Genomic–transcriptomic evolution in lung cancer and metastasis

The evolution of non-small cell lung cancer metastases in TRACERx

(2023) Maise Al Bakir et al.   NATURE

Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA

(2023) Christopher Abbosh et al.   NATURE

The evolution of lung cancer and impact of subclonal selection in TRACERx

(2023) Alexander M. Frankell et al.   NATURE

Evolutionary characterization of lung adenocarcinoma morphology in TRACERx

(2023) Takahiro Karasaki et al.   NATURE MEDICINE

RNA editing underlies genetic risk of common inflammatory diseases

(2022) Qin Li et al.   NATURE

Mechanisms of APOBEC3 mutagenesis in human cancer cells

(2022) Mia Petljak et al.   NATURE

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression

(2022) Shaolong Cao et al.   NATURE BIOTECHNOLOGY

RAS oncogenic activity predicts response to chemotherapy and outcome in lung adenocarcinoma

(2022) Philip East et al.   Nature Communications

The Dual Function of KDM5C in Both Gene Transcriptional Activation and Repression Promotes Breast Cancer Cell Growth and Tumorigenesis

(2021) Hai‐feng Shen et al.   Advanced Science

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

(2021) Stephanie Sungalee et al.   NATURE GENETICS

Tracking Cancer Evolution through the Disease Course

(2021) Chris Bailey et al.   Cancer Discovery

Induction of APOBEC3 exacerbates DNA replication stress and chromosomal instability in early breast and lung cancer evolution

(2021) Subramanian Venkatesan et al.   Cancer Discovery

Using DNA sequencing data to quantify T cell fraction and therapy response

(2021) Robert Bentham et al.   NATURE

Invasive mucinous adenocarcinoma: genetic insights into a lung cancer entity with distinct clinical behavior and genomic features

(2021) Reinhard Buettner   MODERN PATHOLOGY

Multi-omic machine learning predictor of breast cancer therapy response

(2021) Stephen-John Sammut et al.   NATURE

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

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

Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution

(2020) Saioa López et al.   NATURE GENETICS

Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the Friends of Cancer Research TMB Harmonization Project

(2020) Diana M Merino et al.   Journal for ImmunoTherapy of Cancer

Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

(2020) Lindsay M. LaFave et al.   CANCER CELL

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

(2020) Nemanja Despot Marjanovic et al.   CANCER CELL

Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots

(2020) Pégah Jalili et al.   Nature Communications

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches

(2020) Brent S. Pedersen et al.   Genome Medicine

Pervasive chromosomal instability and karyotype order in tumour evolution

(2020) Thomas B. K. Watkins et al.   NATURE

Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency

(2020) Parinaz Mehdipour et al.   NATURE

Histone methyltransferase SETD2 inhibits tumor growth via suppressing CXCL1-mediated activation of cell cycle in lung adenocarcinoma

(2020) You Zhou et al.   Aging-US

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

(2019) Bo Zhou et al.   NUCLEIC ACIDS RESEARCH

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

A clonal expression biomarker associates with lung cancer mortality

(2019) Dhruva Biswas et al.   NATURE MEDICINE

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Targeted Tissue and Cell-Free Tumor DNA Sequencing of Advanced Lung Squamous-Cell Carcinoma Reveals Clinically Significant Prevalence of Actionable Alterations

(2018) Vincent K. Lam et al.   Clinical Lung Cancer

RNA editing derived epitopes function as cancer antigens to elicit immune responses

(2018) Minying Zhang et al.   Nature Communications

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Tracking the Evolution of Non–Small-Cell Lung Cancer

(2017) Mariam Jamal-Hanjani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G

(2017) Shraddha Sharma et al.   PeerJ

Gene expression markers of Tumor Infiltrating Leukocytes

(2017) Patrick Danaher et al.   Journal for ImmunoTherapy of Cancer

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

(2016) Joshua D Campbell et al.   NATURE GENETICS

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme

(2016) Shraddha Sharma et al.   Scientific Reports

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

(2015) Stephen W. Hartley et al.   BMC BIOINFORMATICS

The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers

(2015) Leng Han et al.   CANCER CELL

The landscape of genomic imprinting across diverse adult human tissues

(2015) Yael Baran et al.   GENOME RESEARCH

TheVGAMPackage for Capture-Recapture Data Using the Conditional Likelihood

(2015) Thomas W. Yee et al.   Journal of Statistical Software

The 2015 World Health Organization Classification of Lung Tumors

(2015) William D. Travis et al.   Journal of Thoracic Oncology

Mutations driving CLL and their evolution in progression and relapse

(2015) Dan A. Landau et al.   NATURE

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma

(2015) T H Ho et al.   ONCOGENE

APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages

(2015) Shraddha Sharma et al.   Nature Communications

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma

(2013) Leilei Chen et al.   NATURE MEDICINE

Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function

(2013) Nikolay S. Outchkourov et al.   Cell Reports

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular Epidemiology of EGFR and KRAS Mutations in 3,026 Lung Adenocarcinomas: Higher Susceptibility of Women to Smoking-Related KRAS-Mutant Cancers

(2012) S. Dogan et al.   CLINICAL CANCER RESEARCH

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols