Network biology concepts in complex disease comorbidities

Marfan Syndrome and Related Disorders: 25 Years of Gene Discovery

(2016) Aline Verstraeten et al.   HUMAN MUTATION

Comorbidity Analysis According to Sex and Age in Hypertension Patients in China

(2016) Jiaqi Liu et al.   International Journal of Medical Sciences

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

(2016) Rong Chen et al.   NATURE BIOTECHNOLOGY

A method to decipher pleiotropy by detecting underlying heterogeneity driven by hidden subgroups applied to autoimmune and neuropsychiatric diseases

(2016) Buhm Han et al.   NATURE GENETICS

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

(2016) David Ellinghaus et al.   NATURE GENETICS

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

(2016) Maria Gutierrez-Arcelus et al.   NATURE REVIEWS GENETICS

Unravelling the human genome–phenome relationship using phenome-wide association studies

(2016) William S. Bush et al.   NATURE REVIEWS GENETICS

Health and population effects of rare gene knockouts in adult humans with related parents

(2016) V. M. Narasimhan et al.   SCIENCE

Emerging Role and Therapeutic Implication of Wnt Signaling Pathways in Autoimmune Diseases

(2016) Juan Shi et al.   Journal of Immunology Research

Type 2 Diabetes Mellitus Trajectories and Associated Risks

(2016) Wonsuk Oh et al.   Big Data

Diabetic retinopathy

(2016) Tien Y. Wong et al.   Nature Reviews Disease Primers

Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records

(2016) Riccardo Miotto et al.   Scientific Reports

UBE2L3 Polymorphism Amplifies NF-κB Activation and Promotes Plasma Cell Development, Linking Linear Ubiquitination to Multiple Autoimmune Diseases

(2015) Myles J. Lewis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

(2015) Pau Creixell et al.   CELL

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Molecular and clinical diseasome of comorbidities in exacerbated COPD patients

(2015) Rosa Faner et al.   EUROPEAN RESPIRATORY JOURNAL

Exome-based case–control association study using extreme phenotype design reveals novel candidates with protective effect in diabetic retinopathy

(2015) Corina Shtir et al.   HUMAN GENETICS

Canonical Wnt Signaling in Dendritic Cells Regulates Th1/Th17 Responses and Suppresses Autoimmune Neuroinflammation

(2015) Amol Suryawanshi et al.   JOURNAL OF IMMUNOLOGY

The PPARγ2 Pro12Ala variant is protective against progression of nephropathy in people with type 2 diabetes

(2015) Emanuela Lapice et al.   Journal of Translational Medicine

Personalized medicine: Time for one-person trials

(2015) Nicholas J. Schork   NATURE

The coming era of human phenotyping

(2015)   NATURE BIOTECHNOLOGY

Opportunities for drug repositioning from phenome-wide association studies

(2015) Majid Rastegar-Mojarad et al.   NATURE BIOTECHNOLOGY

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

Pervasive robustness in biological systems

(2015) Marie-Anne Félix et al.   NATURE REVIEWS GENETICS

Protective alleles and modifier variants in human health and disease

(2015) Andrew R. Harper et al.   NATURE REVIEWS GENETICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Basal exon skipping and genetic pleiotropy: A predictive model of disease pathogenesis

(2015) Theodore G. Drivas et al.   Science Translational Medicine

Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

(2015) Hátylas Azevedo et al.   Scientific Reports

Genome-wide copy-number variation study of psychosis in Alzheimer’s disease

(2015) X Zheng et al.   Translational Psychiatry

Causal Drift, Robust Signaling, and Complex Disease

(2015) Andreas Wagner   PLoS One

Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma

(2015) Abhinav Kaushik et al.   PLoS One

Dynamic networks reveal key players in aging

(2014) Fazle E. Faisal et al.   BIOINFORMATICS

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

(2014) Mohammad Moni et al.   BMC BIOINFORMATICS

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

(2014) Tao Zeng et al.   DRUG RESISTANCE UPDATES

Guilt by rewiring: gene prioritization through network rewiring in Genome Wide Association Studies

(2014) L. Hou et al.   HUMAN MOLECULAR GENETICS

The role of the interactome in the maintenance of deleterious variability in human populations

(2014) L. Garcia-Alonso et al.   Molecular Systems Biology

Single-cell technologies for monitoring immune systems

(2014) Pratip K Chattopadhyay et al.   NATURE IMMUNOLOGY

Metformin—mode of action and clinical implications for diabetes and cancer

(2014) Ida Pernicova et al.   Nature Reviews Endocrinology

Cryptic genetic variation: evolution's hidden substrate

(2014) Annalise B. Paaby et al.   NATURE REVIEWS GENETICS

Multimorbidity and rheumatic conditions—enhancing the concept of comorbidity

(2014) Helga Radner et al.   Nature Reviews Rheumatology

Complexity and network dynamics in physiological adaptation: An integrated view

(2014) György Baffy et al.   PHYSIOLOGY & BEHAVIOR

Inverse and Direct Cancer Comorbidity in People with Central Nervous System Disorders: A Meta-Analysis of Cancer Incidence in 577,013 Participants of 50 Observational Studies

(2014) Ferrán Catalá-López et al.   PSYCHOTHERAPY AND PSYCHOSOMATICS

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses

(2014) Kristina Ibáñez et al.   PLoS Genetics

Deeper, longer phenotyping to accelerate the discovery of the genetic architectures of diseases

(2014) Isaac S Kohane   GENOME BIOLOGY

Comorbidities and Polypharmacy

(2014) Thomas G. von Lueder et al.   Heart Failure Clinics

A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

(2013) David R. Blair et al.   CELL

Integrative avenues for exploring the dynamics and evolution of protein interaction networks

(2013) Guillaume Diss et al.   CURRENT OPINION IN BIOTECHNOLOGY

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

The Leu72Met polymorphism of the GHRL gene prevents the development of diabetic nephropathy in Chinese patients with type 2 diabetes mellitus

(2013) Langen Zhuang et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

(2013) Joshua C Denny et al.   NATURE BIOTECHNOLOGY

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

(2013) Jean-Philippe Lambert et al.   NATURE METHODS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Genetic insights into common pathways and complex relationships among immune-mediated diseases

(2013) Miles Parkes et al.   NATURE REVIEWS GENETICS

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

Integration of Protein Abundance and Structure Data Reveals Competition in the ErbB Signaling Network

(2013) C. Kiel et al.   Science Signaling

Single-Stranded DNA-Binding Proteins: Multiple Domains for Multiple Functions

(2013) Thayne H. Dickey et al.   STRUCTURE

Comorbidity: a multidimensional approach

(2013) Enrico Capobianco et al.   TRENDS IN MOLECULAR MEDICINE

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

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

Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

(2013) Sarah A. Pendergrass et al.   PLoS Genetics

Credible Mendelian Randomization Studies: Approaches for Evaluating the Instrumental Variable Assumptions

(2012) M. M. Glymour et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Deep phenotyping for precision medicine

(2012) Peter N. Robinson   HUMAN MUTATION

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

(2012) P. L. Kastritis et al.   Journal of the Royal Society Interface

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Temporal networks

(2012) Petter Holme et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

p53 Dynamics Control Cell Fate

(2012) J. E. Purvis et al.   SCIENCE

The many faces of pleiotropy

(2012) Annalise B. Paaby et al.   TRENDS IN GENETICS

Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability

(2012) Yunpeng Wang et al.   PLoS Computational Biology

Lessons from Model Organisms: Phenotypic Robustness and Missing Heritability in Complex Disease

(2012) Christine Queitsch et al.   PLoS Genetics

Abundant Pleiotropy in Human Complex Diseases and Traits

(2011) Shanya Sivakumaran et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Human Copy Number Variation and Complex Genetic Disease

(2011) Santhosh Girirajan et al.   Annual Review of Genetics

DDN: a caBIG® analytical tool for differential network analysis

(2011) Bai Zhang et al.   BIOINFORMATICS

Inferring pleiotropy by network analysis: linked diseases in the human PPI network

(2011) Thanh-Phuong Nguyen et al.   BMC Systems Biology

The CD6 Multiple Sclerosis Susceptibility Allele Is Associated with Alterations in CD4+ T Cell Proliferation

(2011) D. M. Kofler et al.   JOURNAL OF IMMUNOLOGY

No paradox, no progress: inverse cancer comorbidity in people with other complex diseases

(2011) Rafael Tabarés-Seisdedos et al.   LANCET ONCOLOGY

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

The n-of-1 clinical trial: the ultimate strategy for individualizing medicine?

(2011) Elizabeth O Lillie et al.   Personalized Medicine

Measuring the Evolutionary Rewiring of Biological Networks

(2011) Chong Shou et al.   PLoS Computational Biology

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

(2011) Francisco S. Roque et al.   PLoS Computational Biology

Pervasive Sharing of Genetic Effects in Autoimmune Disease

(2011) Chris Cotsapas et al.   PLoS Genetics

Hsp90 modulates CAG repeat instability in human cells

(2010) David Mittelman et al.   CELL STRESS & CHAPERONES

Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing

(2010) Hansoo Park et al.   NATURE GENETICS

Missing heritability and stochastic genome alterations

(2010) Henry H. Q. Heng   NATURE REVIEWS GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

Defining Comorbidity: Implications for Understanding Health and Health Services

(2009) J. M. Valderas et al.   ANNALS OF FAMILY MEDICINE

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

The Wnt signaling pathway and rheumatoid arthritis

(2009) Francieli de Sousa Rabelo et al.   AUTOIMMUNITY REVIEWS

PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks

(2009) F. Li et al.   BIOINFORMATICS

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

The impact of cellular networks on disease comorbidity

(2009) Juyong Park et al.   Molecular Systems Biology

Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource

(2009) Calliope A Dendrou et al.   NATURE GENETICS

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

Decanalization and the origin of complex disease

(2009) Greg Gibson   NATURE REVIEWS GENETICS

A Dynamic Network Approach for the Study of Human Phenotypes

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

Kinase-Selective Enrichment Enables Quantitative Phosphoproteomics of the Kinome across the Cell Cycle

(2008) Henrik Daub et al.   MOLECULAR CELL

Beta-catenin stabilization extends regulatory T cell survival and induces anergy in nonregulatory T cells

(2008) Yi Ding et al.   NATURE MEDICINE

Molecular and metabolic mechanisms of insulin resistance and β-cell failure in type 2 diabetes

(2008) Deborah M. Muoio et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis

(2008) H. Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

(2008) A. Roguev et al.   SCIENCE

Network Hubs Buffer Environmental Variation in Saccharomyces cerevisiae

(2008) Sasha F Levy et al.   PLOS BIOLOGY

Role of Duplicate Genes in Robustness against Deleterious Human Mutations

(2008) Tzu-Lin Hsiao et al.   PLoS Genetics

Mendelian randomization: Using genes as instruments for making causal inferences in epidemiology

(2007) Debbie A. Lawlor et al.   STATISTICS IN MEDICINE