Systems Pharmacology to Predict Drug Toxicity: Integration Across Levels of Biological Organization

Novel Markers of Kidney Function as Predictors of ESRD, Cardiovascular Disease, and Mortality in the General Population

(2012) Brad C. Astor et al.   AMERICAN JOURNAL OF KIDNEY DISEASES

Metabolomics-on-a-Chip and Predictive Systems Toxicology in Microfluidic Bioartificial Organs

(2012) Laetitia Shintu et al.   ANALYTICAL CHEMISTRY

Benzo[a]pyrene-Induced Changes in MicroRNA–mRNA Networks

(2012) Daneida Lizarraga et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Large-scale mapping of human protein interactome using structural complexes

(2012) Manoj Tyagi et al.   EMBO REPORTS

Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines

(2012) Philippe Chouvarine et al.   PLoS One

Demonstration of Blind Quantum Computing

(2012) S. Barz et al.   SCIENCE

Identification and Pathway Mapping of Furan Target Proteins Reveal Mitochondrial Energy Production and Redox Regulation as Critical Targets of Furan Toxicity

(2012) S. Moro et al.   TOXICOLOGICAL SCIENCES

'Omics analysis of low dose acetaminophen intake demonstrates novel response pathways in humans

(2012) Marlon J.A. Jetten et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Generation and characterization of a mouse model of the metabolic syndrome: apolipoprotein E and aromatase double knockout mice

(2011) Nicola J. A. Scott et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Using Genome-Wide Association Studies to Identify Genes Important in Serious Adverse Drug Reactions

(2011) Ann K. Daly   Annual Review of Pharmacology and Toxicology

Statins as a possible cause of inflammatory and necrotizing myopathies

(2011) Santosh Padala et al.   ATHEROSCLEROSIS

Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network

(2011) Junguk Hur et al.   BMC IMMUNOLOGY

Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches

(2011) Yen Low et al.   CHEMICAL RESEARCH IN TOXICOLOGY

A Novel Preclinical Strategy for Identifying Cardiotoxic Kinase Inhibitors and Mechanisms of Cardiotoxicity

(2011) Hui Cheng et al.   CIRCULATION RESEARCH

Humanized Bone Marrow Mouse Model as a Preclinical Tool to Assess Therapy-Mediated Hematotoxicity

(2011) S. Cai et al.   CLINICAL CANCER RESEARCH

Acute Doxorubicin Toxicity Differentially Alters Cytochrome P450 Expression and Arachidonic Acid Metabolism in Rat Kidney and Liver

(2011) B. N. M. Zordoky et al.   DRUG METABOLISM AND DISPOSITION

Induction of vesicular steatosis by amiodarone and tetracycline is associated with up-regulation of lipogenic genes in heparg cells

(2011) Sébastien Anthérieu et al.   HEPATOLOGY

Phenome-transcriptome correlation unravels anxiety and depression related pathways

(2011) Philipp Gormanns et al.   JOURNAL OF PSYCHIATRIC RESEARCH

Translational bioinformatics: linking knowledge across biological and clinical realms: Figure 1

(2011) Indra Neil Sarkar et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

AMPK Mediates the Initiation of Kidney Disease Induced by a High-Fat Diet

(2011) A.-E. Decleves et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

The distant organ effects of acute kidney injury

(2011) Morgan E. Grams et al.   KIDNEY INTERNATIONAL

Quantification of Activated NF-κB/RelA Complexes Using ssDNA Aptamer Affinity – Stable Isotope Dilution—Selected Reaction Monitoring—Mass Spectrometry

(2011) Yingxin Zhao et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity

(2011) Theonie Anastassiadis et al.   NATURE BIOTECHNOLOGY

Mechanisms of drug-induced liver injury: from bedside to bench

(2011) Shannan Tujios et al.   Nature Reviews Gastroenterology & Hepatology

PhenomeNET: a whole-phenome approach to disease gene discovery

(2011) R. Hoehndorf et al.   NUCLEIC ACIDS RESEARCH

Mouse Phenome Database (MPD)

(2011) Terry P. Maddatu et al.   NUCLEIC ACIDS RESEARCH

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome

(2011) Heng Luo et al.   NUCLEIC ACIDS RESEARCH

Phenobarbital Mediates an Epigenetic Switch at the Constitutive Androstane Receptor (CAR) Target Gene Cyp2b10 in the Liver of B6C3F1 Mice

