Mechanisms of tissue and cell-type specificity in heritable traits and diseases

Repurposing large health insurance claims data to estimate genetic and environmental contributions in 560 phenotypes

(2019) Chirag M. Lakhani et al.   NATURE GENETICS

Tissue-specificity in cancer: The rule, not the exception

(2019) Kevin M. Haigis et al.   SCIENCE

Super-Mendelian inheritance mediated by CRISPR–Cas9 in the female mouse germline

(2019) Hannah A. Grunwald et al.   NATURE

PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components

(2019) Zhipeng Ma et al.   NATURE

Genetic compensation triggered by mutant mRNA degradation

(2019) Mohamed A. El-Brolosy et al.   NATURE

Noncoding deletions reveal a gene that is critical for intestinal function

(2019) Danit Oz-Levi et al.   NATURE

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns

(2018) Laura Magill Sack et al.   CELL

Circuit Design Features of a Stable Two-Cell System

(2018) Xu Zhou et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Tissue-Specific Control of Tissue-Resident Memory T Cells

(2018) Yong Liu et al.   CRITICAL REVIEWS IN IMMUNOLOGY

Two breakthrough gene-targeted treatments for spinal muscular atrophy: challenges remain

(2018) Charlotte J. Sumner et al.   JOURNAL OF CLINICAL INVESTIGATION

Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed

(2018) Ksenya Kveler et al.   NATURE BIOTECHNOLOGY

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

(2018) Eric R. Gamazon et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Mapping the physical network of cellular interactions

(2018) Jean-Charles Boisset et al.   NATURE METHODS

Nusinersen versus Sham Control in Later-Onset Spinal Muscular Atrophy

(2018) Eugenio Mercuri et al.   NEW ENGLAND JOURNAL OF MEDICINE

Alternative splicing isoforms in health and disease

(2018) Hyoung Kyu Kim et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Systematic analysis of complex genetic interactions

(2018) Elena Kuzmin et al.   SCIENCE

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns

(2018) Lisa Bastarache et al.   SCIENCE

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

(2018) Michael J. Gandal et al.   SCIENCE

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

(2018) Alvaro N. Barbeira et al.   Nature Communications

Role of duplicate genes in determining the tissue-selectivity of hereditary diseases

(2018) Ruth Barshir et al.   PLoS Genetics

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders

(2018) Mari E. K. Niemi et al.   NATURE

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

(2018) Towfique Raj et al.   NATURE GENETICS

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

An integrative tissue-network approach to identify and test human disease genes

(2018) Victoria Yao et al.   NATURE BIOTECHNOLOGY

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

BRCA1 ensures genome integrity by eliminating estrogen-induced pathological topoisomerase II–DNA complexes

(2018) Hiroyuki Sasanuma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development cell by cell

(2018) Elizabeth Pennisi   SCIENCE

Tissue-specific and time-dependent clonal expansion of ENU-induced mutant cells in gpt delta mice

(2017) Takafumi Nakayama et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes

(2017) Jeremy R.B. Newman et al.   GENOME RESEARCH

Genetic modifiers of Mendelian disease: Huntington’s disease and the trinucleotide repeat disorders

(2017) Peter A. Holmans et al.   HUMAN MOLECULAR GENETICS

The cell adhesion molecule BT-IgSF is essential for a functional blood–testis barrier and male fertility in mice

(2017) Laura Pelz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tissue adaptation: Implications for gut immunity and tolerance

(2017) Ana M.C. Faria et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Reproducible RNA-seq analysis using recount2

(2017) Leonardo Collado-Torres et al.   NATURE BIOTECHNOLOGY

An integrated expression atlas of miRNAs and their promoters in human and mouse

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

Estimating the causal tissues for complex traits and diseases

(2017) Halit Ongen et al.   NATURE GENETICS

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

Associating cellular epigenetic models with human phenotypes

(2017) Tuuli Lappalainen et al.   NATURE REVIEWS GENETICS

Nusinersen versus Sham Control in Infantile-Onset Spinal Muscular Atrophy

(2017) Richard S. Finkel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

(2017) Alejandro Reyes et al.   NUCLEIC ACIDS RESEARCH

The DifferentialNet database of differential protein–protein interactions in human tissues

(2017) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention

(2017) Cristian Tomasetti et al.   SCIENCE

Concise Review: Induced Pluripotent Stem Cell Research in the Era of Precision Medicine

