Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. - Francisco S. Roque; Peter Bjødstrup Jensen; Henriette Schmock; Marlene Dalgaard; Massimo Andreatta; Thomas Folkmann Hansen; Karen Søeby; Søren Bredkjær; Anders Juul; Thomas Werge; Lars Juhl Jensen; Søren Brunak (PLoS Comput. Biol., 2011)

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. - Massimo Andreatta; Ole Lund; Morten Nielsen 001 (Bioinform., 2013)

Quantifying Significance of MHC II Residues. - Ying Fan; Ruoshui Lu; Lusheng Wang 001; Massimo Andreatta; Shuai Cheng Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Gapped sequence alignment using artificial neural networks: application to the MHC class I system. - Massimo Andreatta; Morten Nielsen 001 (Bioinform., 2016)

NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. - Morten Nielsen 001; Massimo Andreatta (Nucleic Acids Res., 2017)

GibbsCluster: unsupervised clustering and alignment of peptide sequences. - Massimo Andreatta; Bruno Alvarez; Morten Nielsen 001 (Nucleic Acids Res., 2017)

An automated benchmarking platform for MHC class II binding prediction methods. - Massimo Andreatta; Thomas Trolle; Zhen Yan; Jason A. Greenbaum; Bjoern Peters; Morten Nielsen 001 (Bioinform., 2018)

IEDB-AR: immune epitope database - analysis resource in 2019. - Sandeep Kumar Dhanda; Swapnil Mahajan; Sinu Paul; Zhen Yan; Haeuk Kim; Martin Closter Jespersen; Vanessa Isabell Jurtz; Massimo Andreatta; Jason A. Greenbaum; Paolo Marcatili; Alessandro Sette; Morten Nielsen 001; et al. (Nucleic Acids Res., 2019)

STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data. - Massimo Andreatta; Santiago J. Carmona (Bioinform., 2021)

scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets. - Massimo Andreatta; Ariel J. Berenstein; Santiago J. Carmona (Bioinform., 2022)

SPICA: Swiss portal for immune cell analysis. - Massimo Andreatta; Fabrice P. A. David; Christian Iseli; Nicolas Guex; Santiago J. Carmona (Nucleic Acids Res., 2022)