ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species

Contaminant accumulation and biological responses in Atlantic cod (Gadus morhua) caged at a capped waste disposal site in Kollevåg, Western Norway

(2019) Karina Dale et al.   MARINE ENVIRONMENTAL RESEARCH

Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio

(2019) Leonie van Steijn et al.   Zebrafish

BioModels—15 years of sharing computational models in life science

(2019) Rahuman S Malik-Sheriff et al.   NUCLEIC ACIDS RESEARCH

Molecular and Functional Properties of the Atlantic Cod (Gadus morhua) Aryl Hydrocarbon Receptors Ahr1a and Ahr2a

(2019) Libe Aranguren-Abadía et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

RNA-Seq analysis of transcriptome responses in Atlantic cod ( Gadus morhua ) precision-cut liver slices exposed to benzo[ a ]pyrene and 17α-ethynylestradiol

(2018) Fekadu Yadetie et al.   AQUATIC TOXICOLOGY

Whole genome duplications have provided teleosts with many roads to peptide loaded MHC class I molecules

(2018) Unni Grimholt   BMC EVOLUTIONARY BIOLOGY

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Ocean science research is key for a sustainable future

(2018) Martin Visbeck   Nature Communications

Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models

(2018) Méziane Aite et al.   PLoS Computational Biology

The Divergent Genomes of Teleosts

(2018) Vydianathan Ravi et al.   Annual Review of Animal Biosciences

Independent losses of a xenobiotic receptor across teleost evolution

(2018) Marta Eide et al.   Scientific Reports

Automated generation of genome-scale metabolic draft reconstructions based on KEGG

(2018) Emil Karlsen et al.   BMC BIOINFORMATICS

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

Little Fish, Big Data: Zebrafish as a Model for Cardiovascular and Metabolic Disease

(2017) Philipp Gut et al.   PHYSIOLOGICAL REVIEWS

Model-based quantification of metabolic interactions from dynamic microbial-community data

(2017) Mark Hanemaaijer et al.   PLoS One

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

(2017) Sylvain Prigent et al.   PLoS Computational Biology

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

(2016) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

(2015) Zachary A. King et al.   PLoS Computational Biology

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu 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

The emerging use of zebrafish to model metabolic disease

(2013) A. Seth et al.   Disease Models & Mechanisms

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation

(2012) Michaël Bekaert   PLoS One

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Constructing a fish metabolic network model

(2012) Shuzhao Li et al.   GENOME BIOLOGY

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

(2012) Edward Vitkin et al.   GENOME BIOLOGY

Mass spectrometric analyses of microsomal cytochrome P450 isozymes isolated from β-naphthoflavone-treated Atlantic cod (Gadus morhua) liver reveal insights into the cod CYPome

(2011) Odd André Karlsen et al.   AQUATIC TOXICOLOGY

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

An integrative approach towards completing genome-scale metabolic networks

(2009) Nils Christian et al.   Molecular BioSystems

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

PXR and CAR in energy metabolism

(2009) Taira Wada et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology