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: cran: BacArena
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/BacArena
Modeling Framework for Cellular Communities in their
Environments
9 versions
Latest release: over 4 years ago
Papers Mentioning BacArena 19
10.1186/s13059-021-02295-1
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic modelsCited by: 77
Author(s): Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
Software Mentions: 18
Published: over 3 years ago
10.1038/s41598-018-33733-z
Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicalsCited by: 14
Author(s): Matthew Perisin, Christian Sund
Software Mentions: 9
Published: about 6 years ago
10.3390/metabo9020022
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An OverviewCited by: 65
Author(s): Partho Sen, Matej Orešič
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pcbi.1005544
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communitiesCited by: 173
Author(s): Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta
Software Mentions: 4
Published: over 7 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
10.1038/s41396-019-0504-y
The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegansCited by: 62
Author(s): Johannes Zimmermann, Nancy Obeng, Wentao Yang, Barbara Pees, Carola Petersen, Silvio Waschina, Kohar Annie B. Kissoyan, Jack Aidley, Marc P. Hoeppner, Boyke Bunk, Cathrin Spröer, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
Software Mentions: 3
Published: about 5 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
10.3390/microorganisms8020197
Computational Modeling of the Human MicrobiomeCited by: 21
Author(s): Shomeek Chowdhury, Stephen S. Fong
Software Mentions: 2
Published: almost 5 years ago
10.1186/s40168-020-00955-1
Understanding the host-microbe interactions using metabolic modelingCited by: 32
Author(s): Jack Jansma, Sahar El Aidy
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-020-65659-w
ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial CommunitiesCited by: 18
Author(s): Emadoddin Karimian, Ehsan Motamedian
Software Mentions: 2
Published: over 4 years ago
10.1093/bioinformatics/bty561
FLYCOP: metabolic modeling-based analysis and engineering microbial communitiesCited by: 32
Author(s): Beatriz García-Jiménez, José Luis Sánchez García, Juan Nogales
Software Mentions: 2
Published: about 6 years ago
10.3389/fbioe.2020.00574
μBialSim: Constraint-Based Dynamic Simulation of Complex MicrobiomesCited by: 27
Author(s): Denny Popp, Florian Centler
Software Mentions: 1
Published: over 4 years ago
10.3389/fmolb.2021.634479
Metabolic Modeling to Interrogate Microbial Disease: A Tale for ExperimentalistsCited by: 6
Author(s): Fabrice Jean-Pierre, Michael A. Henson, George A. O’Toole
Software Mentions: 1
Published: over 3 years ago
10.1186/s40168-017-0299-x
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbesCited by: 47
Author(s): Kees C. H. van der Ark, Ruben G. A. van Heck, Vítor A. P. Martins dos Santos, Clara Belzer, Willem M. de Vos
Software Mentions: 1
Published: over 7 years ago
10.1016/j.csbj.2020.06.028
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomesCited by: 47
Author(s): Clémence Frioux, Dipali Singh, Tamás Korcsmáros, Falk Hildebrand
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pcbi.1007127
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)Cited by: 40
Author(s): Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or
Software Mentions: 1
Published: over 5 years ago
10.1016/j.csbj.2021.06.048
Modelling microbial communities: Harnessing consortia for biotechnological applicationsCited by: 18
Author(s): Maziya Ibrahim, Lavanya Raajaraam, Karthik Raman
Software Mentions: 1
Published: almost 4 years ago
10.1016/j.csbj.2020.11.035
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling toolsCited by: 14
Author(s): Álvaro Altamirano, Pedro A. Saa, Daniel Garrido
Software Mentions: 1
Published: almost 5 years ago
10.3390/microorganisms9020417
Agent Based Models of Polymicrobial Biofilms and the Microbiome—A ReviewCited by: 10
Author(s): Sherli Koshy-Chenthittayil, Linda Archambault, Dhananjai Senthilkumar, Reinhard Laubenbacher, Pedro Mendes, Anna Dongari-Bagtzoglou
Software Mentions: 1
Published: over 3 years ago