Month: June 2016


[PMID:27288499] [Bioinformatics]

GenVisR: Genomic Visualizations in R

“suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest.”



[PMID:27333808] [Genome Biology]

MUFFINN: cancer gene discovery via network analysis of somatic mutation data

“a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks” “This pathway-centric method shows high sensitivity compared with gene-centric analyses of mutation data.” “is highly predictive for known cancer genes, particularly for genes with low mutation occurrence among cancer patients, with the identification of drivers amongst these genes having substantially higher sensitivity than conventional methods based on gene-centric analysis of mutation data. MUFFINN works effectively with both pan-cancer and individual cancer type samples.”

NGS Simulation Tools

[PMID:27320129] [Nature Reviews Genetics]

A comparison of tools for the simulation of genomic next-generation sequencing data

Review of 23 computational tools for the simulation of NGS data.



[PMID:27311963] [Genome Biology]

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

“a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis.”


Tumor-infiltrating T cell Repertoire

[PMID:27240091] [Nature Genetics]

Landscape of tumor-infiltrating T cell repertoire of human cancers

“a computational method to infer the complementarity-determining region 3 (CDR3) sequences of tumor-infiltrating T cells”. Work from Shirley Liu. It seems the codes are not available.



[PMID:27271197] [Nature Methods]

Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing

“Structural Variant Search (SVS), a method to accurately detect rare somSVs by low-coverage sequencing.”



[PMID:27187206] [Bioinformatics]

SoFIA: a data integration framework for annotating high-throughput datasets

“a framework for workflow-driven data integration with a focus on genomic annotation.”