Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals

Integrating big data and actionable health coaching to optimize wellness

(2015) Leroy Hood et al.   BMC Medicine

Drug-Induced Death Signaling Strategy Rapidly Predicts Cancer Response to Chemotherapy

(2015) Joan Montero et al.   CELL

Using "Big Data" to Dissect Clinical Heterogeneity

(2015) R. B. Altman et al.   CIRCULATION

Obama's Precision Medicine Initiative

(2015) Sharon F. Terry   Genetic Testing and Molecular Biomarkers

Compound signature detection on LINCS L1000 big data

(2015) Chenglin Liu et al.   Molecular BioSystems

Obama 2016 budget calls for Precision Medicine

(2015)   NATURE BIOTECHNOLOGY

UK catapults precision medicine

(2015)   NATURE BIOTECHNOLOGY

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

Diagnosing phenotypes of single-sample individuals by edge biomarkers

(2015) Wanwei Zhang et al.   Journal of Molecular Cell Biology

Precision Medicine in Breast Cancer: Genes, Genomes, and the Future of Genomically Driven Treatments

(2015) Daniel G. Stover et al.   Current Oncology Reports

Predicting Cancer Drug Response: Advancing the DREAM

(2015) R. B. Altman   Cancer Discovery

Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis

(2015) Yuanyuan Li et al.   Scientific Reports

Obama seeks $213m to fund "precision medicine"

(2015) M. McCarthy   BMJ-British Medical Journal

Limited sampling hampers “big data” estimation of species richness in a tropical biodiversity hotspot

(2015) Kristine Engemann et al.   Ecology and Evolution

Obama seeks $213m to fund "precision medicine"

(2015) M. McCarthy   BMJ-British Medical Journal

netClass: an R-package for network based, integrative biomarker signature discovery

(2014) Y. Cun et al.   BIOINFORMATICS

Identifying critical transitions of complex diseases based on a single sample

(2014) Rui Liu et al.   BIOINFORMATICS

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection

(2014) Zhi-Ping Liu et al.   BMC BIOINFORMATICS

Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines

(2014) Liang Li et al.   BMC GENOMICS

Quantitative Optical Imaging of Primary Tumor Organoid Metabolism Predicts Drug Response in Breast Cancer

(2014) A. J. Walsh et al.   CANCER RESEARCH

Progeria: A Paradigm for Translational Medicine

(2014) Leslie B. Gordon et al.   CELL

Prediction of dynamical drug sensitivity and resistance by module network rewiring-analysis based on transcriptional profiling

(2014) Tao Zeng et al.   DRUG RESISTANCE UPDATES

Using drug response data to identify molecular effectors, and molecular “omic” data to identify candidate drugs in cancer

(2014) William C. Reinhold et al.   HUMAN GENETICS

Negative correlation based gene markers identification in integrative gene expression data

(2014) Tao Zeng et al.   International Journal of Data Mining and Bioinformatics

EdgeMarker: Identifying differentially correlated molecule pairs as edge-biomarkers

(2014) Wanwei Zhang et al.   JOURNAL OF THEORETICAL BIOLOGY

Systems biology with omics data

(2014) Luonan Chen   METHODS

Deciphering early development of complex diseases by progressive module network

(2014) Tao Zeng et al.   METHODS

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

(2014) Qiaonan Duan et al.   NUCLEIC ACIDS RESEARCH

Unleashing the potential of NOD- and Toll-like agonists as vaccine adjuvants

(2014) C. Maisonneuve et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Edge biomarkers for classification and prediction of phenotypes

(2014) Tao Zeng et al.   Science China-Life Sciences

GigaDB: promoting data dissemination and reproducibility

(2014) T. P. Sneddon et al.   Database-The Journal of Biological Databases and Curation

Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study

(2014) Mariam Jamal-Hanjani et al.   PLOS BIOLOGY

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines

(2014) Paul Geeleher et al.   GENOME BIOLOGY

Big Biological Data: Challenges and Opportunities

(2014) Yixue Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Prediction and early diagnosis of complex diseases by edge-network

(2013) Xiangtian Yu et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Computational systems biology in the big data era

(2013) Yong Wang et al.   BMC Systems Biology

SHON Is a Novel Estrogen-Regulated Oncogene in Mammary Carcinoma That Predicts Patient Response to Endocrine Therapy

(2013) Y. Jung et al.   CANCER RESEARCH

Collections of Simultaneously Altered Genes as Biomarkers of Cancer Cell Drug Response

(2013) D. L. Masica et al.   CANCER RESEARCH

GWAS Meets TCGA to Illuminate Mechanisms of Cancer Predisposition

(2013) Hyun Seok Kim et al.   CELL

Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

(2013) Iwijn De Vlaminck et al.   CELL

Edgotype: a fundamental link between genotype and phenotype

(2013) Nidhi Sahni et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Network biomarkers reveal dysfunctional gene regulations during disease progression

(2013) Tao Zeng et al.   FEBS Journal

Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data

(2013) Zhi-Ping Liu et al.   IET Systems Biology

Independent Validation of a Model Using Cell Line Chemosensitivity to Predict Response to Therapy

(2013) Wenting Wang et al.   JNCI-Journal of the National Cancer Institute

Early Diagnosis of Complex Diseases by Molecular Biomarkers, Network Biomarkers, and Dynamical Network Biomarkers

(2013) Rui Liu et al.   MEDICINAL RESEARCH REVIEWS

Bringing rigour to translational medicine

(2013) David W. Howells et al.   Nature Reviews Neurology

Variant GADL1 and Response to Lithium Therapy in Bipolar I Disorder

(2013) Chien-Hsiun Chen et al.   NEW ENGLAND JOURNAL OF MEDICINE

Analysis Tool Web Services from the EMBL-EBI

(2013) Hamish McWilliam et al.   NUCLEIC ACIDS RESEARCH

Classification of Time Series Gene Expression in Clinical Studies via Integration of Biological Network

(2013) Liwei Qian et al.   PLoS One

Differential Network Analysis Applied to Preoperative Breast Cancer Chemotherapy Response

(2013) Gregor Warsow et al.   PLoS One

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Commensal Bacteria Control Cancer Response to Therapy by Modulating the Tumor Microenvironment

(2013) N. Iida et al.   SCIENCE

APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems

(2013) Jiguang Wang et al.   Scientific Reports

Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks

(2013) Shao-Yan Sun et al.   Scientific Reports

Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser

(2013) Melissa S. Cline et al.   Scientific Reports

Impact of host and virus genome variability on HCV replication and response to interferon

(2013) Cameron J Schweitzer et al.   Current Opinion in Virology

Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis

(2013) Jing Cui et al.   PLoS Genetics

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Comparison of metagenomic samples using sequence signatures

(2012) Bai Jiang et al.   BMC GENOMICS

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq

(2012) Huijuan Feng et al.   CANCER LETTERS

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Data integration and systems biology approaches for biomarker discovery: Challenges and opportunities for multiple sclerosis

(2012) Pablo Villoslada et al.   JOURNAL OF NEUROIMMUNOLOGY

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

ENCODE leads the way on big data

(2012) Mark Gerstein   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

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

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

A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory

(2012) Leroy Hood et al.   New Biotechnology

Gene Ontology Annotations and Resources

(2012)   NUCLEIC ACIDS RESEARCH

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Translational medicine in China

(2012) JianMin Zhang   Science China-Life Sciences

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

(2012) Christof Winter et al.   PLoS Computational Biology

Personal genomes and precision medicine

(2012) Gareth Highnam et al.   GENOME BIOLOGY

GigaDB: announcing the GigaScience database

(2012) Tam P Sneddon et al.   GigaScience

Preface

(2011) Manolis Kellis et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Improving the efficacy of translational medicine by optimally integrating health care, academia and industry

(2011) Stefan R Bornstein et al.   NATURE MEDICINE

Predictive, personalized, preventive, participatory (P4) cancer medicine

(2011) Leroy Hood et al.   Nature Reviews Clinical Oncology

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

(2011) Yongsheng Huang et al.   PLoS Genetics

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Genome-wide searching of rare genetic variants in WTCCC data

(2010) Tao Feng et al.   HUMAN GENETICS

Expression of Genes Associated with Immunoproteasome Processing of Major Histocompatibility Complex Peptides Is Indicative of Protection with Adjuvanted RTS,S Malaria Vaccine

(2010) Maryanne T. Vahey et al.   JOURNAL OF INFECTIOUS DISEASES

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A new bioinformatics analysis tools framework at EMBL-EBI

(2010) M. Goujon et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

A Government Niche for Translational Medicine and Drug Development

(2010) J. Kaiser   SCIENCE

Translational Medicine and the Value of Biomarker Qualification

(2010) F. M. Goodsaid et al.   Science Translational Medicine

Mathematical Modeling of Molecular Data in Translational Medicine: Theoretical Considerations

(2010) N. F. Marko et al.   Science Translational Medicine

Predictive, preventive, personalized and participatory medicine: back to the future

(2010) Charles Auffray et al.   Genome Medicine

Pathway and network-based analysis of genome-wide association studies in multiple sclerosis

(2009) S. E. Baranzini et al.   HUMAN MOLECULAR GENETICS

Translational Medicine: An Engine of Change for Bringing New Technology to Community Health

(2009) C.-P. Milne et al.   Science Translational Medicine

Alignment and classification of time series gene expression in clinical studies

(2008) T.-h. Lin et al.   BIOINFORMATICS

The prediction of interferon treatment effects based on time series microarray gene expression profiles

(2008) Tao Huang et al.   Journal of Translational Medicine

Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment

(2008) Milton W Taylor et al.   Journal of Translational Medicine

Big data: The next Google

(2008)   NATURE

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology