M. Nielsen

Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing

This study identifies distinct roles of Arabidopsis VEL proteins in Polycomb silencing, showing VRN5 is required for H3K27me2 while VIN3 interacts with VAL1 to regulate H3K27me3.

Extraordinary peptide-binding mode of a songbird MHC class-I molecule suggests mechanism to counter pathogen immune evasion

The study determines the structure of a songbird MHC class I protein, Acar3, and identifies an unusual peptide-binding mode that may enhance immune responses against pathogens.

DiscoTope-3.0 - Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations

DiscoTope-3.0 improves B-cell epitope prediction by using AlphaFold2 models and inverse folding representations, enhancing performance across experimental and predicted structures.

ATRAP - Accurate T cell Receptor Antigen Pairing through data-driven filtering of sequencing information from single-cells

ATRAP filters sequencing artifacts to accurately pair T cell receptors with their cognate peptide-MHC ligands from single-cell data, identifying 1494 high-confidence pairs across 16 donors.

Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome

The paper introduces MHCMotifDecon, a tool for accurately deconvoluting immunopeptidomics data, revealing HLA-DRB3/4/5's significant role in the DR immunopeptidome.

Bi-modal Variational Autoencoders for Metabolite Identification Using Tandem Mass Spectrometry

The paper introduces a bi-modal variational autoencoder to identify metabolites from tandem mass spectrometry data by learning from unpaired molecule structures and spectra.

APRANK: computational prioritization of antigenic proteins and peptides from complete pathogen proteomes

APRANK prioritizes antigenic proteins and peptides from pathogen proteomes using molecular features, successfully predicting antigenicity across multiple disease-causing organisms.

TCRMatch: Predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors

TCRMatch predicts T-cell receptor specificity by comparing sequence similarity to known epitope-specific receptors in the IEDB.

SARS-CoV-2 genome-wide mapping of CD8 T cell recognition reveals strong immunodominance and substantial CD8 T cell activation in COVID-19 patients

This study maps SARS-CoV-2 epitopes recognized by CD8 T cells in COVID-19 patients, showing strong immunodominance and activation, with severe cases having the largest T cell populations.

Sampling SARS-CoV-2 proteomes for predicted CD8 T-cell epitopes as a tool for understanding immunogenic breadth and rational vaccine design

The paper uses predictive models to analyze SARS-CoV-2 proteome diversity and identify potential CD8 T-cell epitopes for vaccine design.

Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response

The paper uses computational models to identify immunogenic regions in the HIV proteome by analyzing HLA diversity and CD8 T-cell immune repertoires, offering a pipeline for vaccine design.

Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19

The paper maps SARS-CoV-2-specific T cell responses in individuals with asymptomatic/mild COVID-19 and finds robust memory T cell responses similar to vaccines, detectable even in antibody-seronegative individuals.

A systematic, unbiased mapping of CD8+ and CD4+ T cell epitopes in Yellow Fever vaccinees

The paper systematically identifies and validates CD8+ and CD4+ T cell epitopes in Yellow Fever vaccinees, revealing immunodominant responses and HLA restrictions with broad population coverage.

HLA-class II specificity assessed by high-density peptide microarray interactions

This study uses high-density peptide microarrays to assess HLA-class II specificity, generating large-scale peptide-MHC-II interaction data to improve prediction tools.

The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution

The study identifies shared immunogenic neoantigens in MSI cancers and finds a negative correlation between indel mutation frequency and neoantigen immunogenicity, suggesting immunoediting during tumor evolution.

Benchmarking predictions of MHC class I restricted T cell epitopes

This study benchmarks T cell epitope prediction tools using a comprehensive dataset of vaccinia virus epitopes, finding that neural network-based methods trained on MHC binding and ligand elution data perform best.

The Life History of Human Foraging: Cross-Cultural and Individual Variation

The paper analyzes hunting skill data from 1,800 individuals to infer age-related productivity patterns and variation in human foraging.

Characterisation of antigenic MHC Class I-restricted T cell epitopes in the glycoprotein of Ebolavirus

This paper identifies nine T cell epitopes in the Ebolavirus glycoprotein and shows they are presented by multiple HLA alleles, suggesting broad immune recognition.

Footprints of antigen processing boost MHC class II natural ligand binding predictions

This study develops MHC class II ligand binding predictors trained on naturally eluted peptides, showing improved performance by incorporating antigen processing rules.

Improved prediction of Bovine Leucocyte Antigens (BoLA) presented ligands by use of MS eluted ligands and in-vitro binding data; impact for the identification T cell epitopes

The paper improves BoLA-I T cell epitope prediction by integrating MS ligand data with in-vitro binding data using a novel pipeline.