Network integration and modelling of dynamic drug responses at multi-omics levels

Yin Yang 1 Suppresses Dilated Cardiomyopathy and Cardiac Fibrosis Through Regulation of Bmp7 and Ctgf

(2019) Chia Yee Tan et al.   CIRCULATION RESEARCH

Upregulation of Yy1 Suppresses Dilated Cardiomyopathy caused by Ttn insufficiency

(2019) Dan Liao et al.   Scientific Reports

Mechanism of doxorubicin cardiotoxicity evaluated by integrating multiple molecular effects into a biophysical model

(2018) M Fernandez-Chas et al.   BRITISH JOURNAL OF PHARMACOLOGY

Expression Profiling of Human Pluripotent Stem Cell-Derived Cardiomyocytes Exposed to Doxorubicin—Integration and Visualization of Multi-Omics Data

(2018) Gustav Holmgren et al.   TOXICOLOGICAL SCIENCES

Bringing in vitro analysis closer to in vivo : Studying doxorubicin toxicity and associated mechanisms in 3D human microtissues with PBPK-based dose modelling

(2018) Marcha Verheijen et al.   TOXICOLOGY LETTERS

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

(2018) Ralf Gilsbach et al.   Nature Communications

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes

(2018) Justin K. Huang et al.   Cell Systems

Toxicogenomics: A 2020 Vision

(2018) Zhichao Liu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Network and Pathway Analysis of Toxicogenomics Data

(2018) Gal Barel et al.   Frontiers in Genetics

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

High-throughput screening of tyrosine kinase inhibitor cardiotoxicity with human induced pluripotent stem cells

(2017) Arun Sharma et al.   Science Translational Medicine

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

(2017) Pekka Kohonen et al.   Nature Communications

Network dynamics-based cancer panel stratification for systemic prediction of anticancer drug response

(2017) Minsoo Choi et al.   Nature Communications

Genetics and genomics of dilated cardiomyopathy and systolic heart failure

(2017) Upasana Tayal et al.   Genome Medicine

Cardiac spheroids as promising in vitro models to study the human heart microenvironment

(2017) Liudmila Polonchuk et al.   Scientific Reports

Post-marketing withdrawal of 462 medicinal products because of adverse drug reactions: a systematic review of the world literature

(2016) Igho J. Onakpoya et al.   BMC Medicine

Reactive oxygen species and fibrosis: further evidence of a significant liaison

(2016) Kati Richter et al.   CELL AND TISSUE RESEARCH

Cardio-Oncology

(2016) Carrie G. Lenneman et al.   CIRCULATION RESEARCH

Characterization of the Changes in Cardiac Structure and Function in Mice Treated With Anthracyclines Using Serial Cardiac Magnetic Resonance ImagingCLINICAL PERSPECTIVE

(2016) Hoshang Farhad et al.   Circulation-Cardiovascular Imaging

Anthracycline-Associated T1 Mapping Characteristics Are Elevated Independent of the Presence of Cardiovascular Comorbidities in Cancer SurvivorsCLINICAL PERSPECTIVE

(2016) Jennifer H. Jordan et al.   Circulation-Cardiovascular Imaging

Proposal for a revised definition of dilated cardiomyopathy, hypokinetic non-dilated cardiomyopathy, and its implications for clinical practice: a position statement of the ESC working group on myocardial and pericardial diseases

(2016) Yigal M. Pinto et al.   EUROPEAN HEART JOURNAL

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments

(2016) Matthias Lienhard et al.   NUCLEIC ACIDS RESEARCH

Multi-omic data integration enables discovery of hidden biological regularities

(2016) Ali Ebrahim et al.   Nature Communications

Modeling Doxorubicin-Induced Cardiotoxicity in Human Pluripotent Stem Cell Derived-Cardiomyocytes

(2016) Agnes Maillet et al.   Scientific Reports

A Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity

(2016) Bernardo L. de Oliveira et al.   PLoS Computational Biology

Identification of genomic biomarkers for anthracycline-induced cardiotoxicity in human iPSC-derived cardiomyocytes: an in vitro repeated exposure toxicity approach for safety assessment

(2015) Umesh Chaudhari et al.   ARCHIVES OF TOXICOLOGY

Direct Reprogramming of RESTing Astrocytes

(2015) Chengzhong Wang et al.   Cell Stem Cell

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

(2015) Tiannan Guo et al.   NATURE MEDICINE

Quantitative and logic modelling of molecular and gene networks

(2015) Nicolas Le Novère   NATURE REVIEWS GENETICS

WITHDRAWN—a resource for withdrawn and discontinued drugs

(2015) Vishal B. Siramshetty et al.   NUCLEIC ACIDS RESEARCH

Development and Characterization of a Scaffold-Free 3D Spheroid Model of Induced Pluripotent Stem Cell-Derived Human Cardiomyocytes

(2015) Philippe Beauchamp et al.   TISSUE ENGINEERING PART C-METHODS

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

(2014) M. J. Nueda et al.   BIOINFORMATICS

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Anthracycline-Dependent Cardiotoxicity and Extracellular Matrix Remodeling

(2014) Dragana Nikitovic et al.   CHEST

Mitochondrial form and function

(2014) Jonathan R. Friedman et al.   NATURE

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Lessons learned from the fate of AstraZeneca's drug pipeline: a five-dimensional framework

(2014) David Cook et al.   NATURE REVIEWS DRUG DISCOVERY

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

(2014) Ralf Gilsbach et al.   Nature Communications

A Computational Model of Reactive Oxygen Species and Redox Balance in Cardiac Mitochondria

(2013) Laura D. Gauthier et al.   BIOPHYSICAL JOURNAL

Oxidative Stress and Sarcomeric Proteins

(2013) Susan F. Steinberg   CIRCULATION RESEARCH

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Cardiovascular toxicity induced by chemotherapy, targeted agents and radiotherapy: ESMO Clinical Practice Guidelines

(2012) G. Curigliano et al.   ANNALS OF ONCOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Doxorubicin-induced cardiomyopathy: From molecular mechanisms to therapeutic strategies

(2012) Yanti Octavia et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

IntScore: a web tool for confidence scoring of biological interactions

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

High purity human-induced pluripotent stem cell-derived cardiomyocytes: electrophysiological properties of action potentials and ionic currents

(2011) Junyi Ma et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Redox Signaling and Cardiac Sarcomeres

(2011) Marius P. Sumandea et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic quantification of peptides/proteins in urine using selected reaction monitoring

(2011) Nathalie Selevsek et al.   PROTEOMICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The origin of fibroblasts and mechanism of cardiac fibrosis

(2010) Guido Krenning et al.   JOURNAL OF CELLULAR PHYSIOLOGY

In this issue

(2010)   NATURE REVIEWS DRUG DISCOVERY

Toxicology for the twenty-first century

(2009) Thomas Hartung   NATURE

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

YY1 Protects Cardiac Myocytes from Pathologic Hypertrophy by Interacting with HDAC5

(2008) Carmen C. Sucharov et al.   MOLECULAR BIOLOGY OF THE CELL

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

(2008) Zoltán Kutalik et al.   NATURE BIOTECHNOLOGY

Transforming Environmental Health Protection

(2008) Francis S. Collins et al.   SCIENCE