How accurate is automated gap filling of metabolic models?

Evaluation of reaction gap-filling accuracy by randomization

(2018) Mario Latendresse et al.   BMC BIOINFORMATICS

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries

(2018) Shu Pan et al.   CURRENT OPINION IN BIOTECHNOLOGY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

(2015) Peter D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

(2014) Leonid Chindelevitch et al.   Nature Communications

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

Ribonucleotide reductases: essential enzymes for bacterial life

(2014) Eduard Torrents   Frontiers in Cellular and Infection Microbiology

Robust flux balance analysis of multiscale biochemical reaction networks

(2013) Yuekai Sun et al.   BMC BIOINFORMATICS

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

The formate channel FocA exports the products of mixed-acid fermentation

(2012) W. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pathway Tools Pathway Prediction Algorithm

(2012) Peter D. Karp et al.   Standards in Genomic Sciences

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

(2012) Edward Vitkin et al.   GENOME BIOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Annotation-based inference of transporter function

(2008) Thomas J. Lee et al.   BIOINFORMATICS

Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov.

(2008) P. Mattarelli et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY