4.6 Article

Integration of Omics Data Sources to Inform Mechanistic Modeling of Immune-Oncology Therapies: A Tutorial for Clinical Pharmacologists

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

ScanNeo: identifying indel-derived neoantigens using RNA-Seq data

Ting-You Wang et al.

BIOINFORMATICS (2019)

Article Immunology

Deciphering CD4+ T cell specificity using novel MHC-TCR chimeric receptors

Jan Kisielow et al.

NATURE IMMUNOLOGY (2019)

Article Biochemical Research Methods

T cell antigen discovery via signaling and antigen-presenting bifunctional receptors

Alok Joglekar et al.

NATURE METHODS (2019)

Article Medicine, Research & Experimental

Neoantigen identification strategies enable personalized immunotherapy in refractory solid tumors

Fangjun Chen et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

Article Biochemical Research Methods

MHCSeqNet: a deep neural network model for universal MHC binding prediction

Poomarin Phloyphisut et al.

BMC BIOINFORMATICS (2019)

Review Genetics & Heredity

Best practices for bioinformatic characterization of neoantigens for clinical utility

Megan M. Richters et al.

GENOME MEDICINE (2019)

Article Biotechnology & Applied Microbiology

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

Brendan Bulik-Sullivan et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas

Susan K. Rathe et al.

SCIENTIFIC REPORTS (2019)

Article Pathology

Normative data for flow cytometry immunophenotyping of benign lymph nodes sampled by surgical biopsy

Gregory David Scott et al.

JOURNAL OF CLINICAL PATHOLOGY (2018)

Article Immunology

The Immune Landscape of Cancer

Vesteinn Thorsson et al.

IMMUNITY (2018)

Article Immunology

Improved methods for predicting peptide binding affinity to MHC class II molecules

Kamilla Kjaergaard Jensen et al.

IMMUNOLOGY (2018)

Article Biochemistry & Molecular Biology

Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer

Nikolaos Zacharakis et al.

NATURE MEDICINE (2018)

Article Biochemistry & Molecular Biology

Phenotype molding of stromal cells in the lung tumor microenvironment

Diether Lambrechts et al.

NATURE MEDICINE (2018)

Article Biochemistry & Molecular Biology

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

Timothy J. O'Donnell et al.

CELL SYSTEMS (2018)

Article Genetics & Heredity

TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis

Jingcheng Wu et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy

Razvan Cristescu et al.

SCIENCE (2018)

Article Medicine, Research & Experimental

IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade

Mark Ayers et al.

JOURNAL OF CLINICAL INVESTIGATION (2017)

Article Multidisciplinary Sciences

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

Max Schelker et al.

NATURE COMMUNICATIONS (2017)

Article Biochemistry & Molecular Biology

Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

Nadeem Riaz et al.

Article Biochemical Research Methods

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

Massimo Andreatta et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

T cell fate and clonality inference from single-cell transcriptomes

Michael J. T. Stubbington et al.

NATURE METHODS (2016)

Letter Biochemical Research Methods

MiXCR: software for comprehensive adaptive immunity profiling

Dmitriy A. Bolotin et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Robust enumeration of cell subsets from tissue expression profiles

Aaron M. Newman et al.

NATURE METHODS (2015)

Article Multidisciplinary Sciences

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

Naiyer A. Rizvi et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life

Joseph J. C. Thome et al.

Article Biochemical Research Methods

Towards error-free profiling of immune repertoires

Mikhail Shugay et al.

NATURE METHODS (2014)

Article Medicine, General & Internal

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

Alexandra Snyder et al.

NEW ENGLAND JOURNAL OF MEDICINE (2014)

Article Pharmacology & Pharmacy

A Mechanistic, Multiscale Mathematical Model of Immunogenicity for Therapeutic Proteins: Part 1-Theoretical Model

X. Chen et al.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2014)

Article Pharmacology & Pharmacy

A Mechanistic, Multiscale Mathematical Model of Immunogenicity for Therapeutic Proteins: Part 2-Model Applications

X. Chen et al.

CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY (2014)

Editorial Material Pharmacology & Pharmacy

Systems Pharmacology for Drug Discovery and Development: Paradigm Shift or Flash in the Pan?

P. Vicini et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2013)

Review Immunology

Oncology Meets Immunology: The Cancer-Immunity Cycle

Daniel S. Chen et al.

IMMUNITY (2013)

Editorial Material Genetics & Heredity

The Cancer Genome Atlas Pan-Cancer analysis project

John N. Weinstein et al.

NATURE GENETICS (2013)

Article Genetics & Heredity

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

Edita Karosiene et al.

IMMUNOGENETICS (2012)

Review Immunology

Coordinated regulation of myeloid cells by tumours

Dmitry I. Gabrilovich et al.

NATURE REVIEWS IMMUNOLOGY (2012)

Article Biochemical Research Methods

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

Morten Nielsen et al.

BMC BIOINFORMATICS (2007)

Article Immunology

Prediction of MHC class I binding peptides using profile motifs

PA Reche et al.

HUMAN IMMUNOLOGY (2002)

Article Biochemical Research Methods

ProPred: prediction of HLA-DR binding sites

H Singh et al.

BIOINFORMATICS (2001)