Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: efmtool

https://packages.ecosyste.ms/registries/pypi.org/packages/efmtool

Python wrapper for efmtool
7 versions
Latest release: almost 2 years ago
1 dependent package
138 downloads last month

Papers Mentioning efmtool 27

How important is thermodynamics for identifying elementary flux modes?
Cited by: 21
Author(s): Sabine Pérès, Mario Jolicœur, C. Moulin, Philippe Dague, Stefan Schuster
Software Mentions: 3
Published: almost 8 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

10.1186/s12934-016-0470-2

Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Cited by: 68
Author(s): Véronique Beckers, Ignacio Poblete‐Castro, Jürgen Tomasch, Christoph Wittmann
Software Mentions: 3
Published: over 8 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: over 12 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

10.1016/j.patter.2020.100177

Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks
Cited by: 9
Author(s): Tom J. Clement, Erik B. Baalhuis, Bas Teusink, Frank J. Bruggeman, Robert Planqué, Daan H. de Groot
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12918-018-0589-3

Dynamic elementary mode modelling of non-steady state flux data
Cited by: 7
Author(s): Abel Folch-Fortuny, Bas Teusink, Huub C. J. Hoefsloot, Age K. Smilde, Alberto Ferrer
Software Mentions: 2
Published: over 6 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

10.1186/1748-7188-7-17

Analysis of Metabolic Subnetworks by Flux Cone Projection
Cited by: 31
Author(s): Sayed-Amir Marashi, László Dávid, Alexander Bockmayr
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0023026

Predicting the Physiological Role of Circadian Metabolic Regulation in the Green Alga Chlamydomonas reinhardtii
Cited by: 7
Author(s): Sascha Schäuble, Ines Heiland, Olga Voytsekh, Maria Mittag, Stefan Schuster
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.1005590

Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes
Cited by: 24
Author(s): Caroline Baroukh, Violette Turon, Olivier Bernard
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1004235

Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
Cited by: 8
Author(s): Thomas P. Prescott, Moritz Lang, Antonis Papachristodoulou
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0129840

Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs
Cited by: 16
Author(s): Christian Jungreuthmayer, David E. Ruckerbauer, Matthias P. Gerstl, Michael Hanscho, Jürgen Zanghellini
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0061648

Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes
Cited by: 16
Author(s): Zita Soons, Eugénio C. Ferreira, Kiran Raosaheb Patil, Isabel Rocha
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0077617

Metabolic Proximity in the Order of Colonization of a Microbial Community
Cited by: 32
Author(s): Varun Mazumdar, Salomon Amar, Daniel Segrè
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0104499

DRUM: A New Framework for Metabolic Modeling under Non-Balanced Growth. Application to the Carbon Metabolism of Unicellular Microalgae
Cited by: 58
Author(s): Caroline Baroukh, Rafael Muñoz-Tamayo, Jean‐Philippe Steyer, Olivier Bernard
Software Mentions: 1
Published: over 10 years ago

10.1186/1748-7188-7-15

Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem
Cited by: 24
Author(s): Sylvain Soliman
Software Mentions: 1
Published: over 12 years ago

10.1038/srep08930

Metabolomics integrated elementary flux mode analysis in large metabolic networks
Cited by: 48
Author(s): Matthias P. Gerstl, David E. Ruckerbauer, Diethard Mattanovich, Christian Jungreuthmayer, Jürgen Zanghellini
Software Mentions: 1
Published: almost 10 years ago

10.1007/s00253-015-6743-6

Macroscopic modeling of mammalian cell growth and metabolism
Cited by: 46
Author(s): Bassem Ben Yahia, Laetitia Malphettes, Elmar Heinzle
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-014-0410-2

Identifying target processes for microbial electrosynthesis by elementary mode analysis
Cited by: 79
Author(s): Frauke Kracke, Jens O. Krömer
Software Mentions: 1
Published: about 10 years ago

10.1186/s12918-014-0094-2

A depth-first search algorithm to compute elementary flux modes by linear programming
Cited by: 26
Author(s): Lake‐Ee Quek, Lars K. Nielsen
Software Mentions: 1
Published: over 10 years ago

10.1186/1752-0509-7-29

Probabilistic strain optimization under constraint uncertainty
Cited by: 7
Author(s): Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun
Software Mentions: 1
Published: over 11 years ago

10.1186/1752-0509-6-103

Designing optimal cell factories: integer programming couples elementary mode analysis with regulation
Cited by: 27
Author(s): Christian Jungreuthmayer, Jürgen Zanghellini
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12918-018-0632-4

Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production
Cited by: 6
Author(s): Juan A. Martínez, Alberto Rodríguez, Fabián Moreno, Noemí Flores, Alvaro R. Lara, Octavio T. Ramı́rez, Guillermo Gosset, Francisco Bolívar
Software Mentions: 1
Published: about 6 years ago

10.1186/s12918-016-0347-3

In silico metabolic network analysis of Arabidopsis leaves
Cited by: 11
Author(s): Véronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver E. Bläsing, Regine Fuchs, Thomas Ehrhardt, Christoph Wittmann
Software Mentions: 1
Published: about 8 years ago

10.1186/1752-0509-6-10

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
Cited by: 63
Author(s): Pablo Carbonell, Davide Fichera, Shashi Bhushan Pandit, Jean-Loup Faulon
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pcbi.1006759

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion
Cited by: 29
Author(s): Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt
Software Mentions: 1
Published: almost 6 years ago