bioconductor: MOMA | Projects | Ecosyste.ms: Papers

10.1016/j.meteno.2015.04.001

Co-evolution of strain design methods based on flux balance and elementary mode analysis
Cited by: 66
Author(s): Daniel Machado, Markus J. Herrgård
Software Mentions: 1
Published: almost 9 years ago

10.3390/metabo2041090

Systematic Applications of Metabolomics in Metabolic Engineering
Cited by: 17
Author(s): Robert A. Dromms, Mark P. Styczynski
Software Mentions: 1
Published: almost 12 years ago

Improved vanillin production in baker's yeast through in silico design
Cited by: 227
Author(s): Ana Rita Brochado, Claudia Matos, Birger Lindberg Møller, Jörgen Hansen, Uffe Hasbro Mortensen, Kiran Raosaheb Patil
Software Mentions: 1
Published: about 14 years ago

10.1186/1475-2859-12-52

Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement
Cited by: 55
Author(s): Di Huang, Shanshan Li, Menglei Xia, Jianping Wen, Xiaoqiang Jia
Software Mentions: 1
Published: over 11 years ago

10.1186/1475-2859-11-101

Rational improvement of the engineered isobutanol-producing Bacillus subtilis by elementary mode analysis
Cited by: 52
Author(s): Shanshan Li, Di Huang, Yong Li, Jianping Wen, Xiaoqiang Jia
Software Mentions: 1
Published: over 12 years ago

10.1186/s12934-017-0787-5

Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus
Cited by: 23
Author(s): Junhua Wang, Cheng Wang, Kejing Song, Jianping Wen
Software Mentions: 1
Published: about 7 years ago

10.1186/s12934-016-0416-8

Designing intracellular metabolism for production of target compounds by introducing a heterologous metabolic reaction based on a Synechosystis sp. 6803 genome-scale model
Cited by: 15
Author(s): Toshiaki Shirai, Takashi Osanai, Akihiko Kondo
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1000744

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions
Cited by: 345
Author(s): Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pcbi.1005140

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
Cited by: 45
Author(s): Daniel Machado, Markus J. Herrgård, Isabel Rocha
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pcbi.0020072

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
Cited by: 118
Author(s): Markus J. Herrgård, Stephen S. Fong, Bernhard Ø. Palsson
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pcbi.1004434

Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
Cited by: 2
Author(s): Claudio Altafini, Giuseppe Facchetti
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.0030192

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli
Cited by: 82
Author(s): Osbaldo Resendis‐Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado‐Vides, Bernhard Ø. Palsson
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pcbi.1000308

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
Cited by: 192
Author(s): Vinay Satish Kumar, Costas D. Maranas
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1007310

p13CMFA: Parsimonious 13C metabolic flux analysis
Cited by: 9
Author(s): Carles Foguet, Anusha Jayaraman, Silvia Marín, Vitaly A. Selivanov, Pablo Moreno-Ger, Ramón Messeguer, Pedro de Atauri, Marta Cascante
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1000236

Spontaneous Reaction Silencing in Metabolic Optimization
Cited by: 42
Author(s): Takashi Nishikawa, Natali Gulbahce, Adilson E. Motter
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pcbi.0040036

Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens
Cited by: 73
Author(s): Daniel Segura, Radhakrishnan Mahadevan, Katy Juárez, Derek R. Lovley
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pcbi.1006687

Cellular determinants of metabolite concentration ranges
Cited by: 7
Author(s): Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1002047

Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis
Cited by: 56
Author(s): Yun Lee, Fang Chen, Lina Gallego‐Giraldo, Richard A. Dixon, Eberhard O. Voit
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1002363

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
Cited by: 314
Author(s): Ali R. Zomorrodi, Costas D. Maranas
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pcbi.1007319

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
Cited by: 27
Author(s): Charles Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0063707

Characterization of the Metabolic Requirements in Yeast Meiosis
Cited by: 13
Author(s): Debjit Ray, Ping Ye
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0191835

Predicting the accumulation of storage compounds by Rhodococcus jostii RHA1 in the feast-famine growth cycles using genome-scale flux balance analysis
Cited by: 11
Author(s): Mohammad Tajparast, Dominic Frigon
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0028503

Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer
Cited by: 89
Author(s): Kazimierz O. Wrzeszczyński, Vinay Varadan, James R. Byrnes, Elena Lum, Sitharthan Kamalakaran, Douglas A. Levine, Nevenka Dimitrova, Michael Q. Zhang, Robert Lucito
Software Mentions: 1
Published: almost 13 years ago

10.3390/cancers13030425

Cysteine and Folate Metabolism Are Targetable Vulnerabilities of Metastatic Colorectal Cancer
Cited by: 12
Author(s): Josep Tarragó‐Celada, Carles Foguet, Míriam Tarrado‐Castellarnau, Silvia Marín, Xavier Hernandez‐Alias, Jordi Perarnau, Fionnuala Morrish, David M. Hockenbery, Roger R. Gomis, Eytan Ruppin, Mariia Yuneva, Pedro de Atauri, Marta Cascante
Software Mentions: 1
Published: almost 4 years ago

10.3389/fbioe.2019.00033

New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering
Cited by: 140
Author(s): María Santos-Merino, Amit Kumar Singh, Daniel C. Ducat
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.03076

Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production
Cited by: 23
Author(s): Zhen Ma, Chao Ye, Weiwei Deng, Mengmeng Xu, Qiong Wang, Gao-Qiang Liu, Feng Wang, Liming Li, Zhenghong Xu, Guiyang Shi, Zhongyang Ding
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2017.02060

Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing
Cited by: 65
Author(s): Qiang Yan, Stephen S. Fong
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2017.02299

From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality
Cited by: 32
Author(s): Jan‐Ulrich Kreft, Caroline M. Plugge, Clara Prats, Johan H. J. Leveau, Weiwen Zhang, Ferdi L. Hellweger
Software Mentions: 1
Published: almost 7 years ago

Ecosyste.ms: Papers

Projects: bioconductor: MOMA

Papers Mentioning MOMA 128