Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

Interpreting pathways to discover cancer driver genes with Moonlight

(2020) Antonio Colaprico et al.   Nature Communications

Durvalumab with or without tremelimumab in patients with recurrent or metastatic head and neck squamous cell carcinoma: EAGLE, a randomized, open-label phase III study

(2020) R.L. Ferris et al.   ANNALS OF ONCOLOGY

Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis

(2020) Bo Wen et al.   Nature Communications

PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations

(2019) Bo Wen et al.   GENOME RESEARCH

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

(2019) Mohamed Mounir et al.   PLoS Computational Biology

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

TMT labeling for the masses: A robust and cost-efficient, in-solution labeling approach

(2019) Jana Zecha et al.   MOLECULAR & CELLULAR PROTEOMICS

Graph algorithms for condensing and consolidating gene set analysis results

(2019) Sara R. Savage et al.   MOLECULAR & CELLULAR PROTEOMICS

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline

(2019) David D. Shteynberg et al.   JOURNAL OF PROTEOME RESEARCH

Palbociclib and cetuximab in platinum-resistant and in cetuximab-resistant human papillomavirus-unrelated head and neck cancer: a multicentre, multigroup, phase 2 trial

(2019) Douglas Adkins et al.   LANCET ONCOLOGY

Insights into impact of DNA copy number alteration and methylation on the proteogenomic landscape in human ovarian cancer via a multi-omics integrative analysis

(2019) Xiaoyu Song et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

(2019) David J. Clark et al.   CELL

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics

(2018) David J. Clark et al.   JOURNAL OF PROTEOME RESEARCH

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

(2018) Philipp Mertins et al.   Nature Protocols

Gene signatures and expression of miRNAs associated with efficacy of panitumumab in a head and neck cancer phase II trial

(2018) Marco Siano et al.   ORAL ONCOLOGY

NAA80 is actin’s N-terminal acetyltransferase and regulates cytoskeleton assembly and cell motility

(2018) Adrian Drazic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

Assembly and activation of the Hippo signalome by FAT1 tumor suppressor

(2018) Daniel Martin et al.   Nature Communications

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

(2018) Qingsong Gao et al.   Cell Reports

PDV: an integrative proteomics data viewer

(2018) Kai Li et al.   BIOINFORMATICS

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2018) Freddie Bray et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Contact inhibitory Eph signaling suppresses EGF-promoted cell migration by decoupling EGFR activity from vesicular recycling

(2018) Wayne Stallaert et al.   Science Signaling

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

(2018) James M. McFarland et al.   Nature Communications

Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma

(2018) Christina Karamboulas et al.   Cell Reports

Basal subtype is predictive for response to cetuximab treatment in patient-derived xenografts of squamous cell head and neck cancer

(2017) Konrad Klinghammer et al.   INTERNATIONAL JOURNAL OF CANCER

Ki67 Proliferation Index as a Tool for Chemotherapy Decisions During and After Neoadjuvant Aromatase Inhibitor Treatment of Breast Cancer: Results From the American College of Surgeons Oncology Group Z1031 Trial (Alliance)

(2017) Matthew J. Ellis et al.   JOURNAL OF CLINICAL ONCOLOGY

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results

(2017) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Emerging functions of the EGFR in cancer

(2017) Sara Sigismund et al.   Molecular Oncology

Distinct kinetics of serine and threonine dephosphorylation are essential for mitosis

(2017) Jamin B. Hein et al.   NATURE CELL BIOLOGY

Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas

(2017) Simon Papillon-Cavanagh et al.   NATURE GENETICS

Plk1 regulates contraction of postmitotic smooth muscle cells and is required for vascular homeostasis

(2017) Guillermo de Cárcer et al.   NATURE MEDICINE

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

LinkedOmics: analyzing multi-omics data within and across 32 cancer types

(2017) Suhas V Vasaikar et al.   NUCLEIC ACIDS RESEARCH

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

(2017) Kenneth Daily et al.   Scientific Data

Epidermal Growth Factor Receptor Cell Proliferation Signaling Pathways

(2017) et al.   Cancers

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann et al.   BIOINFORMATICS

Safety and clinical activity of pembrolizumab for treatment of recurrent or metastatic squamous cell carcinoma of the head and neck (KEYNOTE-012): an open-label, multicentre, phase 1b trial

