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

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Cited 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 chemicals
Cited by: 14
Author(s): Matthew Perisin, Christian Sund
Software Mentions: 9
Published: almost 6 years ago

10.3390/metabo9020022

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
Cited by: 65
Author(s): Partho Sen, Matej Orešič
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1005544

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Cited 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 Auxotrophies
Cited 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 elegans
Cited 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 metabolism
Cited by: 13
Author(s): Lillian Dillard, Dawson Payne, Jason A. Papin
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8020197

Computational Modeling of the Human Microbiome
Cited by: 21
Author(s): Shomeek Chowdhury, Stephen S. Fong
Software Mentions: 2
Published: over 4 years ago

10.1186/s40168-020-00955-1

Understanding the host-microbe interactions using metabolic modeling
Cited by: 32
Author(s): Jack Jansma, Sahar El Aidy
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-65659-w

ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
Cited 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 communities
Cited 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 Microbiomes
Cited 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 Experimentalists
Cited 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 microbes
Cited 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: about 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 genomes
Cited by: 47
Author(s): Clémence Frioux, Dipali Singh, Tamás Korcsmáros, Falk Hildebrand
Software Mentions: 1
Published: over 4 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 applications
Cited by: 18
Author(s): Maziya Ibrahim, Lavanya Raajaraam, Karthik Raman
Software Mentions: 1
Published: over 3 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 tools
Cited by: 14
Author(s): Álvaro Altamirano, Pedro A. Saa, Daniel Garrido
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms9020417

Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review
Cited 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