(2017) Takashi Hamazaki et al.   STEM CELLS

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

The Synucleinopathies: Twenty Years On

(2017) Michel Goedert et al.   Journal of Parkinsons Disease

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors

(2016) Wael Jdey et al.   CLINICAL CANCER RESEARCH

RB1: a prototype tumor suppressor and an enigma

(2016) Nicholas J. Dyson   GENES & DEVELOPMENT

Genetic determinants of myocardial dysfunction

(2016) Xianchi Li et al.   JOURNAL OF MEDICAL GENETICS

Genetics in Parkinson disease: Mendelian versus non-Mendelian inheritance

(2016) Dena G. Hernandez et al.   JOURNAL OF NEUROCHEMISTRY

Gene‐specific correlation of RNA and protein levels in human cells and tissues

(2016) Fredrik Edfors et al.   Molecular Systems Biology

Transcriptomics resources of human tissues and organs

(2016) M. Uhlen et al.   Molecular Systems Biology

Tissue biology perspective on macrophages

(2016) Yasutaka Okabe et al.   NATURE IMMUNOLOGY

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

Insights on the pathophysiology of Alzheimer's disease: The crosstalk between amyloid pathology, neuroinflammation and the peripheral immune system

(2016) Sandro Dá Mesquita et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues

(2016) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

(2016) Gregorio Alanis-Lobato et al.   NUCLEIC ACIDS RESEARCH

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Distribution of miRNA expression across human tissues

(2016) Nicole Ludwig et al.   NUCLEIC ACIDS RESEARCH

The Human Phenotype Ontology in 2017

(2016) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Two genes substitute for the mouse Y chromosome for spermatogenesis and reproduction

(2016) Y. Yamauchi et al.   SCIENCE

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

(2016) X. Lan et al.   SCIENCE

Functional redundancy of the kinases MEK1 and MEK2: Rescue of theMek1mutant phenotype byMek2knock-in reveals a protein threshold effect

(2016) Rifdat Aoidi et al.   Science Signaling

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

(2016) Charles E. Breeze et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

(2016) André Schultz et al.   PLoS Computational Biology

A Bystander Mechanism Explains the Specific Phenotype of a Broadly Expressed Misfolded Protein

(2016) Lauren Klabonski et al.   PLoS Genetics

Functional redundancy of the kinases MEK1 and MEK2: Rescue of theMek1mutant phenotype byMek2knock-in reveals a protein threshold effect

(2016) Rifdat Aoidi et al.   Science Signaling

The International Human Epigenome Consortium Data Portal

(2016) David Bujold et al.   Cell Systems

Tissue Specificity of Human Disease Module

(2016) Maksim Kitsak et al.   Scientific Reports

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions

(2015) Katrin Sameith et al.   BMC BIOLOGY

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma

(2015) Amitabh Sharma et al.   HUMAN MOLECULAR GENETICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

DASHR: database of small human noncoding RNAs

(2015) Yuk Yee Leung et al.   NUCLEIC ACIDS RESEARCH

Effect of predicted protein-truncating genetic variants on the human transcriptome

(2015) M. A. Rivas et al.   SCIENCE

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Higher-order genetic interactions and their contribution to complex traits

(2015) Matthew B. Taylor et al.   TRENDS IN GENETICS

Towards tissue-specific pharmacology: insights from the calcium-sensing receptor as a paradigm for GPCR (patho)physiological bias

(2015) Katie Leach et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Haploinsufficiency for BRCA1 leads to cell-type-specific genomic instability and premature senescence

(2015) Maja Sedic et al.   Nature Communications

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

Human protein interaction networks across tissues and diseases

(2015) Esti Yeger-Lotem et al.   Frontiers in Genetics

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

(2014) Warren A. Kibbe et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases

(2014) Ruth Barshir et al.   PLoS Computational Biology

Cancer Evolution Is Associated with Pervasive Positive Selection on Globally Expressed Genes

(2014) Sheli L. Ostrow et al.   PLoS Genetics

Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes

(2013) Jacqueline K. White et al.   CELL

Molecular mechanisms of paralogous compensation and the robustness of cellular networks

(2013) Guillaume Diss et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users

(2012) Ana Rath et al.   HUMAN MUTATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

(2012) Oded Magger et al.   PLoS Computational Biology

Tissue-Specific Proteins and Functional Implications

(2011) Dorothea Emig et al.   JOURNAL OF PROTEOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

 40p53 controls the switch from pluripotency to differentiation by regulating IGF signaling in ESCs

(2010) E. Ungewitter et al.   GENES & DEVELOPMENT

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Tissue Selectivity in Multiple Endocrine Neoplasia Type 1-Associated Tumorigenesis

(2009) A. Gracanin et al.   CANCER RESEARCH

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies

(2009) Hemant Khanna et al.   NATURE GENETICS

Genetics of Type 1A Diabetes

(2009) Patrick Concannon et al.   NEW ENGLAND JOURNAL OF MEDICINE

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Exposing the fitness contribution of duplicated genes

(2008) Alexander DeLuna et al.   NATURE GENETICS

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network properties of genes harboring inherited disease mutations

(2008) I. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA