Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

Predicting Dynamic Metabolic Demands in the Photosynthetic EukaryoteChlorella vulgaris

(2017) Cristal Zuñiga et al.   PLANT PHYSIOLOGY

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

(2017) Ke Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

(2017) Natalie Millán-Aguiñaga et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

(2016) Maike K. Aurich et al.   Frontiers in Physiology

Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation

(2015) C. A. Contador et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery

(2015) Paul R. Jensen et al.   NATURAL PRODUCT REPORTS

Identification of Alp1U and Lom6 as epoxy hydrolases and implications for kinamycin and lomaiviticin biosynthesis

(2015) Bin Wang et al.   Nature Communications

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

(2014) Wai Ong et al.   BMC Systems Biology

Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway

(2014) Taylor K. S. Richter et al.   ENVIRONMENTAL MICROBIOLOGY

Prediction of intracellular metabolic states from extracellular metabolomic data

(2014) Maike K. Aurich et al.   Metabolomics

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Discovery of the lomaiviticin biosynthetic gene cluster in Salinispora pacifica

(2014) Jeffrey E. Janso et al.   TETRAHEDRON

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Insight into the “-Omics” Based Engineering of Streptomycetes for Secondary Metabolite Overproduction

(2013) Amit Kumar Chaudhary et al.   Biomed Research International

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Selective Overproduction of the Proteasome Inhibitor Salinosporamide A via Precursor Pathway Regulation

(2011) Anna Lechner et al.   CHEMISTRY & BIOLOGY

Microdiversity and evidence for high dispersal rates in the marine actinomycete ‘Salinispora pacifica’

(2011) Kelle C. Freel et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

(2011) Mohammad Tauqeer Alam et al.   FEBS LETTERS

The diazofluorene antitumor antibiotics: Structural elucidation, biosynthetic, synthetic, and chemical biological studies

(2011) Seth B. Herzon et al.   NATURAL PRODUCT REPORTS

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

(2011) Jan Schellenberger et al.   Nature Protocols

A preliminary investigation on the growth requirement for monovalent cations, divalent cations and medium ionic strength of marine actinomycete Salinispora

(2010) Ginger Tsueng et al.   APPLIED MICROBIOLOGY AND 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

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Impact of Natural Products on Developing New Anti-Cancer Agents†

(2009) Gordon M. Cragg et al.   CHEMICAL REVIEWS

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

(2009) Adam M. Feist et al.   METABOLIC ENGINEERING

Applications of genome-scale metabolic reconstructions

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

Exploration and engineering of biosynthetic pathways in the marine actinomycete Salinispora tropica

(2009) Markus Nett et al.   PURE AND APPLIED CHEMISTRY

A low-sodium-salt formulation for the fermentation of salinosporamides by Salinispora tropica strain NPS21184

(2008) Ginger Tsueng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Growth of Salinispora tropica strains CNB440, CNB476, and NPS21184 in nonsaline, low-sodium media

(2008) Ginger Tsueng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY