Proteogenomic landscape of squamous cell lung cancer

Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer

(2018) Elizabeth A. McMillan et al.   CELL

Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross-linking

(2018) Alessandro Porrello et al.   Nature Communications

Whole Exome and Transcriptome Analyses Integrated with Microenvironmental Immune Signatures of Lung Squamous Cell Carcinoma

(2018) Jeong-Sun Seo et al.   Cancer Immunology Research

Nivolumab Versus Docetaxel in Previously Treated Patients With Advanced Non–Small-Cell Lung Cancer: Two-Year Outcomes From Two Randomized, Open-Label, Phase III Trials (CheckMate 017 and CheckMate 057)

(2017) Leora Horn et al.   JOURNAL OF CLINICAL ONCOLOGY

Lung Adenocarcinoma and Squamous Cell Carcinoma Gene Expression Subtypes Demonstrate Significant Differences in Tumor Immune Landscape

(2017) Hawazin Faruki et al.   Journal of Thoracic Oncology

Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue

(2017) Deanna L. Plubell et al.   MOLECULAR & CELLULAR PROTEOMICS

Translation from unconventional 5′ start sites drives tumour initiation

(2017) Ataman Sendoel et al.   NATURE

WNT signalling in prostate cancer

(2017) Virginia Murillo-Garzón et al.   Nature Reviews Urology

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens

(2017) Walter F Lenoir et al.   NUCLEIC ACIDS RESEARCH

Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms

(2017) Paul A. Stewart et al.   PROTEOMICS

Neutrophils dominate the immune cell composition in non-small cell lung cancer

(2017) Julia Kargl et al.   Nature Communications

ΔNp63 Inhibits Oxidative Stress-Induced Cell Death, Including Ferroptosis, and Cooperates with the BCL-2 Family to Promote Clonogenic Survival

(2017) Gary X. Wang et al.   Cell Reports

Silence of fibronectin 1 increases cisplatin sensitivity of non-small cell lung cancer cell line

(2016) Weiwei Gao et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The p53 family orchestrates the regulation of metabolism: physiological regulation and implications for cancer therapy

(2016) Marco Napoli et al.   BRITISH JOURNAL OF CANCER

Identification and Characterization of MCM3 as a Kelch-like ECH-associated Protein 1 (KEAP1) Substrate

(2016) Kathleen M. Mulvaney et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Multiplatform-based molecular subtypes of non-small-cell lung cancer

(2016) F Chen et al.   ONCOGENE

Squamous Cell Lung Cancer: From Tumor Genomics to Cancer Therapeutics

(2015) D. R. Gandara et al.   CLINICAL CANCER RESEARCH

Objective Measurement and Clinical Significance of TILs in Non–Small Cell Lung Cancer

(2015) Kurt A. Schalper et al.   JNCI-Journal of the National Cancer Institute

NRF2 regulates serine biosynthesis in non–small cell lung cancer

(2015) Gina M DeNicola et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Nivolumab versus Docetaxel in Advanced Squamous-Cell Non–Small-Cell Lung Cancer

(2015) Julie Brahmer et al.   NEW ENGLAND JOURNAL OF MEDICINE

T-cell exhaustion in the tumor microenvironment

(2015) Y Jiang et al.   Cell Death & Disease

Objective Measurement and Clinical Significance of TILs in Non–Small Cell Lung Cancer

(2015) Kurt A. Schalper et al.   JNCI-Journal of the National Cancer Institute

Proteomic analysis of colon and rectal carcinoma using standard and customized databases

(2015) Robbert J.C. Slebos et al.   Scientific Data

PROGgeneV2: enhancements on the existing database

(2015) Chirayu Pankaj Goswami et al.   BMC CANCER

Conducting Meta-Analyses inRwith themetaforPackage

(2015) Wolfgang Viechtbauer   Journal of Statistical Software

A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma

(2015) Paul A. Stewart et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

IAPP-driven metabolic reprogramming induces regression of p53-deficient tumours in vivo

(2014) Avinashnarayan Venkatanarayan et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Tertiary lymphoid structures in cancer and beyond

(2014) Marie-Caroline Dieu-Nosjean et al.   TRENDS IN IMMUNOLOGY

Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact

(2014) Lei Li et al.   Nature Communications

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Iterative rank-order normalization of gene expression microarray data

(2013) Eric A Welsh et al.   BMC BIOINFORMATICS

Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer

(2013) M. E. Abazeed et al.   CANCER RESEARCH

Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification

(2013) Mikhail M. Savitski et al.   JOURNAL OF PROTEOME RESEARCH

PTPN12 promotes resistance to oxidative stress and supports tumorigenesis by regulating FOXO signaling

(2013) I S Harris et al.   ONCOGENE

FHL2 Silencing Reduces Wnt Signaling and Osteosarcoma Tumorigenesis In Vitro and In Vivo

(2013) Julia Brun et al.   PLoS One

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer

(2012) Jamie K. Teer et al.   BIOINFORMATICS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Functions of S100 Proteins

(2012) R. Donato et al.   CURRENT MOLECULAR MEDICINE

Matrix architecture defines the preferential localization and migration of T cells into the stroma of human lung tumors

(2012) Hélène Salmon et al.   JOURNAL OF CLINICAL INVESTIGATION

In-depth Proteomic Analysis of Nonsmall Cell Lung Cancer to Discover Molecular Targets and Candidate Biomarkers

(2012) Takefumi Kikuchi et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Lyn is a redox sensor that mediates leukocyte wound attraction in vivo

(2011) Sa Kan Yoo et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

Lung Squamous Cell Carcinoma mRNA Expression Subtypes Are Reproducible, Clinically Important, and Correspond to Normal Cell Types

(2010) M. D. Wilkerson et al.   CLINICAL CANCER RESEARCH

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Cysteine Redox Potential Determines Pro-Inflammatory IL-1β Levels

(2009) Smita S. Iyer et al.   PLoS One

Cross-Species Comparison of Human and Mouse Intestinal Polyps Reveals Conserved Mechanisms in Adenomatous Polyposis Coli (APC)-Driven Tumorigenesis

(2008) Claudia Gaspar et al.   AMERICAN JOURNAL OF PATHOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY