A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification

A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification

(2019) Ren-Hua Chung et al.   GigaScience

Integrative omics for health and disease

(2018) Konrad J. Karczewski et al.   NATURE REVIEWS GENETICS

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

Quantifying the regulatory effect size ofcis-acting genetic variation using allelic fold change

(2017) Pejman Mohammadi et al.   GENOME RESEARCH

Genetic architecture: the shape of the genetic contribution to human traits and disease

(2017) Nicholas J. Timpson et al.   NATURE REVIEWS GENETICS

InterSIM: Simulation tool for multiple integrative ‘omic datasets’

(2016) Prabhakar Chalise et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools

(2015) Owen J. L. Rackham et al.   BIOINFORMATICS

SimSeq: a nonparametric approach to simulation of RNA-sequence datasets

(2015) Sam Benidt et al.   BIOINFORMATICS

Complex and multi-allelic copy number variation in human disease

(2015) Christina L. Usher et al.   Briefings in Functional Genomics

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer

(2015) Matthew Ruffalo et al.   PLoS Computational Biology

Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions

(2014) Jason H. Moore et al.   GENETIC EPIDEMIOLOGY

SeqSIMLA2: Simulating Correlated Quantitative Traits Accounting for Shared Environmental Effects in User-Specified Pedigree Structure

(2014) Ren-Hua Chung et al.   GENETIC EPIDEMIOLOGY

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data

(2014) Mehmet Kemal Samur   PLoS One

Interplay of Interlocus Gene Conversion and Crossover in Segmental Duplications Under a Neutral Scenario

(2014) Diego A. Hartasánchez et al.   G3-Genes Genomes Genetics

ATHENA: the analysis tool for heritable and environmental network associations

(2013) Emily R. Holzinger et al.   BIOINFORMATICS

ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network

(2013) Dokyoon Kim et al.   BioData Mining

Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies

(2012) Emily R Holzinger et al.   PHARMACOGENOMICS

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

(2011) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HAPGEN2: simulation of multiple disease SNPs

(2011) Zhan Su et al.   BIOINFORMATICS

A Statistical Framework for eQTL Mapping Using RNA-seq Data

(2011) Wei Sun   BIOMETRICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Integrating diverse genomic data using gene sets

(2011) Svitlana Tyekucheva et al.   GENOME BIOLOGY

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY