Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes

(2014) Aleksej Zelezniak et al.   PLoS Computational Biology

Polyamine Transport by the Polyspecific Organic Cation Transporters OCT1, OCT2, and OCT3

(2013) Monica Sala-Rabanal et al.   MOLECULAR PHARMACEUTICS

Systematic identification of proteins that elicit drug side effects

(2013) M. Kuhn et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Effects of widely used drugs on micronutrients: A story rarely told

(2013) Dimitrios Samaras et al.   NUTRITION

Integrated Analysis of Drug-Induced Gene Expression Profiles Predicts Novel hERG Inhibitors

(2013) Joseph J. Babcock et al.   PLoS One

Common Variation in the NOS1AP Gene Is Associated With Drug-Induced QT Prolongation and Ventricular Arrhythmia

(2012) Yalda Jamshidi et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Novel rare variants in congenital cardiac arrhythmia genes are frequent in drug-induced torsades de pointes

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Building the process-drug–side effect network to discover the relationship between biological Processes and side effects

(2011) Sejoon Lee et al.   BMC BIOINFORMATICS

Linkage of Organic Anion Transporter-1 to Metabolic Pathways through Integrated “Omics”-driven Network and Functional Analysis

(2011) Sun-Young Ahn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

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Diseases in a dish: modeling human genetic disorders using induced pluripotent cells

(2011) Gustavo Tiscornia et al.   NATURE MEDICINE

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

(2011) Jan Schellenberger et al.   Nature Protocols

Phase II failures: 2008–2010

(2011) John Arrowsmith   NATURE REVIEWS DRUG DISCOVERY

Phase III and submission failures: 2007–2010

(2011) John Arrowsmith   NATURE REVIEWS DRUG DISCOVERY

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

(2011) Xing-Ming Zhao et al.   PLoS Computational Biology

Effect of metformin on oxidative stress, nitrosative stress and inflammatory biomarkers in type 2 diabetes patients

(2010) Arpita Chakraborty et al.   DIABETES RESEARCH AND CLINICAL PRACTICE

Reflect: A practical approach to web semantics

(2010) Seán I. O’Donoghue et al.   Journal of Web Semantics

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Effect of Supplemental Folic Acid in Pregnancy on Childhood Asthma: A Prospective Birth Cohort Study

(2009) M. J. Whitrow et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

GPD1L links redox state to cardiac excitability by PKC-dependent phosphorylation of the sodium channel SCN5A

(2009) Carmen R. Valdivia et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Antiarrhythmic Effects of Some Antioxidant Vitamins in Rats Injected with Epinephrine

(2009) Rajat Sethi et al.   Cardiovascular Toxicology

Cancer Incidence and Mortality After Treatment With Folic Acid and Vitamin B12

(2009) Marta Ebbing   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Identifying the proteins to which small-molecule probes and drugs bind in cells

(2009) S.-E. Ong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

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

Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae

(2009) Patrick H. Bradley et al.   PLoS Computational Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Similar compounds searching system by using the gene expression microarray database

(2008) Hiroyoshi Toyoshiba et al.   TOXICOLOGY LETTERS

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology