bioconductor: MOMA | Projects | Ecosyste.ms: Papers

10.1186/1752-0509-7-125

sybil – Efficient constraint-based modelling in R
Cited by: 105
Author(s): Gabriel Gelius-Dietrich, Abdelmoneim Amer Desouki, Claus Jonathan Fritzemeier, Martin J. Lercher
Software Mentions: 9
Published: about 11 years ago

10.3389/fbioe.2021.612893

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering
Cited by: 4
Author(s): Somtirtha Roy, Tijana Radivojević, Mark Forrer, Jose Manuel Martí, Vamshi Jonnalagadda, Tyler W. H. Backman, William Morrell, Hector Plahar, Joonhoon Kim, Nathan J. Hillson, Héctor García Martín
Software Mentions: 6
Published: almost 4 years ago

10.1128/mSystems.00230-18

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth
Cited by: 74
Author(s): A. Succurro, Daniel Segrè, Oliver Ebenhöh
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0147651

Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Cited by: 13
Author(s): Andrew S Krueger, Christian Munck, Gautam Dantas, George M. Church, James E. Galagan, Joseph Lehár, Morten Otto Alexander Sommer
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2105-11-213

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Cited by: 505
Author(s): Jan Schellenberger, Junyoung O. Park, Tom M Conrad, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 14 years ago

10.1186/s13059-021-02289-z

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
Cited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: almost 4 years ago

10.3389/fbioe.2020.00279

Dynamic Modeling of CHO Cell Metabolism Using the Hybrid Cybernetic Approach With a Novel Elementary Mode Analysis Strategy
Cited by: 13
Author(s): Juan A. Martínez, Dubhe Bulté, Martha A. Contreras, Laura A. Palomares, Octavio T. Ramı́rez
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.633073

In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products
Cited by: 2
Author(s): Albert Enrique Tafur Rangel, Wendy Ríos, Daisy Mejía, Carmen Ojeda, Richard A. Carlson, Jorge M. Gómez, Andrés Fernando González Barrios
Software Mentions: 3
Published: over 3 years ago

10.1093/gbe/evab125

Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System
Cited by: 9
Author(s): Carlos Santana-Molina, Fernando Gutiérrez, Damien P. Devos
Software Mentions: 3
Published: over 3 years ago

10.3390/metabo11020113

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases
Cited by: 2
Author(s): Julia Koblitz, Sabine Eva Will, S Alexander Riemer, Thomas Ulas, Meina Neumann‐Schaal, Dietmar Schomburg
Software Mentions: 3
Published: almost 4 years ago

10.1186/1752-0509-5-101

Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production
Cited by: 62
Author(s): Jong Myoung Park, Tae Yong Kim, Sang Yup Lee
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0098187

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue
Cited by: 277
Author(s): Jakob Hedegaard, Kasper Thorsen, Mette K. Lund, Anne-Mette K. Hein, Stephen Hamilton-Dutoit, Søren Vang, Iver Nordentoft, Karin Birkenkamp‐Demtröder, Mogens Kruhøffer, Henrik Hager, Bjarne Knudsen, Claus Lindbjerg Andersen, Karina D. Sørensen, Jakob Skou Pedersen, Torben F. Ørntoft, Lars Dyrskjøt
Software Mentions: 3
Published: over 10 years ago

10.3390/metabo10080303

Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis
Cited by: 42
Author(s): Svetlana Volkova, Marta R. A. Matos, Matthias Mattanovich, Igor Marín de Mas
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-47935-6

Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast
Cited by: 7
Author(s): Deya Alzoubi, Abdelmoneim Amer Desouki, Martin J. Lercher
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-63235-w

iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model
Cited by: 15
Author(s): Saeideh Khodaee, Yazdan Asgari, Mehdi Totonchi, Mohammad Hossein Karimi‐Jafari
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2393-13-246

Estimating the prevalence of obstetric fistula: a systematic review and meta-analysis
Cited by: 151
Author(s): Alma J Adler, Carine Ronsmans, Clara Calvert, Véronique Filippi
Software Mentions: 3
Published: almost 11 years ago

10.1042/EBC20180045

Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering
Cited by: 11
Author(s): Sophie Landon, Joshua Rees-Garbutt, Lucia Marucci, Claire Grierson
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms8111793

Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Cited by: 10
Author(s): Jinxin Zhao, Yan Zhu, Ji-Ru Han, Yu Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
Software Mentions: 3
Published: about 4 years ago

10.1186/1752-0509-6-71

i AK692: A genome-scale metabolic model of Spirulina platensis C1
Cited by: 35
Author(s): Amornpan Klanchui, Chiraphan Khannapho, Atchara Phodee, Supapon Cheevadhanarak, Asawin Meechai
Software Mentions: 2
Published: over 12 years ago

10.1186/s13059-016-0968-2

Mapping the landscape of metabolic goals of a cell
Cited by: 31
Author(s): Qi Zhao, Arion I. Stettner, Ed Reznik, Ioannis Ch. Paschalidis, Daniel Segrè
Software Mentions: 2
Published: over 8 years ago

10.1016/j.gpb.2017.07.002

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation
Cited by: 13
Author(s): Soheil Jahangiri, Limsoon Wong, Changiz Eslahchi
Software Mentions: 2
Published: almost 7 years ago

10.1093/gigascience/giy021

Genome-scale metabolic modeling of responses to polymyxins inPseudomonas aeruginosa
Cited by: 39
Author(s): Yan Zhu, Tobias Czauderna, Jinxin Zhao, Matthias Klapperstueck, Mohd Hafidz Mahamad Maifiah, Mei‐Ling Han, Jing Lü, Björn Sommer, Tony Velkov, Trevor Lithgow, Jiangning Song, Falk Schreiber, Jian Li
Software Mentions: 2
Published: over 6 years ago

10.1093/bioinformatics/btt364

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks
Cited by: 8
Author(s): Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-017-06918-1

Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production
Cited by: 20
Author(s): Heng Zhang, Chao Ye, Nan Xu, Chuntao Chen, Xiao Chen, Fanshu Yuan, Yunhua Xu, Jiazhi Yang, Dongping Sun
Software Mentions: 2
Published: over 7 years ago

10.1089/ast.2016.1551

The Mars Organic Molecule Analyzer (MOMA) Instrument: Characterization of Organic Material in Martian Sediments
Cited by: 164
Author(s): Fred Goesmann, W. B. Brinckerhoff, F. Raulin, W. Goetz, Ryan M. Danell, Stéphanie Getty, Sandra Siljeström, Helge Mißbach, Harald Steininger, Ricardo Arévalo, Arnaud Buch, Caroline Freissinet, Andrej Grubisic, Uwe J. Meierhenrich, V. Pinnick, Fabien Stalport, Cyril Szopa, Jorge L. Vago, Robert Lindner, Mitchell D. Schulte, J. R. Brucato, Daniel P. Glavin, N. Grand, Xiang Li, F. H. W. van Amerom
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.0010046

Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs
Cited by: 137
Author(s): Karthik Raman, P. T. Ravi Rajagopalan, Nagasuma Chandra
Software Mentions: 2
Published: about 19 years ago

10.1093/bioinformatics/btab013

MEWpy: a computational strain optimization workbench in Python
Cited by: 10
Author(s): Vítor Pereira, Fernando Cruz, Miguel Rocha
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-76302-z

Inhabited subsurface wet smectites in the hyperarid core of the Atacama Desert as an analog for the search for life on Mars
Cited by: 21
Author(s): Armando Azua‐Bustos, Alberto González Fairén, Carlos González-Silva, Daniel Carrizo, Miguel Ángel Fernández-Martínez, Cristián Arenas-Fajardo, M. Fernández-Sampedro, Carolina Gil-Lozano, Laura Sánchez-García, Carmen Ascaso, Jacek Wierzchoś, E. B. Rampe
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-80561-1

Exploring gene knockout strategies to identify potential drug targets using genome-scale metabolic models
Cited by: 10
Author(s): Abhijit Paul, Rajat Anand, Sonali Porey Karmakar, Surender Rawat, Nandadulal Bairagi, Samrat Chatterjee
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1008125

In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli
Cited by: 7
Author(s): Laura de Arroyo Garcia, Patrik R. Jones
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-84114-y

Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism
Cited by: 5
Author(s): Christopher Pries, Zahra Razaghi-Moghadam, Joachim Kopka, Zoran Nikoloski
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/bts401

Random sampling of elementary flux modes in large-scale metabolic networks
Cited by: 68
Author(s): Daniel Machado, Zita Soons, Kiran Raosaheb Patil, Eugénio C. Ferreira, Isabel Rocha
Software Mentions: 2
Published: about 12 years ago

10.1186/1752-0509-4-45

OptFlux: an open-source software platform for in silico metabolic engineering
Cited by: 324
Author(s): Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha
Software Mentions: 2
Published: over 14 years ago

10.1128/mSystems.00157-18

Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
Cited by: 28
Author(s): Yan Zhu, Jinxin Zhao, Mohd Hafidz Mahamad Maifiah, Tony Velkov, Falk Schreiber, Jian Li
Software Mentions: 2
Published: over 5 years ago

10.1186/1752-0509-4-156

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
Cited by: 102
Author(s): Arnau Montagud, Emilio Navarro, Pedro Fernández de Córdoba, Javier F. Urchueguı́a, Kiran Raosaheb Patil
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pcbi.1004363

A Method to Constrain Genome-Scale Models with 13C Labeling Data
Cited by: 51
Author(s): Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam P. Arkin, Jay D. Keasling
Software Mentions: 2
Published: about 9 years ago

10.1186/s12918-015-0190-y

Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition
Cited by: 24
Author(s): Mohammad Tajparast, Dominic Frigon
Software Mentions: 2
Published: over 9 years ago

10.1186/s13068-017-0709-0

Efficient estimation of the maximum metabolic productivity of batch systems
Cited by: 8
Author(s): Peter C. St. John, Michael F. Crowley, Yannick J. Bomble
Software Mentions: 2
Published: almost 8 years ago

10.1089/ast.2016.1533

Habitability on Early Mars and the Search for Biosignatures with the ExoMars Rover
Cited by: 350
Author(s): Jorge L. Vago, Francès Westall, A. J. Coates, R. Jaumann, Oleg Korablev, Valérie Ciarletti, И. Г. Митрофанов, Jean-Luc Josset, M. C. De Sanctis, Jean‐Pierre Bibring, Fernando Rull, Fred Goesmann, Harald Steininger, W. Goetz, W. B. Brinckerhoff, Cyril Szopa, F. Raulin, Howell G. M. Edwards, Lyle G. Whyte, Alberto González Fairén, J. C. Bridges, Ernst Hauber, G. G. Ori, Stéphanie C. Werner, D. Loizeau, R. O. Kuzmin, R. M. E. Williams, J. Flahaut, F. Forget, D. Rodionov, H. Svedhem, E. Sefton‐Nash, Gerhard Kminek, L. Lorenzoni, Luc Joudrier, В. А. Михайлов, Alexander Zashchirinskiy, S. Alexashkin, F. Calantropio, Andrea Merlo, Pantelis Poulakis, Olivier Witasse, Olivier Bayle, Silvia Bayón, Uwe J. Meierhenrich, John Carter, Juan Manuel García‐Ruiz, P. Baglioni, A. F. C. Haldemann, Andrew Ball, A. Debus, Robert Lindner, Frédéric Haessig, D. Monteiro, R. Trautner, Christoph Voland, Pierre Rebeyre, D. Goulty, F. Didot, Stephen Durrant, Eric Zekri, D. Koschny, Andrea De Toni, Gianfranco Visentin, Martin Zwick, M. van Winnendael, Martín Azkarate, Christophe Carreau
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-9-499

Natural computation meta-heuristics for the in silico optimization of microbial strains
Cited by: 101
Author(s): Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12859-014-0420-0

An integrated network visualization framework towards metabolic engineering applications
Cited by: 6
Author(s): Alberto Noronha, Paulo Vilaça, Miguel Rocha
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1000329

Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak?
Cited by: 76
Author(s): Zhi Wang, Jianzhi Zhang
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12918-017-0515-0

OptPipe - a pipeline for optimizing metabolic engineering targets
Cited by: 13
Author(s): András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie‐France Sagot, Jan Marienhagen, Susana Vinga
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12918-014-0137-8

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina
Cited by: 64
Author(s): Chao Ye, Nan Xu, Haiqin Chen, Yong Q. Chen, Wei Chen, Li Liu
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0043401

Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus
Cited by: 41
Author(s): Thomas Ulas, S Alexander Riemer, Melanie Zaparty, Bettina Siebers, Dietmar Schomburg
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0024162

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques
Cited by: 78
Author(s): Joonhoon Kim, Jennifer L. Reed, Christos T. Maravelias
Software Mentions: 2
Published: about 13 years ago

10.5936/csbj.201210006

DEVELOPING A YEAST CELL FACTORY FOR THE PRODUCTION OF TERPENOIDS
Cited by: 53
Author(s): Sotirios C. Kampranis, Antonios M. Makris
Software Mentions: 2
Published: about 12 years ago

10.5936/csbj.201210016

EMERGING ENGINEERING PRINCIPLES FOR YIELD IMPROVEMENT IN MICROBIAL CELL DESIGN
Cited by: 9
Author(s): Santiago Comba, Ana Arabolaza, Hugo Gramajo
Software Mentions: 2
Published: about 12 years ago

10.3389/fmicb.2013.00200

Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast
Cited by: 11
Author(s): Ashok Misra, Matthew F. Conway, Joseph Johnnie, Tabish M. Qureshi, Bao Lige, Anne M. Derrick, Eddy Chukwura Agbo, Ganesh Sriram
Software Mentions: 2
Published: almost 12 years ago

10.1186/1752-0509-5-91

Analysis of complex metabolic behavior through pathway decomposition
Cited by: 24
Author(s): Kuhn Ip, Caroline Colijn, Desmond S. Lun
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-016-3311-0

Modelling microbial metabolic rewiring during growth in a complex medium
Cited by: 12
Author(s): Marco Fondi, Emanuele Bosi, Luana Presta, Diletta Natoli, Renato Fani
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-12-28

FASIMU: flexible software for flux-balance computation series in large metabolic networks
Cited by: 57
Author(s): Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann−Georg Holzhütter
Software Mentions: 2
Published: almost 14 years ago

10.3390/microorganisms7040101

Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria
Cited by: 8
Author(s): Sabina Żołędowska, Luana Presta, Marco Fondi, Francesca Decorosi, Luciana Giovannetti, Alessio Mengoni, Ewa Łojkowska
Software Mentions: 2
Published: over 5 years ago

10.15252/msb.20177739

An integrated computational and experimental study uncovers <scp>FUT</scp> 9 as a metabolic driver of colorectal cancer
Cited by: 35
Author(s): Noam Auslander, Chelsea E. Cunningham, Behzad M. Toosi, Emily McEwen, Keren Yizhak, Frederick S. Vizeacoumar, Sreejit Parameswaran, N Gonen, Tanya Freywald, Kalpana K. Bhanumathy, Andrew Freywald, Franco J. Vizeacoumar, Eytan Ruppin
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1008185

Genetic buffering and potentiation in metabolism
Cited by: 4
Author(s): Juan F. Poyatos
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2017.02290

Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium
Cited by: 4
Author(s): Miguel Ponce-de-León, Daniel Tamarit, Jorge Calle-Espinosa, Matteo Mori, Amparo Latorre, Francisco Montero, Juli Peretó
Software Mentions: 1
Published: almost 7 years ago

