Single nucleotide variant counts computed from RNA sequencing and cellular traffic into human kidney allografts

The Banff 2017 Kidney Meeting Report: Revised diagnostic criteria for chronic active T cell-mediated rejection, antibody-mediated rejection, and prospects for integrative endpoints for next-generation clinical trials

(2018) M. Haas et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

(2017) Ashis Saha et al.   GENOME RESEARCH

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

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

(2017) Barbara E Stranger et al.   NATURE GENETICS

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

(2017) Max Schelker et al.   Nature Communications

The Banff 2015 Kidney Meeting Report: Current Challenges in Rejection Classification and Prospects for Adopting Molecular Pathology

(2016) A. Loupy et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA

(2016) Matt R. Paul et al.   BMC GENOMICS

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues

(2016) Heather E. Wheeler et al.   PLoS Genetics

Assessing allele-specific expression across multiple tissues from RNA-seq read data

(2015) Matti Pirinen et al.   BIOINFORMATICS

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

(2015) Eric R Gamazon et al.   NATURE GENETICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients

(2015) Casey Dorr et al.   PLoS One

Genome measures used for quality control are dependent on gene function and ancestry

(2014) Jing Wang et al.   BIOINFORMATICS

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

(2013) Ting Gong et al.   BIOINFORMATICS

Three-stage quality control strategies for DNA re-sequencing data

(2013) Y. Guo et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Factors influencing long-term outcome after kidney transplantation

(2013) Christophe Legendre et al.   TRANSPLANT INTERNATIONAL

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

MicroRNA Sequence Profiles of Human Kidney Allografts With or Without Tubulointerstitial Fibrosis

(2012) Iddo Z. Ben-Dov et al.   TRANSPLANTATION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Identification of lesions indicating rejection in kidney transplant biopsies: tubulitis is severely under-detected by conventional microscopy

(2011) M. Elshafie et al.   NEPHROLOGY DIALYSIS TRANSPLANTATION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS