published in:

Nature Reviews Microbiology, 2011, v. 9, n. 1, p. 39, doi. 10.1038/nrmicro2456

By:

Mahadevan, Radhakrishnan;
Palsson, Bernhard Ø.;
Lovley, Derek R.

Publication type:

Article

A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell.

Published in:

Biotechnology & Bioengineering, 2014, v. 111, n. 4, p. 709, doi. 10.1002/bit.25137

By:

Bourdakos, Nicholas;
Marsili, Enrico;
Mahadevan, Radhakrishnan

Publication type:

Article

The design of long-term effective uranium bioremediation strategy using a community metabolic model.

Published in:

Biotechnology & Bioengineering, 2012, v. 109, n. 10, p. 2475, doi. 10.1002/bit.24528

By:

Zhuang, K.;
Ma, E.;
Lovley, Derek R.;
Mahadevan, Radhakrishnan

Publication type:

Article

Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture.

Published in:

Biotechnology & Bioengineering, 2007, v. 97, n. 5, p. 1190, doi. 10.1002/bit.21332

By:

Hjersted, Jared L.;
Henson, Michael A.;
Mahadevan, Radhakrishnan

Publication type:

Article

Estimating optimal profiles of genetic alterations using constraint-based models.

Published in:

Biotechnology & Bioengineering, 2005, v. 89, n. 2, p. 243, doi. 10.1002/bit.20349

By:

Gadkar, Kapil G.;
Doyle III, Francis J.;
Edwards, Jeremy S.;
Mahadevan, Radhakrishnan

Publication type:

Article

Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.

Published in:

Biotechnology & Bioengineering, 2004, v. 86, n. 3, p. 317, doi. 10.1002/bit.20011

By:

Wiback, Sharon J.;
Mahadevan, Radhakrishnan;
Palsson, Bernhard Ø.

Publication type:

Article

Evaluating the feasibility of medium-chain oleochemical synthesis using microbial chain elongation.

Published in:

Journal of Industrial Microbiology & Biotechnology, 2024, v. 51, p. 1, doi. 10.1093/jimb/kuae027

By:

Agena, Ethan;
Gois, Ian M;
Bowers, Connor M;
Mahadevan, Radhakrishnan;
Scarborough, Matthew J;
Lawson, Christopher E

Publication type:

Article

Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid.

Published in:

Journal of Industrial Microbiology & Biotechnology, 2018, v. 45, n. 8, p. 735, doi. 10.1007/s10295-018-2053-1

By:

Balderas-Hernández, Victor E.;
Correia, Kevin;
Mahadevan, Radhakrishnan

Publication type:

Article

Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling.

Published in:

BMC Research Notes, 2010, v. 3, p. 125, doi. 10.1186/1756-0500-3-125

By:

Garg, Srinath;
Yang, Laurence;
Mahadevan, Radhakrishnan

Publication type:

Article

Control-relevant scheduling of polymer grade transitions.

Published in:

AIChE Journal, 2002, v. 48, n. 8, p. 1754, doi. 10.1002/aic.690480816

By:

Mahadevan, Radhakrishnan;
Doyle, Francis J.;
Allcock, Andrew C.

Publication type:

Article

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 4, p. 1, doi. 10.1371/journal.pcbi.1005409

By:

Klamt, Steffen;
Regensburger, Georg;
Gerstl, Matthias P.;
Jungreuthmayer, Christian;
Schuster, Stefan;
Mahadevan, Radhakrishnan;
Zanghellini, Jürgen;
Müller, Stefan

Publication type:

Article

Genome-Scale Metabolic Modeling Reveals Sequential Dysregulation of Glutathione Metabolism in Livers from Patients with Alcoholic Hepatitis.

Published in:

Metabolites (2218-1989), 2022, v. 12, n. 12, p. 1157, doi. 10.3390/metabo12121157

By:

Manchel, Alexandra;
Mahadevan, Radhakrishnan;
Bataller, Ramon;
Hoek, Jan B.;
Vadigepalli, Rajanikanth

Publication type:

Article

A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution.

Published in:

Biotechnology for Biofuels, 2020, v. 13, n. 1, p. 1, doi. 10.1186/s13068-020-01753-5

By:

Liu, Yilan;
Chen, Jinjin;
Khusnutdinova, Anna N.;
Correia, Kevin;
Diep, Patrick;
Batyrova, Khorcheska A.;
Nemr, Kayla;
Flick, Robert;
Stogios, Peter;
Yakunin, Alexander F.;
Mahadevan, Radhakrishnan

Publication type:

Article

Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from D ehalococcoides mccartyi.

Published in:

Microbial Biotechnology, 2016, v. 9, n. 1, p. 47, doi. 10.1111/1751-7915.12315

By:

Islam, M. Ahsanul;
Tchigvintsev, Anatoli;
Yim, Veronica;
Savchenko, Alexei;
Yakunin, Alexander F.;
Mahadevan, Radhakrishnan;
Edwards, Elizabeth A.

Publication type:

Article

Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

Published in:

Microbial Biotechnology, 2009, v. 2, n. 2, p. 274, doi. 10.1111/j.1751-7915.2009.00087.x

By:

Scheibe, Timothy D.;
Mahadevan, Radhakrishnan;
Yilin Fang;
Garg, Srinath;
Long, Philip E.;
Lovley, Derek R.

Publication type:

Article

Macrophage Immunomodulation Through New Polymers that Recapitulate Functional Effects of Itaconate as a Power House of Innate Immunity.

Published in:

Advanced Functional Materials, 2021, v. 31, n. 6, p. 1, doi. 10.1002/adfm.202003341

By:

Davenport Huyer, Locke;
Mandla, Serena;
Wang, Yufeng;
Campbell, Scott B.;
Yee, Bess;
Euler, Christian;
Lai, Benjamin F.;
Bannerman, A. Dawn;
Lin, Dawn S. Y.;
Montgomery, Miles;
Nemr, Kayla;
Bender, Timothy;
Epelman, Slava;
Mahadevan, Radhakrishnan;
Radisic, Milica

Publication type:

Article

Leaching characteristics of nickeliferous pyrrhotite tailings from the Sudbury, Ontario area.

Published in:

Canadian Metallurgical Quarterly, 2017, v. 56, n. 4, p. 372, doi. 10.1080/00084433.2017.1361162

By:

Garg, Srinath;
Judd, Kurtis;
Mahadevan, Radhakrishnan;
Edwards, Elizabeth;
Papangelakis, Vladimiros G.

Publication type:

Article

SARS-CoV-2 receptor-binding mutations and antibody contact sites.

Published in:

Antibody Therapeutics, 2021, v. 4, n. 3, p. 149, doi. 10.1093/abt/tbab015

By:

Mejdani, Marios;
Haddadi, Kiandokht;
Pham, Chester;
Mahadevan, Radhakrishnan

Publication type:

Article

Automation assisted anaerobic phenotyping for metabolic engineering.

Published in:

Microbial Cell Factories, 2021, v. 20, n. 1, p. 1, doi. 10.1186/s12934-021-01675-3

By:

Raj, Kaushik;
Venayak, Naveen;
Diep, Patrick;
Golla, Sai Akhil;
Yakunin, Alexander F.;
Mahadevan, Radhakrishnan

Publication type:

Article

A scalable method for parameter identification in kinetic models of metabolism using steady-state data.

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5216, doi. 10.1093/bioinformatics/btz445

By:

Srinivasan, Shyam;
Cluett, William R;
Mahadevan, Radhakrishnan

Publication type:

Article

Model-based design of bistable cell factories for metabolic engineering.

Published in:

Bioinformatics, 2018, v. 34, n. 8, p. 1363, doi. 10.1093/bioinformatics/btx769

By:

Srinivasan, Shyam;
Cluett, William R;
Mahadevan, Radhakrishnan

Publication type:

Article

Genome-scale strain designs based on regulatory minimal cut sets.

Published in:

Bioinformatics, 2015, v. 31, n. 17, p. 2844, doi. 10.1093/bioinformatics/btv217

By:

Mahadevan, Radhakrishnan;
von Kamp, Axel;
Klamt, Steffen

Publication type:

Article

Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39778-7

By:

Venkatesan, Meenakshi;
Fruci, Michael;
Verellen, Lou Ann;
Skarina, Tatiana;
Mesa, Nathalie;
Flick, Robert;
Pham, Chester;
Mahadevan, Radhakrishnan;
Stogios, Peter J.;
Savchenko, Alexei

Publication type:

Article

Ensemble modeling of cancer metabolism.