(2011) Harri Lempiäinen et al.   PLoS One

Comparative Gene Expression Profiles Induced by PPARγ and PPARα/γ Agonists in Human Hepatocytes

(2011) Alexandra Rogue et al.   PLoS One

The Implications of Relationships between Human Diseases and Metabolic Subpathways

(2011) Xia Li et al.   PLoS One

Integrated Proteomic and Transcriptomic Investigation of the Acetaminophen Toxicity in Liver Microfluidic Biochip

(2011) Jean Matthieu Prot et al.   PLoS One

Humanized mice with ectopic artificial liver tissues

(2011) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting Adverse Drug Events Using Pharmacological Network Models

(2011) A. Cami et al.   Science Translational Medicine

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

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

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

Drug targets: single-cell transcriptomics hastens unbiased discovery

(2011) Tamas Bartfai et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

(2011) Lun Yang et al.   PLoS Computational Biology

A Phenomics-Based Strategy Identifies Loci on APOC1, BRAP, and PLCG1 Associated with Metabolic Syndrome Phenotype Domains

(2011) Christy L. Avery et al.   PLoS Genetics

Developing a kidney and urinary pathway knowledge base

(2011) Simon Jupp et al.   Journal of Biomedical Semantics

The Chemical Basis of Pharmacology

(2010) Michael J. Keiser et al.   BIOCHEMISTRY

Bayesian rule learning for biomedical data mining

(2010) Vanathi Gopalakrishnan et al.   BIOINFORMATICS

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

(2010) Y. Yamanishi et al.   BIOINFORMATICS

Understanding lactic acidosis in paracetamol (acetaminophen) poisoning

(2010) Anoop D. Shah et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

Modeling Liver-Related Adverse Effects of Drugs UsingkNearest Neighbor Quantitative Structure−Activity Relationship Method

(2010) Amie D. Rodgers et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Dynamic MicroRNA Expression Programs During Cardiac Differentiation of Human Embryonic Stem Cells

(2010) Kitchener D. Wilson et al.   Circulation-Cardiovascular Genetics

The Need for Precompetitive Integrative Bionetwork Disease Model Building

(2010) S H Friend   CLINICAL PHARMACOLOGY & THERAPEUTICS

Probabilistic Risk Analysis: Improving Early Drug Development Decision Making

(2010) P N Mudd et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Prediction of Adverse Drug Reactions Using Decision Tree Modeling

(2010) F Hammann et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform

(2010) Sunita J. Shukla et al.   DRUG DISCOVERY TODAY

Epigenetic Changes Induced by Air Toxics: Formaldehyde Exposure Alters miRNA Expression Profiles in Human Lung Cells

(2010) Julia E. Rager et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation

(2010) Yunlong Liu et al.   Epigenetics

Investigation of low-dose ritonavir on human peripheral blood mononuclear cells using gene expression whole genome microarrays

(2010) Saliha Yilmaz et al.   GENOMICS

Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data

(2010) Xinan Yang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes

(2010) Leonidas G. Alexopoulos et al.   MOLECULAR & CELLULAR PROTEOMICS

Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation

(2010) Benjamin D. Cosgrove et al.   Molecular BioSystems

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

PhenoHM: human–mouse comparative phenome–genome server

(2010) Divya Sardana et al.   NUCLEIC ACIDS RESEARCH

A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways

(2010) Izhar Wallach et al.   PLoS One

Reconstituting Organ-Level Lung Functions on a Chip

(2010) D. Huh et al.   SCIENCE

Systems Pharmacology of Arrhythmias

(2010) S. I. Berger et al.   Science Signaling

EU Framework 6 Project: Predictive Toxicology (PredTox)—overview and outcome

(2010) Laura Suter et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks

(2010) Joel T. Dudley et al.   Journal of Cardiovascular Translational Research

Likelihood ratios for genome medicine

(2010) Alexander A Morgan et al.   Genome Medicine

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Ontology-driven indexing of public datasets for translational bioinformatics

(2009) Nigam H Shah et al.   BMC BIOINFORMATICS

Comparison of concept recognizers for building the Open Biomedical Annotator

(2009) Nigam H Shah et al.   BMC BIOINFORMATICS

Definition, conservation and epigenetics of housekeeping and tissue-enriched genes

(2009) Xinwei She et al.   BMC GENOMICS

Serum Metabolomics Reveals Irreversible Inhibition of Fatty Acid β-Oxidation through the Suppression of PPARα Activation as a Contributing Mechanism of Acetaminophen-Induced Hepatotoxicity

(2009) Chi Chen et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Defining ‘Signal’ and its Subtypes in Pharmacovigilance Based on a Systematic Review of Previous Definitions

(2009) Manfred Hauben et al.   DRUG SAFETY

Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans

(2009) A. H. Harrill et al.   GENOME RESEARCH

Acetaminophen dosing of humans results in blood transcriptome and metabolome changes consistent with impaired oxidative phosphorylation

(2009) Rick D. Fannin et al.   HEPATOLOGY

Fragment-Based Prediction of the Clinical Occurrence of Long QT Syndrome and Torsade de Pointes

(2009) Matthew Clark et al.   Journal of Chemical Information and Modeling

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

(2009) Andreas Bender et al.   Journal of Chemical Information and Modeling

Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis

(2009) Josef Scheiber et al.   Journal of Chemical Information and Modeling

Drug Effects Viewed from a Signal Transduction Network Perspective

(2009) Anton F. Fliri et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Japanese toxicogenomics project: Application of toxicogenomics

(2009) Takeki Uehara et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

A network view of disease and compound screening

(2009) Eric E. Schadt et al.   NATURE REVIEWS DRUG DISCOVERY

Phenomics: the systematic study of phenotypes on a genome-wide scale

(2009) R.M. Bilder et al.   NEUROSCIENCE

Signaling Pathways Controlling Pluripotency and Early Cell Fate Decisions of Human Induced Pluripotent Stem Cells

(2009) Ludovic Vallier et al.   STEM CELLS

The Liver Toxicity Biomarker Study: Phase I Design and Preliminary Results

(2009) Robert N. Mcburney et al.   TOXICOLOGIC PATHOLOGY

Population-Based Discovery of Toxicogenomics Biomarkers for Hepatotoxicity Using a Laboratory Strain Diversity Panel

(2009) Alison H. Harrill et al.   TOXICOLOGICAL SCIENCES

Acute doxorubicin cardiotoxicity alters cardiac cytochrome P450 expression and arachidonic acid metabolism in rats

(2009) Beshay N.M. Zordoky et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Increased sensitivity for troglitazone-induced cytotoxicity using a human in vitro co-culture model

(2009) Ylva Edling et al.   TOXICOLOGY IN VITRO

Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome

(2009) Lun Yang et al.   PLoS Computational Biology

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

(2009) Li Xie et al.   PLoS Computational Biology

Phase II study of sequentially administered low-dose mitomycin-C (MMC) and irinotecan (CPT-11) in women with metastatic breast cancer (MBC)

(2008) E. Mrozek et al.   ANNALS OF ONCOLOGY

Phenomics: Building Scaffolds for Biological Hypotheses in the Post-Genomic Era

(2008) Robert M. Bilder   BIOLOGICAL PSYCHIATRY

Tissue slices for the evaluation of metabolism-based toxicity with the example of diclofenac

(2008) Alison E.M. Vickers   CHEMICO-BIOLOGICAL INTERACTIONS

A Phase I Pharmacokinetic and Pharmacodynamic Correlative Study of the Antisense Bcl-2 Oligonucleotide G3139, in Combination with Carboplatin and Paclitaxel, in Patients with Advanced Solid Tumors

(2008) G. Liu et al.   CLINICAL CANCER RESEARCH

Mitochondrial dysfunction and delayed hepatotoxicity: another lesson from troglitazone

(2008) N. L. Julie et al.   DIABETOLOGIA

Deletion of Apoptosis Signal-Regulating Kinase 1 Attenuates Acetaminophen-Induced Liver Injury by Inhibiting c-Jun N-Terminal Kinase Activation

(2008) Hayato Nakagawa et al.   GASTROENTEROLOGY

Discovery and implementation of transcriptional biomarkers of synthetic LXR agonists in peripheral blood cells

(2008) Elizabeth A DiBlasio-Smith et al.   Journal of Translational Medicine

Large-scale chemical dissection of mitochondrial function

(2008) Bridget K Wagner et al.   NATURE BIOTECHNOLOGY

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Development of a Phospholipidosis Database and Predictive Quantitative Structure-Activity Relationship (QSAR) Models

(2008) Naomi L. Kruhlak et al.   TOXICOLOGY MECHANISMS AND METHODS