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: sybil

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/sybil

Efficient Constrained Based Modelling
20 versions
Latest release: over 3 years ago
9 dependent packages

Papers Mentioning sybil 12

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

10.1186/1752-0509-7-125

sybil – Efficient constraint-based modelling in R
Cited by: 105
Author(s): Gabriel Gelius-Dietrich, Abdelmoneim Amer Desouki, Claus Jonathan Fritzemeier, Martin J. Lercher
Software Mentions: 9
Published: almost 11 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: about 6 years ago

10.1371/journal.pone.0236890

Defining the nutritional input for genome-scale metabolic models: A roadmap
Cited by: 21
Author(s): Γεώργιος Μαρίνος, Christoph Kaleta, Silvio Waschina
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0119016

Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain
Cited by: 17
Author(s): Anand Gavai, Farahaniza Supandi, Hannes Hettling, Paul Murrell, Jack A. M. Leunissen, Hans van Beek
Software Mentions: 7
Published: over 9 years ago

10.1186/s12918-014-0130-2

MetaNET - a web-accessible interactive platform for biological metabolic network analysis
Cited by: 8
Author(s): Pankaj Narang, Shawez Khan, Anmol Jaywant Hemrom, Andrew M. Lynn
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pcbi.1009157

Data integration uncovers the metabolic bases of phenotypic variation in yeast
Cited by: 2
Author(s): Marianyela Petrizzelli, Dominique de Vienne, Thibault Nidelet, Camille Noûs, Christine Dillmann
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1005036

Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
Cited by: 23
Author(s): Daniel Hartleb, Florian Jarre, Martin J. Lercher
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-47935-6

Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast
Cited by: 7
Author(s): Deya Alzoubi, Abdelmoneim Amer Desouki, Martin J. Lercher
Software Mentions: 3
Published: about 5 years ago

10.1186/s13068-016-0665-0

Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction
Cited by: 19
Author(s): Sandra Castillo, Dorothee Barth, Mikko Arvas, Tiina Pakula, Esa Pitkänen, Peter Blomberg, Tuulikki Seppänen‐Laakso, Heli Nygrén, Dhinakaran Sivasiddarthan, Merja Penttilä, Merja Oja
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.biotechadv.2018.10.004

Synthetic biology tools for engineering Yarrowia lipolytica
Cited by: 108
Author(s): Macarena Larroude, Tristan Rossignol, Jean‐Marc Nicaud, Rodrigo Ledesma-Amaro
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-018-35092-1

Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations
Cited by: 5
Author(s): Deya Alzoubi, Abdelmoneim Amer Desouki, Martin J. Lercher
Software Mentions: 2
Published: almost 6 years ago