A molecular phenotypic map of malignant pleural mesothelioma

First-line nivolumab plus ipilimumab in unresectable malignant pleural mesothelioma (CheckMate 743): a multicentre, randomised, open-label, phase 3 trial

(2021) Paul Baas et al.   LANCET

Challenges in lung and thoracic pathology: molecular advances in the classification of pleural mesotheliomas

(2021) Lynnette Fernandez-Cuesta et al.   VIRCHOWS ARCHIV

Whole-genome doubling confers unique genetic vulnerabilities on tumour cells

(2021) Ryan J. Quinton et al.   NATURE

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

(2020) Isidro Cortés-Ciriano et al.   NATURE GENETICS

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers

(2020) Hoon Kim et al.   NATURE GENETICS

Improved Indel Detection in DNA and RNA via Realignment with ABRA2

(2019) Lisle E Mose et al.   BIOINFORMATICS

Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications

(2019) Yuna Blum et al.   Nature Communications

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Tumor diversity and the trade-off between universal cancer tasks

(2019) Jean Hausser et al.   Nature Communications

Redefining malignant pleural mesothelioma types as a continuum uncovers immune-vascular interactions

(2019) Nicolas Alcala et al.   EBioMedicine

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Integrative Molecular Characterization of Malignant Pleural Mesothelioma

(2018) Julija Hmeljak et al.   Cancer Discovery

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types

(2017) Sejoon Lee et al.   NUCLEIC ACIDS RESEARCH

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations

(2017) Victor Renault et al.   PLoS One

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Bevacizumab for newly diagnosed pleural mesothelioma in the Mesothelioma Avastin Cisplatin Pemetrexed Study (MAPS): a randomised, controlled, open-label, phase 3 trial

(2016) Gérard Zalcman et al.   LANCET

Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations

(2016) Raphael Bueno et al.   NATURE GENETICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition

(2015) M. P. Mak et al.   CLINICAL CANCER RESEARCH

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH