TAP 1.0: A robust immunoinformatic tool for the prediction of tumor T-cell antigens based on AAindex properties

Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data

(2020) Birkir Reynisson et al.   JOURNAL OF PROTEOME RESEARCH

iTTCA-Hybrid: Improved and robust identification of tumor T cell antigens by utilizing hybrid feature representation

(2020) Phasit Charoenkwan et al.   ANALYTICAL BIOCHEMISTRY

Epitope Prediction by Novel Immunoinformatics Approach: A State-of-the-art Review

(2019) Ehsan Raoufi et al.   International Journal of Peptide Research and Therapeutics

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

TTAgP 1.0: A computational tool for the specific prediction of tumor T cell antigens

(2019) Jorge Félix Beltrán Lissabet et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

(2018) Weilong Zhao et al.   PLoS Computational Biology

A benchmark study of k-mer counting methods for high-throughput sequencing

(2018) Swati C Manekar et al.   GigaScience

Predicting antimicrobial peptides by using increment of diversity with quadratic discriminant analysis method

(2017) Pengmian Feng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Ten quick tips for machine learning in computational biology

(2017) Davide Chicco   BioData Mining

Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation

(2017) Marek Wieczorek et al.   Frontiers in Immunology

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

An overview of bioinformatics tools for epitope prediction: Implications on vaccine development

(2015) Ruth E. Soria-Guerra et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Landscape of Tumor Antigens in T Cell Immunotherapy

(2015) S. Ilyas et al.   JOURNAL OF IMMUNOLOGY

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+T cell epitopes

(2015) Diego Chowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

(2014) Lars Olsen et al.   BMC Medical Genomics

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

A new method for identifying bivariate differential expression in high dimensional microarray data using quadratic discriminant analysis

(2011) Jorge M Arevalillo et al.   BMC BIOINFORMATICS

Hydrophobicity as a driver of MHC class I antigen processing

(2011) Lan Huang et al.   EMBO JOURNAL

Ipilimumab plus Dacarbazine for Previously Untreated Metastatic Melanoma

(2011) Caroline Robert et al.   NEW ENGLAND JOURNAL OF MEDICINE

Improved Survival with Ipilimumab in Patients with Metastatic Melanoma

(2010) F. Stephen Hodi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Classification of antimicrobial peptide using diversity measure with quadratic discriminant analysis

(2009) Wei Chen et al.   JOURNAL OF MICROBIOLOGICAL METHODS