10.3389/fonc.2014.00046

Evidence for a Functional Link between Chromosomal Breakpoints and Aberrant DNA Methylation in Cancer
Cited by: 4
Author(s): Sven Bilke, Yevgeniy Gindin
Software Mentions: 1
Published: over 10 years ago

10.3389/fonc.2012.00197

Major Chromosomal Breakpoint Intervals in Breast Cancer Co-Localize with Differentially Methylated Regions
Cited by: 30
Author(s): Man-Hung Eric Tang, Vinay Varadan, Sitharthan Kamalakaran, Michael Q. Zhang, Nevenka Dimitrova, James Hicks
Software Mentions: 1
Published: almost 13 years ago

10.3389/fpls.2015.00049

Integration of metabolomics data into metabolic networks
Cited by: 45
Author(s): Nadine Töpfer, Sabrina Kleeßen, Zoran Nikoloski
Software Mentions: 1
Published: almost 10 years ago

10.3389/fpls.2020.00325

The Geomagnetic Field Is a Contributing Factor for an Efficient Iron Uptake in Arabidopsis thaliana
Cited by: 15
Author(s): Monirul Islam, Massimo E. Maffei, Gianpiero Vigani
Software Mentions: 1
Published: over 4 years ago

10.1186/gb-2008-9-9-r140

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions
Cited by: 51
Author(s): Evan S. Snitkin, Andrew T. Dudley, Daniel M. Janse, Kaisheen Wong, George M. Church, Daniel Segrè
Software Mentions: 1
Published: almost 17 years ago

10.1186/gb-2012-13-9-r78

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
Cited by: 80
Author(s): Joonhoon Kim, Jennifer L. Reed
Software Mentions: 1
Published: almost 13 years ago

10.3390/polym10060653

Crystal Orientation of Poly(l-Lactic Acid) Induced by Magnetic Alignment of a Nucleating Agent
Cited by: 5
Author(s): Ryosuke Kusumi, Sachi Teranishi, Fumiko Kimura, Masahisa Wada, Tsunehisa Kimura, Yoshiki Horikawa, Tadakazu Kawai
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-66240-1

ORIGIN: a novel and compact Laser Desorption – Mass Spectrometry system for sensitive in situ detection of amino acids on extraterrestrial surfaces
Cited by: 23
Author(s): N. F. W. Ligterink, Valentine Grimaudo, Pavel Moreno‐García, Rustam Lukmanov, Marek Tulej, I. Leya, Robert Lindner, Peter Würz, Charles S. Cockell, P. Ehrenfreund, Andreas Riedo
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-68715-7

Investigating the biological potential of galactic cosmic ray-induced radiation-driven chemical disequilibrium in the Martian subsurface environment
Cited by: 4
Author(s): Dimitra Atri
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-73846-y

ExoMars Raman Laser Spectrometer (RLS): development of chemometric tools to classify ultramafic igneous rocks on Mars
Cited by: 22
Author(s): Marco Veneranda, Guillermo López‐Reyes, José Antonio Manrique, Aurelio Sanz‐Arranz, E.A. Lalla, Menelaos Konstantinidis, Andoni Moral, Jesús Medina, Fernando Rull
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-81014-z

ExoFiT trial at the Atacama Desert (Chile): Raman detection of biomarkers by representative prototypes of the ExoMars/Raman Laser Spectrometer
Cited by: 9
Author(s): Marco Veneranda, Guillermo López‐Reyes, Jesús Sáiz, José Antonio Manrique, Aurelio Sanz‐Arranz, Jesús Medina, Andoni Moral, Laura Seoane, S. Ibarmia, Fernando Rull
Software Mentions: 1
Published: almost 4 years ago

10.3390/s18124264

Sensor Distribution Optimization for Structural Impact Monitoring Based on NSGA-II and Wavelet Decomposition
Cited by: 10
Author(s): Peng Li, Liuwei Huang, Jiachao Peng
Software Mentions: 1
Published: almost 6 years ago

10.1186/1742-4682-4-48

Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia
Cited by: 72
Author(s): Tunahan Çakır, Selma Alsan, Hale Saybaşιlι, Ata Akın, Kutlu Ö. Ülgen
Software Mentions: 1
Published: almost 17 years ago

10.7554/eLife.03641

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer
Cited by: 108
Author(s): Keren Yizhak, Edoardo Gaude, Sylvia E. Le Dévédec, Yedael Y. Waldman, Gideon Y. Stein, Bob van de Water, Christian Frezza, Eytan Ruppin
Software Mentions: 1
Published: about 10 years ago

10.3390/ijms21217903

The Microenvironment of Decellularized Extracellular Matrix from Heart Failure Myocardium Alters the Balance between Angiogenic and Fibrotic Signals from Stromal Primitive Cells
Cited by: 13
Author(s): Immacolata Belviso, Francesco Angelini, Franca Di Meglio, Vittorio Picchio, Anna Maria Sacco, Cristina Nocella, Veronica Romano, Daria Nurzynska, Giacomo Frati, Ciro Maiello, Elisa Messina, Stefania Montagnani, Francesca Pagano, Clotilde Castaldo, Isotta Chimenti
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms22137192

Systematic Understanding of Recent Developments in Bacterial Cellulose Biosynthesis at Genetic, Bioprocess and Product Levels
Cited by: 13
Author(s): Gizem Buldum, Athanasios Mantalaris
Software Mentions: 1
Published: over 3 years ago

10.1089/ast.2018.1868

Functional Properties of Amino Acid Side Chains as Biomarkers of Extraterrestrial Life
Cited by: 23
Author(s): Christos D. Georgiou
Software Mentions: 1
Published: about 6 years ago

10.1016/j.isci.2020.101818

A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria
Cited by: 27
Author(s): Supreeta Vijayakumar, Pattanathu Rahman, Claudio Angione
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-018-2352-6

Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd
Cited by: 9
Author(s): Takeyuki Tamura
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2105-14-S2-S17

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints
Cited by: 45
Author(s): Shaogang Ren, Bo Zeng, Xiaoning Qian
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-6-308

Evolutionary programming as a platform for in silico metabolic engineering
Cited by: 398
Author(s): Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen
Software Mentions: 1
Published: almost 19 years ago

10.1186/s12859-015-0866-8

Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner
Cited by: 3
Author(s): Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos, Francisco S. Melo
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-14-344

Partial inhibition and bilevel optimization in flux balance analysis
Cited by: 5
Author(s): Giuseppe Facchetti, Claudio Altafini
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-9-97

Using a logical model to predict the growth of yeast
Cited by: 20
Author(s): Ken Whelan, Ross D. King
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12864-015-2042-y

Reconstruction and analysis of the genome-scale metabolic model of schizochytrium limacinum SR21 for docosahexaenoic acid production
Cited by: 40
Author(s): Chao Ye, Weihua Qiao, Xiaobin Yu, Xiao‐Jun Ji, He Huang, Jackie L. Collier, Li Liu
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2180-5-39

Modeling Lactococcus lactis using a genome-scale flux model
Cited by: 227
Author(s): Ana Paula Oliveira, Jens Nielsen, Jochen Förster
Software Mentions: 1
Published: over 19 years ago

10.1186/1752-0509-5-145

Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects
Cited by: 18
Author(s): Wu‐Hsiung Wu, Feng Sheng Wang, Mau Song Chang
Software Mentions: 1
Published: about 13 years ago

10.1186/1752-0509-6-S1-S11

Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example
Cited by: 1
Author(s): Rudong Li, Lei Liu
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-6-16

Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations
Cited by: 29
Author(s): Sabrina Kleeßen, Zoran Nikoloski
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-7-98

An objective function exploiting suboptimal solutions in metabolic networks
Cited by: 26
Author(s): Edwin H. Wintermute, Tami D. Lieberman, Pamela A. Silver
Software Mentions: 1
Published: almost 12 years ago

10.1186/1752-0509-6-8

FAME, the Flux Analysis and Modeling Environment
Cited by: 73
Author(s): Joost Boele, Brett G. Olivier, Bas Teusink
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12918-014-0086-2

Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca
Cited by: 17
Author(s): Niti Vanee, J. Paul Brooks, Victor Spicer, Dmitriy Shamshurin, Oleg V. Krokhin, John A. Wilkins, Yu Deng, Stephen S. Fong
Software Mentions: 1
Published: over 10 years ago

10.1002/bem.22123

Reduction of the geomagnetic field delaysArabidopsis thalianaflowering time through downregulation of flowering-related genes
Cited by: 34
Author(s): Chiara Agliassa, Ravishankar Narayana, Cinzia M. Bertea, Christopher T. Rodgers, Massimo E. Maffei
Software Mentions: 1
Published: over 6 years ago

10.1002/bies.200900128

Improved network performance via antagonism: From synthetic rescues to multi‐drug combinations
Cited by: 33
Author(s): Adilson E. Motter
Software Mentions: 1
Published: almost 15 years ago

10.1093/bioinformatics/bty1065

Characterizing and ranking computed metabolic engineering strategies
Cited by: 15
Author(s): Philipp Schneider, Steffen Klamt
Software Mentions: 1
Published: almost 6 years ago

10.1093/bioinformatics/btaa163

NIHBA: a network interdiction approach for metabolic engineering design
Cited by: 6
Author(s): Shouyong Jiang, Yong Wang, Marcus Kaiser, Natalio Krasnogor
Software Mentions: 1
Published: over 4 years ago

10.3390/biology9020030

Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness
Cited by: 6
Author(s): Michel Lavoie, Blanche Saint-Béat, Jan Strauss, Sébastien Guérin, Antoine Allard, Simon Hardy, Angela Falciatore, Johann Lavaud
Software Mentions: 1
Published: almost 5 years ago

10.1093/biostatistics/kxu030

Joint synthesis of multiple correlated outcomes in networks of interventions
Cited by: 33
Author(s): Orestis Efthimiou, Dimitris Mavridis, Richard D Riley, Andrea Cipriani, Georgia Salanti
Software Mentions: 1
Published: over 10 years ago

10.1186/s13068-015-0291-2

Model-driven intracellular redox status modulation for increasing isobutanol production in Escherichia coli
Cited by: 29
Author(s): Jiao Liu, Haishan Qi, Wang Cheng, Jianping Wen
Software Mentions: 1
Published: over 9 years ago

10.1186/s13068-018-1028-9

Mathematical models of lignin biosynthesis
Cited by: 28
Author(s): Mojdeh Faraji, Luís L. Fonseca, Luis L. Escamilla‐Treviño, Jaime Barros-Ríos, Nancy L. Engle, Zamin K. Yang, Timothy J. Tschaplinski, Richard A. Dixon, Eberhard O. Voit
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13068-019-1518-4

In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling
Cited by: 30
Author(s): Minsuk Kim, Beom Gi Park, Eun-Jung Kim, Joonwon Kim, Byung‐Gee Kim
Software Mentions: 1
Published: over 5 years ago

10.3390/life5021127

Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality
Cited by: 13
Author(s): Hyun‐Seob Song, Ryan McClure, Hans C. Bernstein, Christopher C. Overall, Eric A. Hill, Alex Beliaev
Software Mentions: 1
Published: over 9 years ago

10.3390/life4040535

Biota and Biomolecules in Extreme Environments on Earth: Implications for Life Detection on Mars
Cited by: 28
Author(s): Joost W. Aerts, Wilfred F. M. Röling, Andreas Elsaesser, P. Ehrenfreund
Software Mentions: 1
Published: about 10 years ago

10.3390/life10110299

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels
Cited by: 15
Author(s): Maria Priscila Franco Lacerda, Eun‐Suok Oh, Carrie A. Eckert
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: MOMA

Papers Mentioning MOMA 128