Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability

Exploring the Differential Expression and Prognostic Significance of the COL11A1 Gene in Human Colorectal Carcinoma: An Integrated Bioinformatics Approach

(2021) Ritwik Patra et al.   Frontiers in Genetics

Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes

(2021) Grégory Ehx et al.   IMMUNITY

caAtlas: An immunopeptidome atlas of human cancer

(2021) Xinpei Yi et al.   iScience

MAPDP: a cloud-based computational platform for immunopeptidomics analyses

(2020) Mathieu Courcelles et al.   JOURNAL OF PROTEOME RESEARCH

Landscape of transcriptome variations uncovering known and novel driver events in colorectal carcinoma

(2020) Giovanna Pira et al.   Scientific Reports

Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer

(2020) Qingchuan Zhao et al.   Cancer Immunology Research

Relationships Between Immune Landscapes, Genetic Subtypes and Responses to Immunotherapy in Colorectal Cancer

(2020) Emilie Picard et al.   Frontiers in Immunology

Mass Spectrometry-Based Identification of MHC-Associated Peptides

(2020) Sachin Kote et al.   Cancers

Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

(2020) Jean-David Larouche et al.   Genome Medicine

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability

(2020) Peng Jia et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling

(2020) Sibylle Pfammatter et al.   ANALYTICAL CHEMISTRY

Crosstalk Between the MSI Status and Tumor Microenvironment in Colorectal Cancer

(2020) Anqi Lin et al.   Frontiers in Immunology

A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens

(2020) Robin Minati et al.   Frontiers in Immunology

The prognostic value of tumor-infiltrating lymphocytes in colorectal cancer differs by anatomical subsite: a systematic review and meta-analysis

(2019) Yamei Zhao et al.   World Journal of Surgical Oncology

Discovery and characterization of actionable tumor antigens

(2019) Grégory Ehx et al.   Genome Medicine

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs

(2019) Marie-Pierre Hardy et al.   Scientific Reports

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space

(2019) Masato Ogishi et al.   Frontiers in Immunology

Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

(2019) Alice Newey et al.   Journal for ImmunoTherapy of Cancer

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4

(2019) Jitske van den Bulk et al.   Genome Medicine

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

(2018) Markus W. Löffler et al.   CANCER RESEARCH

Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts Using Two Isolation Methods

(2018) Joël Lanoix et al.   PROTEOMICS

The Prognostic Value of Tumor-Infiltrating lymphocytes in Stage II Colon Cancer. A Nationwide Population-Based Study

(2018) Ann C. Eriksen et al.   Translational Oncology

Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis

(2018) Megan E. Forrest et al.   Scientific Reports

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

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

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

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

Colorectal cancer vaccines: Tumor-associated antigens vs neoantigens

(2018) Sandra Wagner et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies

(2017) Kaja C. G. Berg et al.   Molecular Cancer

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Gene expression markers of Tumor Infiltrating Leukocytes

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

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

Global patterns and trends in colorectal cancer incidence and mortality

(2016) Melina Arnold et al.   GUT

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Central tolerance to self revealed by the autoimmune regulator

(2015) Alice Y. Chan et al.   Annals of the New York Academy of Sciences

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

(2015) Xiaohui Yan et al.   CANCER CELL

Microsatellite Instability Testing and Its Role in the Management of Colorectal Cancer

(2015) Hisato Kawakami et al.   CURRENT TREATMENT OPTIONS IN ONCOLOGY

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Oncogenic cancer/testis antigens: prime candidates for immunotherapy

(2015) Morten F. Gjerstorff et al.   Oncotarget

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints

(2014) Nicolas J. Llosa et al.   Cancer Discovery

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Exploring the MHC-peptide matrix of central tolerance in the human thymus

(2013) Eleni Adamopoulou et al.   Nature Communications

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

(2013) Kosuke Yoshihara et al.   Nature Communications

Epigenetic and genetic features of 24 colon cancer cell lines

(2013) D Ahmed et al.   Oncogenesis

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Cetuximab Plus Irinotecan, Fluorouracil, and Leucovorin As First-Line Treatment for Metastatic Colorectal Cancer: Updated Analysis of Overall Survival According to Tumor KRAS and BRAF Mutation Status

(2011) Eric Van Cutsem et al.   JOURNAL OF CLINICAL ONCOLOGY

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

T Cells Targeting Carcinoembryonic Antigen Can Mediate Regression of Metastatic Colorectal Cancer but Induce Severe Transient Colitis

(2010) Maria R Parkhurst et al.   MOLECULAR THERAPY

Molecular Mechanisms of IFN-γ to Up-Regulate MHC Class I Antigen Processing and Presentation

(2009) Fang Zhou   INTERNATIONAL REVIEWS OF IMMUNOLOGY

KRAS Mutations and Sensitivity to Epidermal Growth Factor Receptor Inhibitors in Colorectal Cancer: Practical Application of Patient Selection

(2009) Antonio Jimeno et al.   JOURNAL OF CLINICAL ONCOLOGY

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

(2009) David A. Barbie et al.   NATURE