Integration of bioinformatics and machine learning strategies identifies APM-related gene signatures to predict clinical outcomes and therapeutic responses for breast cancer patients

Molecular subtyping of breast cancer intrinsic taxonomy with oligonucleotide microarray and NanoString nCounter

(2021) Yen-Jen Chen et al.   BIOSCIENCE REPORTS

MiRNA-based model for predicting the TMB level in colon adenocarcinoma based on a LASSO logistic regression method

(2021) Zhengtian Li et al.   MEDICINE

Establishment and Validation of an Individualized Cell Cycle Process-Related Gene Signature to Predict Cancer-Specific Survival in Patients with Bladder Cancer

(2020) Run Shi et al.   Cancers

Cytotoxic CD4+ T Cells in Bladder Cancer—A New License to Kill

(2020) Adrian G. Sacher et al.   CANCER CELL

Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma

(2020) Zhan-yu Xu et al.   PeerJ

De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection

(2020) Daria Beshnova et al.   Science Translational Medicine

POTN: A Human Leukocyte Antigen-A2 Immunogenic Peptides Screening Model and Its Applications in Tumor Antigens Prediction

(2020) Qingqing Meng et al.   Frontiers in Immunology

Gene signature of antigen processing and presentation machinery predicts response to checkpoint blockade in non-small cell lung cancer (NSCLC) and melanoma

(2020) Jeffrey C Thompson et al.   Journal for ImmunoTherapy of Cancer

Breast Cancer Risk and Insulin Resistance: Post Genome-Wide Gene–Environment Interaction Study Using a Random Survival Forest

(2019) Su Yon Jung et al.   CANCER RESEARCH

Intratumoral Activity of the CXCR3 Chemokine System Is Required for the Efficacy of Anti-PD-1 Therapy

(2019) Melvyn T. Chow et al.   IMMUNITY

Expression of MHC class I, HLA-A and HLA-B identifies immune-activated breast tumors with favorable outcome

(2019) María del Mar Noblejas-López et al.   OncoImmunology

Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-Years for 29 Cancer Groups, 1990 to 2017

(2019) et al.   JAMA Oncology

HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation

(2019) Jatin Arora et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction

(2019) Shixiang Wang et al.   eLife

Targeting the TIGIT-PVR immune checkpoint axis as novel therapeutic option in breast cancer

(2019) Hauke Stamm et al.   OncoImmunology

Development of a membrane lipid metabolism–based signature to predict overall survival for personalized medicine in ccRCC patients

(2019) Maode Bao et al.   EPMA Journal

Defective HLA class I antigen processing machinery in cancer

(2018) Lei Cai et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

(2018) Mirjana Efremova et al.   Nature Communications

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

(2018) K. G. Paulson et al.   Nature Communications

Evaluating biological activity of compounds by transcription factor activity profiling

(2018) Alexander Medvedev et al.   Science Advances

Identification and validation of novel microenvironment-based immune molecular subgroups of head and neck squamous cell carcinoma: implications for immunotherapy

(2018) Y -P Chen et al.   ANNALS OF ONCOLOGY

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Atezolizumab and Nab-Paclitaxel in Advanced Triple-Negative Breast Cancer

(2018) Peter Schmid et al.   NEW ENGLAND JOURNAL OF MEDICINE

High PD-L1 Expression Is Closely Associated With Tumor-Infiltrating Lymphocytes and Leads to Good Clinical Outcomes in Chinese Triple Negative Breast Cancer Patients

(2017) NiJiati AiErken et al.   International Journal of Biological Sciences

HLA-E-expressing pluripotent stem cells escape allogeneic responses and lysis by NK cells

(2017) Germán G Gornalusse et al.   NATURE BIOTECHNOLOGY

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

(2017) Martin Lauss et al.   Nature Communications

Mining expression and prognosis of topoisomerase isoforms in non-small-cell lung cancer by using Oncomine and Kaplan–Meier plotter

(2017) Guo-Xin Hou et al.   PLoS One

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis

(2016) Andrea Schietinger et al.   IMMUNITY

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

(2016) Jesse M. Zaretsky et al.   NEW ENGLAND JOURNAL OF MEDICINE

Targeting of topoisomerases for prognosis and drug resistance in ovarian cancer

(2016) Yang Bai et al.   Journal of Ovarian Research

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Eradication of Large Solid Tumors by Gene Therapy with a T-Cell Receptor Targeting a Single Cancer-Specific Point Mutation

(2015) M. Leisegang et al.   CLINICAL CANCER RESEARCH

Immune checkpoint modulation: Rational design of combination strategies

(2015) Dmitriy Zamarin et al.   PHARMACOLOGY & THERAPEUTICS

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

(2014) R. Salgado et al.   ANNALS OF ONCOLOGY

PD-L1 Expression in Triple-Negative Breast Cancer

(2014) E. A. Mittendorf et al.   Cancer Immunology Research

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis

(2013) Colin Clarke et al.   CARCINOGENESIS

MHC Class I Antigen Processing and Presenting Machinery: Organization, Function, and Defects in Tumor Cells

(2013) P. Leone et al.   JNCI-Journal of the National Cancer Institute

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

(2011) Kuo-Jang Kao et al.   BMC CANCER

microRNA-Associated Progression Pathways and Potential Therapeutic Targets Identified by Integrated mRNA and microRNA Expression Profiling in Breast Cancer

(2011) F. M. Buffa et al.   CANCER RESEARCH

DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

Relationship between HLA class I antigen processing machinery component expression and the clinicopathologic characteristics of bladder carcinomas

(2009) Helen P. Cathro et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS