GenNet framework: interpretable deep learning for predicting phenotypes from genetic data

Objectives, design and main findings until 2020 from the Rotterdam Study

(2020) M. Arfan Ikram et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Deep neural network improves the estimation of polygenic risk scores for breast cancer

(2020) Adrien Badré et al.   JOURNAL OF HUMAN GENETICS

Exome sequencing and characterization of 49,960 individuals in the UK Biobank

(2020) Cristopher V. Van Hout et al.   NATURE

Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements

(2020) Tiffany Amariuta et al.   NATURE GENETICS

A biologically-informed polygenic score identifies endophenotypes and clinical conditions associated with the insulin receptor function on specific brain regions

(2019) Shantala A. Hari Dass et al.   EBioMedicine

Genome-wide association study identifies 30 loci associated with bipolar disorder

(2019) Eli A. Stahl et al.   NATURE GENETICS

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Visible Machine Learning for Biomedicine

(2018) Michael K. Yu et al.   CELL

Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

(2018) Tom Young et al.   IEEE Computational Intelligence Magazine

Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability

(2018) Pirro G. Hysi 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

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

(2018) Loic Yengo et al.   HUMAN MOLECULAR GENETICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

A survey on deep learning in medical image analysis

(2017) Geert Litjens et al.   MEDICAL IMAGE ANALYSIS

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

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

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

(2016) Santhilal Subhash et al.   BMC BIOINFORMATICS

HASE: Framework for efficient high-dimensional association analyses

(2016) G. V. Roshchupkin et al.   Scientific Reports

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

A polygenic burden of rare disruptive mutations in schizophrenia

(2014) Shaun M. Purcell et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

INRICH: interval-based enrichment analysis for genome-wide association studies

(2012) Phil H. Lee et al.   BIOINFORMATICS

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

(2012) M. Visser et al.   GENOME RESEARCH

Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations

(2012) Sophie I. Candille et al.   PLoS One

DISC1-binding proteins in neural development, signalling and schizophrenia

(2011) Nicholas J. Bradshaw et al.   NEUROPHARMACOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder

(2009) Peter Holmans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Eye color and the prediction of complex phenotypes from genotypes

(2009) Fan Liu et al.   CURRENT BIOLOGY

The Neurodevelopmental Hypothesis of Schizophrenia, Revisited

(2009) S. H. Fatemi et al.   SCHIZOPHRENIA BULLETIN

Three Genome-wide Association Studies and a Linkage Analysis Identify HERC2 as a Human Iris Color Gene

(2008) Manfred Kayser et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation

(2008) Jiali Han et al.   PLoS Genetics