Published in:

Frontiers in Physiology, 2012, v. 3, p. 1, doi. 10.3389/fphys.2012.00135

By:

Khazaei, Tahmineh;
McGuigan, Alison;
Mahadevan, Radhakrishnan

Publication type:

Article

An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2019, v. 13, n. 4, p. 1042, doi. 10.1038/s41396-018-0333-4

By:

Wang, Po-Hsiang;
Correia, Kevin;
Ho, Han-Chen;
Venayak, Naveen;
Nemr, Kayla;
Flick, Robert;
Mahadevan, Radhakrishnan;
Edwards, Elizabeth A.

Publication type:

Article

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2017, v. 11, n. 3, p. 626, doi. 10.1038/ismej.2016.158

By:

Wang, Po-Hsiang;
Tang, Shuiquan;
Nemr, Kayla;
Flick, Robert;
Yan, Jun;
Mahadevan, Radhakrishnan;
F Yakunin, Alexander;
Löffler, Frank E;
Edwards, Elizabeth A

Publication type:

Article

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2011, v. 5, n. 2, p. 305, doi. 10.1038/ismej.2010.117

By:

Zhuang, Kai;
Izallalen, Mounir;
Mouser, Paula;
Richter, Hanno;
Risso, Carla;
Mahadevan, Radhakrishnan;
Lovley, Derek R

Publication type:

Article

Genome-scale constraint-based modeling of Geobacter metallireducens.

Published in:

BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-15

By:

Jun Sun;
Sayyar, Bahareh;
Butler, Jessica E.;
Pharkya, Priti;
Fahland, Tom R.;
Famili, Iman;
Schilling, Christophe H.;
Lovley, Derek R.;
Mahadevan, Radhakrishnan

Publication type:

Article

Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium.

Published in:

Proteins, 2013, v. 81, n. 6, p. 1031, doi. 10.1002/prot.24227

By:

Zheng, Hongyan;
Beliavsky, Alina;
Tchigvintsev, Anatoli;
Brunzelle, Joseph S.;
Brown, Greg;
Flick, Robert;
Evdokimova, Elena;
Wawrzak, Zdzislaw;
Mahadevan, Radhakrishnan;
Anderson, Wayne F.;
Savchenko, Alexei;
Yakunin, Alexander F.

Publication type:

Article

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 444, doi. 10.1186/1471-2164-13-444

By:

Hitoshi Suzuki;
MacDonald, Jacqueline;
Syed, Khajamohiddin;
Salamov, Asaf;
Chiaki Hori;
Aerts, Andrea;
Henrissat, Bernard;
Wiebenga, Ad;
vanKuyk, Patricia A.;
Barry, Kerrie;
Lindquist, Erika;
LaButti, Kurt;
Lapidus, Alla;
Lucas, Susan;
Coutinho, Pedro;
Yunchen Gong;
Masahiro Samejima;
Radhakrishnan Mahadevan;
Abou-Zaid, Mamdouh;
de Vries, Ronald P.

Publication type:

Article

A gap-filling algorithm for prediction of metabolic interactions in microbial communities.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.pcbi.1009060

By:

Giannari, Dafni;
Ho, Cleo Hanchen;
Mahadevan, Radhakrishnan

Publication type:

Article

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 8, p. 1, doi. 10.1371/journal.pcbi.1009110

By:

Zhu, Leo;
Pei, William;
Thiele, Ines;
Mahadevan, Radhakrishnan

Publication type:

Article

SYSTEMS BIOLOGY: THE SYNERGISTIC INTERPLAY BETWEEN BIOLOGY AND MATHEMATICS.

Published in:

Canadian Journal of Chemical Engineering, 2008, v. 86, n. 2, p. 127, doi. 10.1002/cjce.20025

By:

Dhurjati, Prasad;
Mahadevan, Radhakrishnan

Publication type:

Article

Redesigning metabolism based on orthogonality principles.

Published in:

Nature Communications, 2017, v. 8, n. 5, p. 15188, doi. 10.1038/ncomms15188

By:

Pandit, Aditya Vikram;
Srinivasan, Shyam;
Mahadevan, Radhakrishnan

Publication type:

Article

Systematizing the different notions of growth‐coupled product synthesis and a single framework for computing corresponding strain designs.

Published in:

Biotechnology Journal, 2021, v. 16, n. 12, p. 1, doi. 10.1002/biot.202100236

By:

Schneider, Philipp;
Mahadevan, Radhakrishnan;
Klamt, Steffen

Publication type:

Article

Pan‐Genome‐Scale Network Reconstruction: Harnessing Phylogenomics Increases the Quantity and Quality of Metabolic Models.

Published in:

Biotechnology Journal, 2020, v. 15, n. 10, p. 1, doi. 10.1002/biot.201900519

By:

Correia, Kevin;
Mahadevan, Radhakrishnan

Publication type:

Article

Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics.

Published in:

Microbial Cell Factories, 2015, v. 14, n. 1, p. 1, doi. 10.1186/s12934-015-0252-2

By:

Gold, Nicholas D.;
Gowen, Christopher M.;
Lussier, Francois-Xavier;
Cautha, Sarat C.;
Mahadevan, Radhakrishnan;
Martin, Vincent J. J.

Publication type:

Article

Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000887

By:

Islam, M. Ahsanul;
Edwards, Elizabeth A.;
Mahadevan, Radhakrishnan

Publication type:

Article

Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 2, p. 1, doi. 10.1371/journal.pcbi.0040036

By:

Segura, Daniel;
Mahadevan, Radhakrishnan;
Juárez, Katy;
Lovley, Derek R.

Publication type:

Article

Economics of membrane occupancy and respiro-fermentation.

Published in:

Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.34

By:

Zhuang, Kai;
Vemuri, Goutham N;
Mahadevan, Radhakrishnan

Publication type:

Article

Sub-optimal phenotypes of double-knockout mutants of Escherichia coli depend on the order of gene deletions.

Published in:

Integrative Biology, 2015, v. 7, n. 8, p. 930, doi. 10.1039/c5ib00096c

By:

Gawand, Pratish;
Said Abukar, Fatumina;
Venayak, Naveen;
Partow, Siavash;
Motter, Adilson E.;
Mahadevan, Radhakrishnan

Publication type:

Article

Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.

Published in:

Integrative Biology, 2015, v. 7, n. 8, p. 869, doi. 10.1039/c5ib00095e

By:

Islam, M. Ahsanul;
Zengler, Karsten;
Edwards, Elizabeth A.;
Mahadevan, Radhakrishnan;
Stephanopoulos, Gregory

Publication type:

Article

Design principles for generating robust gene expression patterns in dynamic engineered tissues.

Published in:

Integrative Biology, 2013, v. 5, n. 3, p. 578, doi. 10.1039/c3ib20274g

By:

Javaherian, Sahar;
Anesiadis, Nikolaos;
Mahadevan, Radhakrishnan;
McGuigan, Alison P.

Publication type:

Article

KinMod database: a tool for investigating metabolic regulation.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac081

By:

Haddadi, Kiandokht;
Barghout, Rana Ahmed;
Mahadevan, Radhakrishnan

Publication type:

Article

AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution.

Published in:

Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/baz022

By:

Correia, Kevin;
Yu, Shi M;
Mahadevan, Radhakrishnan

Publication type:

Article

New Insights into Dehalococcoides mccartyi Metabolism from a Reconstructed Metabolic Network-Based Systems-Level Analysis of D. mccartyi Transcriptomes.

Published in:

PLoS ONE, 2014, v. 9, n. 4, p. 1, doi. 10.1371/journal.pone.0094808

By:

Islam, M. Ahsanul;
Waller, Alison S.;
Hug, Laura A.;
Provart, Nicholas J.;
Edwards, Elizabeth A.;
Mahadevan, Radhakrishnan

Publication type:

Article

When Do Two‐Stage Processes Outperform One‐Stage Processes?

Published in:

Biotechnology Journal, 2018, v. 13, n. 2, p. 1, doi. 10.1002/biot.201700539

By:

Klamt, Steffen;
Mahadevan, Radhakrishnan;
Hädicke, Oliver

Publication type:

Article

Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids.

Published in:

Biotechnology Journal, 2017, v. 12, n. 11, p. 1, doi. 10.1002/biot.201600751

By:

Khusnutdinova, Anna N.;
Flick, Robert;
Popovic, Ana;
Brown, Greg;
Tchigvintsev, Anatoli;
Nocek, Boguslaw;
Correia, Kevin;
Joo, Jeong C.;
Mahadevan, Radhakrishnan;
Yakunin, Alexander F.

Publication type:

Article

Constructing kinetic models of metabolism at genome-scales: A review.

Published in:

Biotechnology Journal, 2015, v. 10, n. 9, p. 1345, doi. 10.1002/biot.201400522

By:

Srinivasan, Shyam;
Cluett, William R.;
Mahadevan, Radhakrishnan

Publication type:

Article