Genomic and evolutionary classification of lung cancer in never smokers

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

(2021) Jian Carrot-Zhang et al.   Cell Reports

In silico saturation mutagenesis of cancer genes

(2021) Ferran Muiños et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

Tobacco smoking and somatic mutations in human bronchial epithelium

(2020) Kenichi Yoshida et al.   NATURE

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung 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

Genomic landscape of lung adenocarcinoma in East Asians

(2020) Jianbin Chen et al.   NATURE GENETICS

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

(2020) Saioa López et al.   NATURE GENETICS

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

(2020) Ashley M. Laughney et al.   NATURE MEDICINE

Mutation signatures specific to DNA alkylating agents in yeast and cancers

(2020) Natalie Saini et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Konrad J. Karczewski et al.   NATURE

Activation of the receptor tyrosine kinase, RET, improves long-term hematopoietic stem cell outgrowth and potency

(2020) William Grey et al.   BLOOD

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

(2020) Bin Zhu et al.   Nature Communications

Afatinib for the treatment of EGFR mutation-positive NSCLC: A review of clinical findings

(2020) R Donald Harvey et al.   JOURNAL OF ONCOLOGY PHARMACY PRACTICE

Mutational signature SBS8 predominantly arises due to late replication errors in cancer

(2020) Vinod Kumar Singh et al.   Communications Biology

First-Line Nivolumab Plus Ipilimumab in Advanced Non–Small-Cell Lung Cancer (CheckMate 568): Outcomes by Programmed Death Ligand 1 and Tumor Mutational Burden as Biomarkers

(2019) Neal Ready et al.   JOURNAL OF CLINICAL ONCOLOGY

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

(2019) Mia Petljak et al.   CELL

A Compendium of Mutational Signatures of Environmental Agents

(2019) Jill E. Kucab et al.   CELL

TelomereHunter – in silico estimation of telomere content and composition from cancer genomes

(2019) Lars Feuerbach et al.   BMC BIOINFORMATICS

Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma

(2019) Jake June-Koo Lee et al.   CELL

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer

(2019) Myrthe Jager et al.   GENOME RESEARCH

Mechanisms, Hallmarks, and Implications of Stem Cell Quiescence

(2019) Inchul J. Cho et al.   Stem Cell Reports

The Ubiquitin Proteasome System Is a Key Regulator of Pluripotent Stem Cell Survival and Motor Neuron Differentiation

(2019) Monique Bax et al.   Cells

SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events

(2019) Erik N. Bergstrom et al.   BMC GENOMICS

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

(2019) Johan Staaf et al.   NATURE MEDICINE

The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity

(2019) Jude Canon et al.   NATURE

ARID1A promotes genomic stability through protecting telomere cohesion

(2019) Bo Zhao et al.   Nature Communications

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Pathogenic Germline Variants in 10,389 Adult Cancers

(2018) Kuan-lin Huang et al.   CELL

Genome doubling shapes the evolution and prognosis of advanced cancers

(2018) Craig M. Bielski et al.   NATURE GENETICS

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden

(2018) Matthew D. Hellmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole-genome sequencing reveals genomic signatures associated with the inflammatory microenvironments in Chinese NSCLC patients

(2018) Cheng Wang et al.   Nature Communications

Status of KRAS in iPSCs Impacts upon Self-Renewal and Differentiation Propensity

(2018) Kenji Kubara et al.   Stem Cell Reports

CharGer: clinical Characterization of Germline variants

(2018) Adam D Scott et al.   BIOINFORMATICS

ERBB2 -Mutated Metastatic Non–Small Cell Lung Cancer: Response and Resistance to Targeted Therapies

(2017) Jody C. Chuang et al.   Journal of Thoracic Oncology

Genomic deletion of malic enzyme 2 confers collateral lethality in pancreatic cancer

(2017) Prasenjit Dey et al.   NATURE

Systematic analysis of telomere length and somatic alterations in 31 cancer types

(2017) Floris P Barthel et al.   NATURE GENETICS

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures

(2017) Helen Davies et al.   NATURE MEDICINE

Tracking the Evolution of Non–Small-Cell Lung Cancer

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

Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

(2017) Eric Letouzé et al.   Nature Communications

UPS-indel: a Universal Positioning System for Indels

(2017) Mohammad Shabbir Hasan et al.   Scientific Reports

Principles of Reconstructing the Subclonal Architecture of Cancers

(2017) Stefan C. Dentro et al.   Cold Spring Harbor Perspectives in Medicine

Suppression of the SWI/SNF Component Arid1a Promotes Mammalian Regeneration

(2016) Xuxu Sun et al.   Cell Stem Cell

Afatinib versus gefitinib as first-line treatment of patients with EGFR mutation-positive non-small-cell lung cancer (LUX-Lung 7): a phase 2B, open-label, randomised controlled trial

(2016) Keunchil Park et al.   LANCET ONCOLOGY

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

(2016) Joshua D Campbell et al.   NATURE GENETICS

Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study

(2016) Jianxin Shi et al.   PLOS MEDICINE

Mitochondrial DNA copy number variation across human cancers

(2016) Ed Reznik et al.   eLife

TP53 Mutation Spectrum in Smokers and Never Smoking Lung Cancer Patients

(2016) Ann R. Halvorsen et al.   Frontiers in Genetics

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

A systematic analysis of the resistance and sensitivity of HER2YVMAreceptor tyrosine kinase mutant to tyrosine kinase inhibitors in HER2-positive lung cancer

(2015) Xiaokun Shen et al.   JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Frequent alterations in cytoskeleton remodelling genes in primary and metastatic lung adenocarcinomas

(2015) Kui Wu et al.   Nature Communications

Co-occurring Genomic Alterations Define Major Subsets of KRAS-Mutant Lung Adenocarcinoma with Distinct Biology, Immune Profiles, and Therapeutic Vulnerabilities

(2015) F. Skoulidis et al.   Cancer Discovery

Hmga2 is required for canonical WNT signaling during lung development

(2014) Indrabahadur Singh et al.   BMC BIOLOGY

p53 as a target for the treatment of cancer

(2014) Michael J. Duffy et al.   CANCER TREATMENT REVIEWS

The neurotrophic factor receptor RET drives haematopoietic stem cell survival and function

(2014) Diogo Fonseca-Pereira et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Estimating telomere length from whole genome sequence data

(2014) Zhihao Ding et al.   NUCLEIC ACIDS RESEARCH

Two nested developmental waves demarcate a compartment boundary in the mouse lung

(2014) Denise Martinez Alanis et al.   Nature Communications

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids

(2014) Lynnette Fernandez-Cuesta et al.   Nature Communications

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

(2014) Niccolo Bolli et al.   Nature Communications

Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

(2014) S. M. Dewhurst et al.   Cancer Discovery

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Ubiquitin-activating enzyme UBA1 is required for cellular response to DNA damage

(2012) Pavel Moudry et al.   CELL CYCLE

Microenvironmental regulation of stem cells in intestinal homeostasis and cancer

(2011) Jan Paul Medema et al.   NATURE

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Coexistence of Quiescent and Active Adult Stem Cells in Mammals

(2010) L. Li et al.   SCIENCE

Transcriptional regulation of RET by Nkx2-1, Phox2b, Sox10, and Pax3

(2009) Thomas Y.Y. Leon et al.   JOURNAL OF PEDIATRIC SURGERY