Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

Plasma cell-free DNA variant analysis compared with methylated DNA analysis in renal cell carcinoma

(2020) Kathryn Lasseter et al.   GENETICS IN MEDICINE

Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA

(2019) Shu Yi Shen et al.   Nature Protocols

The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients

(2018) Oliver A. Zill et al.   CLINICAL CANCER RESEARCH

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

(2018) Shu Yi Shen et al.   NATURE

Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker

(2018) Abu Ali Ibn Sina et al.   Nature Communications

Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease

(2018) Joshua Moss et al.   Nature Communications

Detection and surveillance of bladder cancer using urine tumor DNA

(2018) Jonathan C. Dudley et al.   Cancer Discovery

Evolution of Circulating Tumor DNA Profile from First-line to Subsequent Therapy in Metastatic Renal Cell Carcinoma

(2017) Sumanta K. Pal et al.   EUROPEAN UROLOGY

Bosniak Classification for Complex Renal Cysts Reevaluated: A Systematic Review

(2017) Ivo G. Schoots et al.   JOURNAL OF UROLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer

(2016) Inessa Skrypkina et al.   DISEASE MARKERS

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Sex differences of leukocytes DNA methylation adjusted for estimated cellular proportions

(2015) Masatoshi Inoshita et al.   Biology of Sex Differences

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Small Renal Mass

(2010) Inderbir S. Gill et al.   NEW ENGLAND JOURNAL OF MEDICINE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS