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

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Cited 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: over 5 years ago

10.3390/metabo11040232

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
Cited 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 analysis
Cited 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 set
Cited 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: about 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 Pathogen
Cited 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 Bacteria
Cited 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: about 3 years ago

10.1186/s12896-021-00702-w

Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri
Cited by: 6
Author(s): Hao Luo, Peishun Li, Hao Wang, Stefan Roos, Boyang Ji, Jens Nielsen
Software Mentions: 2
Published: about 3 years ago

10.1039/d0mo00154f

Mechanistic models of microbial community metabolism
Cited by: 13
Author(s): Lillian Dillard, Dawson Payne, Jason A. Papin
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-69509-7

Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
Cited 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: about 4 years ago

10.1371/journal.pcbi.1006971

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Cited 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 Modeling
Cited 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