(2016) Tanguy Y Seiwert et al.   LANCET ONCOLOGY

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

(2016) Jing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

The rules and impact of nonsense-mediated mRNA decay in human cancers

(2016) Rik G H Lindeboom et al.   NATURE GENETICS

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

moFF: a robust and automated approach to extract peptide ion intensities

(2016) Andrea Argentini et al.   NATURE METHODS

Recurrent chimeric fusion RNAs in non-cancer tissues and cells

(2016) Mihaela Babiceanu et al.   NUCLEIC ACIDS RESEARCH

Divergent viral presentation among human tumors and adjacent normal tissues

(2016) Song Cao et al.   Scientific Reports

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

(2016) Nathan Salomonis et al.   Stem Cell Reports

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

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Polo-like kinase 1 inhibits DNA damage response during mitosis

(2015) Jan Benada et al.   CELL CYCLE

Epigenetic silencing of neurofilament genes promotes an aggressive phenotype in breast cancer

(2015) Marilia Freitas Calmon et al.   Epigenetics

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Large-scale profiling of microRNAs for The Cancer Genome Atlas

(2015) Andy Chu et al.   NUCLEIC ACIDS RESEARCH

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Targeting Cdc20 as a novel cancer therapeutic strategy

(2015) Lixia Wang et al.   PHARMACOLOGY & THERAPEUTICS

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

(2015) Eric W. Deutsch et al.   Proteomics Clinical Applications

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution

(2015) S. Kasar et al.   Nature Communications

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

(2015) Yuan Gao et al.   GENOME BIOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Performance evaluation of DNA copy number segmentation methods

(2014) Morgane Pierre-Jean et al.   BRIEFINGS IN BIOINFORMATICS

Prognostic Biomarkers in Phase II Trial of Cetuximab-Containing Induction and Chemoradiation in Resectable HNSCC: Eastern Cooperative Oncology Group E2303

(2014) A. Psyrri et al.   CLINICAL CANCER RESEARCH

Integrative Analysis of Head and Neck Cancer Identifies Two Biologically Distinct HPV and Three Non-HPV Subtypes

(2014) M. K. Keck et al.   CLINICAL CANCER RESEARCH

Randomized Phase III Trial of Concurrent Accelerated Radiation Plus Cisplatin With or Without Cetuximab for Stage III to IV Head and Neck Carcinoma: RTOG 0522

(2014) K. Kian Ang et al.   JOURNAL OF CLINICAL ONCOLOGY

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

(2014) Navin Rauniyar et al.   JOURNAL OF PROTEOME RESEARCH

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Sangtae Kim et al.   Nature Communications

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes

(2013) Vonn Walter 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

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

(2012) Matteo Benelli et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Automatic Relevance Determination in Nonnegative Matrix Factorization with the /spl beta/-Divergence

(2012) V. Y. F. Tan et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Cortactin in cell migration and cancer at a glance

(2012) S. M. MacGrath et al.   JOURNAL OF CELL SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

MGMT promoter methylation is predictive of response to radiotherapy and prognostic in the absence of adjuvant alkylating chemotherapy for glioblastoma

(2011) A. L. Rivera et al.   NEURO-ONCOLOGY

Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation

(2011) Saw Yen Ow et al.   PROTEOMICS

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

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Oncogenic Activity of Ect2 Is Regulated through Protein Kinase Cι-mediated Phosphorylation

(2010) Verline Justilien et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Mammalian Target of Rapamycin Complex 1 (mTORC1) Activity Is Associated with Phosphorylation of Raptor by mTOR

(2009) Lifu Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Regulation of Chk2 Ubiquitination and Signaling through Autophosphorylation of Serine 379

(2008) C. M. Lovly et al.   MOLECULAR AND CELLULAR BIOLOGY

Platinum-Based Chemotherapy plus Cetuximab in Head and Neck Cancer

(2008) Jan B. Vermorken et al.   NEW ENGLAND JOURNAL OF MEDICINE

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH