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Genome-scale gene/reaction essentiality and synthetic lethality analysis

Molecular systems biology, 2009-08, Vol.5 (1), p.301-301

2009

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A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

Nature communications, 2016-12, Vol.7 (1), p.13806-13806, Article 13806

2016

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From directed evolution to computational enzyme engineering—A review

AIChE journal, 2020-03, Vol.66 (3), p.n/a

2020

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OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities

PLoS computational biology, 2012-02, Vol.8 (2), p.e1002363-e1002363

2012

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OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

PLoS computational biology, 2010-04, Vol.6 (4), p.e1000744-e1000744

2010

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SteadyCom: Predicting microbial abundances while ensuring community stability

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005539-e1005539

2017

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Recent advances in the reconstruction of metabolic models and integration of omics data

Current opinion in biotechnology, 2014-10, Vol.29 (C), p.39-45

2014

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Pathway design using de novo steps through uncharted biochemical spaces

Nature communications, 2018-01, Vol.9 (1), p.184-15, Article 184

2018

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Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration

Metabolic engineering, 2015-05, Vol.29 (C), p.86-96

2015

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Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism

PloS one, 2011-07, Vol.6 (7), p.e21784-e21784

2011

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k-OptForce: integrating kinetics with flux balance analysis for strain design

PLoS computational biology, 2014-02, Vol.10 (2), p.e1003487-e1003487

2014

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Synthetic biology of cyanobacteria: unique challenges and opportunities

Frontiers in microbiology, 2013, Vol.4, p.246-246

2013

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OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes

PloS one, 2014-08, Vol.9 (8), p.e105954-e105954

2014

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MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

BMC bioinformatics, 2012-01, Vol.13 (1), p.6-6, Article 6

2012

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Optimization based automated curation of metabolic reconstructions

BMC bioinformatics, 2007-06, Vol.8 (1), p.212-212, Article 212

2007

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Artificial water channels enable fast and selective water permeation through water-wire networks

Nature nanotechnology, 2020-01, Vol.15 (1), p.73-79

2020

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Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models

Metabolic engineering, 2018-05, Vol.47 (C), p.190-199

2018

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dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009448-e1009448

2021

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A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

Metabolic engineering, 2014-09, Vol.25, p.50-62

2014

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MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes

ACS synthetic biology, 2018-02, Vol.7 (2), p.462-473

2018

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d‑OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

ACS synthetic biology, 2014-04, Vol.3 (4), p.247-257

2014

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PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore

Nature communications, 2018-09, Vol.9 (1), p.3661-10, Article 3661

2018

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Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

Biotechnology and bioengineering, 2003-12, Vol.84 (6), p.647-657

2003

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Engineering biology approaches for food and nutrient production by cyanobacteria

Current opinion in biotechnology, 2021-02, Vol.67 (C), p.1-6

2021

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CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database

Journal of chemical information and modeling, 2014-12, Vol.54 (12), p.3417-3438

2014

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Genome-scale gene/reaction essentiality and synthetic lethality analysis

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

From directed evolution to computational enzyme engineering—A review

OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities

OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

SteadyCom: Predicting microbial abundances while ensuring community stability

Recent advances in the reconstruction of metabolic models and integration of omics data

Pathway design using de novo steps through uncharted biochemical spaces

Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration

Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism

k-OptForce: integrating kinetics with flux balance analysis for strain design

Synthetic biology of cyanobacteria: unique challenges and opportunities

OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

Optimization based automated curation of metabolic reconstructions

Artificial water channels enable fast and selective water permeation through water-wire networks

Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes

d‑OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

Engineering biology approaches for food and nutrient production by cyanobacteria

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database

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