MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

Finding metabolic pathways using atom tracking

(2010) Allison P. Heath et al.   BIOINFORMATICS

What makes an enzyme promiscuous?

(2010) Ann Babtie et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Metabolomic Changes Accompanying Transformation and Acquisition of Metastatic Potential in a Syngeneic Mouse Mammary Tumor Model

(2010) Xin Lu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Decision tree supported substructure prediction of metabolites from GC-MS profiles

(2010) Jan Hummel et al.   Metabolomics

Global metabolite profiling of agarose degradation by Saccharophagus degradans 2-40

(2010) Min Hye Shin et al.   New Biotechnology

Long-Chain Fatty Acid Combustion Rate Is Associated with Unique Metabolite Profiles in Skeletal Muscle Mitochondria

(2010) Erin L. Seifert et al.   PLoS One

Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits

(2010) B. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acute and Short-term Effects of Secondhand Smoke on Lung Function and Cytokine Production

(2009) Andreas D. Flouris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

(2009) Tobias Kind et al.   ANALYTICAL CHEMISTRY

Inferring branching pathways in genome-scale metabolic networks

(2009) Esa Pitkänen et al.   BMC Systems Biology

Modulation of pentose phosphate pathway during cell cycle progression in human colon adenocarcinoma cell line HT29

(2009) Pedro Vizán et al.   INTERNATIONAL JOURNAL OF CANCER

Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate inBacillus subtilis

(2009) Roelco J. Kleijn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic Pathfinding Using RPAIR Annotation

(2009) Karoline Faust et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effects of Smoking on the Developing Lung: Insights from a Biologic Model for Lung Development, Homeostasis, and Repair

(2009) Virender K. Rehan et al.   LUNG

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

SMPDB: The Small Molecule Pathway Database

(2009) Alex Frolkis et al.   NUCLEIC ACIDS RESEARCH

The NCBI BioSystems database

(2009) Lewis Y. Geer et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

(2009) J. Xia et al.   NUCLEIC ACIDS RESEARCH

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API

(2009) Nobuaki Kono et al.   PLoS One

Dysregulated gene expression networks in human acute myelogenous leukemia stem cells

(2009) R. Majeti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human gut microbiome adopts an alternative state following small bowel transplantation

(2009) A. L. Hartman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prenatal exposure to environmental tobacco smoke alters gene expression in the developing murine hippocampus

(2009) Partha Mukhopadhyay et al.   REPRODUCTIVE TOXICOLOGY

The conservation and evolutionary modularity of metabolism

(2009) José M Peregrín-Alvarez et al.   GENOME BIOLOGY

The public road to high-quality curated biological pathways

(2008) M ADRIAENS et al.   DRUG DISCOVERY TODAY

Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites

(2008) Masaaki Kotera et al.   Journal of Chemical Information and Modeling

Metabolite profiling of human colon carcinoma – deregulation of TCA cycle and amino acid turnover

(2008) Carsten Denkert et al.   Molecular Cancer

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

Quality control for plant metabolomics: reporting MSI-compliant studies

(2008) Oliver Fiehn et al.   PLANT JOURNAL

Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry

(2008) Oliver Fiehn   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

iPath: interactive exploration of biochemical pathways and networks

(2008) Ivica Letunic et al.   TRENDS IN BIOCHEMICAL SCIENCES

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY

Depiction of metabolome changes in histidine-starvedEscherichia coliby CE-TOFMS

(2007) Yoshiaki Ohashi et al.   Molecular BioSystems