Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research

New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data

(2017) Grigoriy Gogoshin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Organization principles of biological networks: An explorative study

(2016) Havva Kohestani et al.   BIOSYSTEMS

Comparative genome-scale modelling ofStaphylococcus aureusstrains identifies strain-specific metabolic capabilities linked to pathogenicity

(2016) Emanuele Bosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tailoring therapies—improving the management of early breast cancer: St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2015

(2015) A. S. Coates et al.   ANNALS OF ONCOLOGY

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

TBX1 protein interactions and microRNA-96-5p regulation controls cell proliferation during craniofacial and dental development: implications for 22q11.2 deletion syndrome

(2015) S. Gao et al.   HUMAN MOLECULAR GENETICS

NaviCell Web Service for network-based data visualization

(2015) Eric Bonnet et al.   NUCLEIC ACIDS RESEARCH

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

A Regulatory Network Involving β-Catenin, e-Cadherin, PI3k/Akt, and Slug Balances Self-Renewal and Differentiation of Human Pluripotent Stem Cells In Response to Wnt Signaling

(2015) Tyng-Shyan Huang et al.   STEM CELLS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

FGFR3 mutation causes abnormal membranous ossification in achondroplasia

(2014) Federico Di Rocco et al.   HUMAN MOLECULAR GENETICS

Predicting interactome network perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia

(2014) Leon Juvenal Hajingabo et al.   MOLECULAR BIOLOGY OF THE CELL

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle 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

Exploiting combinatorial patterns in cancer genomic data for personalized therapy and new target discovery

(2014) Michael Schubert et al.   PHARMACOGENOMICS

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

(2014) Roser Corominas et al.   Nature Communications

Targeted omics and systems medicine: personalising care

(2014) Huan Zhang et al.   Lancet Respiratory Medicine

Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network

(2014) Benjamin P. Keith et al.   Frontiers in Genetics

Personalizing the treatment of women with early breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2013

(2013) A. Goldhirsch et al.   ANNALS OF ONCOLOGY

Identification of cancer fusion drivers using network fusion centrality

(2013) Chia-Chin Wu et al.   BIOINFORMATICS

Cancer heterogeneity: implications for targeted therapeutics

(2013) R Fisher et al.   BRITISH JOURNAL OF CANCER

Identification of Human Protein Interaction Domains using an ORFeome-based Yeast Two-hybrid Fragment Library

(2013) Selma Waaijers et al.   JOURNAL OF PROTEOME RESEARCH

Network Biology editorial 2013

(2013) Edward Marcotte et al.   Molecular BioSystems

Pharmacogenomics of breast cancer therapy: An update

(2013) Kelly Westbrook et al.   PHARMACOLOGY & THERAPEUTICS

Randomized Phase III Placebo-Controlled Trial of Letrozole Plus Oral Temsirolimus As First-Line Endocrine Therapy in Postmenopausal Women With Locally Advanced or Metastatic Breast Cancer

(2012) Antonio C. Wolff et al.   JOURNAL OF CLINICAL ONCOLOGY

Improving Endocrine Therapy for Breast Cancer: It's Not That Simple

(2012) E. Claire Dees et al.   JOURNAL OF CLINICAL ONCOLOGY

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Critical Truths About Power Laws

(2012) M. P. H. Stumpf et al.   SCIENCE

Human diseases through the lens of network biology

(2012) Laura I. Furlong   TRENDS IN GENETICS

Chapter 5: Network Biology Approach to Complex Diseases

(2012) Dong-Yeon Cho et al.   PLoS Computational Biology

Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms

(2012) Fredrik Barrenäs et al.   GENOME BIOLOGY

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

(2011) Shan Zhao et al.   Annual Review of Pharmacology and Toxicology

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Fenofibrate suppresses growth of the human hepatocellular carcinoma cell via PPARα-independent mechanisms

(2011) Daisuke Yamasaki et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer

(2011) L. Li et al.   GENOME RESEARCH

Phosphatidylinositol 3-Kinase and Antiestrogen Resistance in Breast Cancer

(2011) Todd W. Miller et al.   JOURNAL OF CLINICAL ONCOLOGY

The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer

(2011) Yan Xu et al.   MOLECULAR BIOLOGY REPORTS

A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers

(2011) Siwanon Jirawatnotai et al.   NATURE

Everolimus in Postmenopausal Hormone-Receptor–Positive Advanced Breast Cancer

(2011) José Baselga et al.   NEW ENGLAND JOURNAL OF MEDICINE

Network biology: a direct approach to study biological function

(2011) Frank Emmert-Streib et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Decade of Systems Biology

(2010) Han-Yu Chuang et al.   Annual Review of Cell and Developmental Biology

Mechanisms of Endocrine Resistance in Breast Cancer

(2010) C. Kent Osborne et al.   Annual Review of Medicine

Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

(2010) Jie Zhang et al.   BMC BIOINFORMATICS

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

Metabolic Network Analysis of Pseudomonas aeruginosa during Chronic Cystic Fibrosis Lung Infection

(2010) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

The Impact of Gene Expression Regulation on Evolution of Extracellular Signaling Pathways

(2010) Varodom Charoensawan et al.   MOLECULAR & CELLULAR PROTEOMICS

Construction of a Large Extracellular Protein Interaction Network and Its Resolution by Spatiotemporal Expression Profiling

(2010) Stephen Martin et al.   MOLECULAR & CELLULAR PROTEOMICS

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

(2010) Matthew D. Dyer et al.   PLoS One

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

(2009) Kevin R. Brown et al.   BIOINFORMATICS

Novel Agents on the Horizon for Cancer Therapy

(2009) W. W. Ma et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Genome-Wide Promoter Analysis of the SOX4 Transcriptional Network in Prostate Cancer Cells

(2009) C. D. Scharer et al.   CANCER RESEARCH

Revealing promiscuous drug–target interactions by chemical proteomics

(2009) Marcus Bantscheff et al.   DRUG DISCOVERY TODAY

Lapatinib Combined With Letrozole Versus Letrozole and Placebo As First-Line Therapy for Postmenopausal Hormone Receptor–Positive Metastatic Breast Cancer

(2009) Stephen Johnston et al.   JOURNAL OF CLINICAL ONCOLOGY

Trastuzumab Plus Anastrozole Versus Anastrozole Alone for the Treatment of Postmenopausal Women With Human Epidermal Growth Factor Receptor 2–Positive, Hormone Receptor–Positive Metastatic Breast Cancer: Results From the Randomized Phase III TAnDEM Study

(2009) Bella Kaufman et al.   JOURNAL OF CLINICAL ONCOLOGY

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Targeting of immune signalling networks by bacterial pathogens

(2009) Igor E. Brodsky et al.   NATURE CELL BIOLOGY

Bridging the gap between systems biology and medicine

(2009) Gilles Clermont et al.   Genome Medicine

A Dynamic Network Approach for the Study of Human Phenotypes

(2009) César A. Hidalgo et al.   PLoS Computational Biology

VisANT: an integrative framework for networks in systems biology

(2008) Z. Hu et al.   BRIEFINGS IN BIOINFORMATICS

Cancer driver mutations in protein kinase genes

(2008) Ali Torkamani et al.   CANCER LETTERS

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells

(2008) Xiaosong Liu et al.   CELL RESEARCH

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE