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: BOFdat
https://packages.ecosyste.ms/registries/pypi.org/packages/BOFdat
Package to generate biomass objective function stoichiometric coefficients from experimental data
7 versions
Latest release: about 5 years ago
17 downloads last month
Papers Mentioning BOFdat 11
10.1371/journal.pcbi.1006644
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media typesCited by: 35
Author(s): Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared T. Broddrick, Karsten Zengler, Jaehyung Kim
Software Mentions: 7
Published: almost 6 years ago
10.3390/metabo11040232
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple AuxotrophiesCited by: 7
Author(s): Alina Renz, Lina Widerspick, Andreas Dräger
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-021-02289-z
Addressing uncertainty in genome-scale metabolic model reconstruction and analysisCited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: over 3 years ago
10.15252/msb.202010099
Genome‐scale metabolic modeling reveals key features of a minimal gene setCited by: 12
Author(s): Jean-Christophe Lachance, Dominick Matteau, Joëlle Brodeur, Colton J. Lloyd, Nathan Mih, Zachary A. King, Thomas F. Knight, Adam M. Feist, Jonathan M. Monk, Jaehyung Kim, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.00116
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic PathogenCited by: 9
Author(s): Christian Salgård Jensen, Charles J. Norsigian, Xin Fang, Xiaohui Chen Nielsen, Jens Jørgen Christensen, Bernhard Ø. Palsson, Jonathan M. Monk
Software Mentions: 2
Published: over 4 years ago
10.3390/metabo11080491
Modelling hCDKL5 Heterologous Expression in BacteriaCited by: 5
Author(s): Marco Fondi, Stefano Gonzi, Mikołaj Dziurzyński, Paola Turano, Veronica Ghini, Marzia Calvanese, Andrea Colarusso, Concetta Lauro, Ermenegilda Parrilli, Maria Luisa Tutino
Software Mentions: 2
Published: over 3 years ago
10.1186/s12896-021-00702-w
Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteriCited by: 6
Author(s): Hao Luo, Peishun Li, Hao Wang, Stefan Roos, Boyang Ji, Jens Nielsen
Software Mentions: 2
Published: over 3 years ago
10.1039/d0mo00154f
Mechanistic models of microbial community metabolismCited by: 13
Author(s): Lillian Dillard, Dawson Payne, Jason A. Papin
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-020-69509-7
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediationCited by: 17
Author(s): Shany Ofaim, Raphy Zarecki, Seema Porob, Daniella Gat, Tamar Lahav, Yechezkel Kashi, Radi Aly, Hanan Eizenberg, Zeev Ronen, Shiri Freilich
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pcbi.1006971
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental dataCited by: 69
Author(s): Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence T. Yang, Anand V. Sastry, Yara Seif, Jaehyung Kim, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques
Software Mentions: 1
Published: over 5 years ago
10.3389/fbioe.2021.602464
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic ModelingCited by: 5
Author(s): Kusum Dhakar, Raphy Zarecki, Daniella van Bommel, Nadav Knossow, Shlomit Medina, Başak Öztürk, Radi Aly, Hanan Eizenberg, Zeev Ronen, Shiri Freilich
Software Mentions: 1
Published: over 3 years ago