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ArticlesPeer ReviewedFull Text
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets
Author / Creator:Nielsen, Morten ; Andreatta, Massimo
Publisher:England: BioMed Central Ltd
Journal title:Genome medicine, 2016-03, Vol.8 (1), p.33-33, Article 33
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Interpretation of T cell states from single-cell transcriptomics data using reference atlases
Author / Creator:Andreatta, Massimo ; Corria-Osorio, Jesus ; Müller, Sören ; Cubas, Rafael ; Coukos, George ; Carmona, Santiago J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-05, Vol.12 (1), p.2965-2965, Article 2965
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A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections
Author / Creator:Andreatta, Massimo ; Tjitropranoto, Ariel ; Sherman, Zachary ; Kelly, Michael C ; Ciucci, Thomas ; Carmona, Santiago J
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2022-07, Vol.11
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Semi-supervised integration of single-cell transcriptomics data
Author / Creator:Andreatta, Massimo ; Hérault, Léonard ; Gueguen, Paul ; Gfeller, David ; Berenstein, Ariel J. ; Carmona, Santiago J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-01, Vol.15 (1), p.872-13, Article 872
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Footprints of antigen processing boost MHC class II natural ligand predictions
Author / Creator:Barra, Carolina ; Alvarez, Bruno ; Paul, Sinu ; Sette, Alessandro ; Peters, Bjoern ; Andreatta, Massimo ; Buus, Søren ; Nielsen, Morten
Publisher:England: BioMed Central Ltd
Journal title:Genome medicine, 2018-11, Vol.10 (1), p.84-84, Article 84
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Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts
Author / Creator:Roque, Francisco S. ; Jensen, Peter B. ; Schmock, Henriette ; Dalgaard, Marlene ; Andreatta, Massimo ; Hansen, Thomas ; Søeby, Karen ; Bredkjær, Søren ; Juul, Anders ; Werge, Thomas ; Jensen, Lars J. ; Brunak, Søren
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2011-08, Vol.7 (8), p.e1002141-e1002141
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NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data
Author / Creator:Andreatta, Massimo ; Schafer-Nielsen, Claus ; Lund, Ole ; Buus, Søren ; Nielsen, Morten
Publisher:United States: Public Library of Science
Journal title:PloS one, 2011-11, Vol.6 (11), p.e26781-e26781
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In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
Author / Creator:Andreatta, Massimo ; Nielsen, Morten ; Møller Aarestrup, Frank ; Lund, Ole
Publisher:United States: Public Library of Science
Journal title:PloS one, 2010-10, Vol.5 (10), p.e13680-e13680
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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
Author / Creator:Andreatta, Massimo ; Karosiene, Edita ; Rasmussen, Michael ; Stryhn, Anette ; Buus, Søren ; Nielsen, Morten
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:Immunogenetics (New York), 2015-11, Vol.67 (11-12), p.641-650
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Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8+ T cells
Author / Creator:Corria-Osorio, Jesus ; Carmona, Santiago J. ; Stefanidis, Evangelos ; Andreatta, Massimo ; Ortiz-Miranda, Yaquelin ; Muller, Tania ; Rota, Ioanna A. ; Crespo, Isaac ; Seijo, Bili ; Castro, Wilson ; Jimenez-Luna, Cristina ; Scarpellino, Leonardo ; Ronet, Catherine ; Spill, Aodrenn ; Lanitis, Evripidis ; Romero, Pedro ; Luther, Sanjiv A. ; Irving, Melita ; Coukos, George
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2023-05, Vol.24 (5), p.869-883
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Activation of the transcription factor NFAT5 in the tumor microenvironment enforces CD8+ T cell exhaustion
Author / Creator:Tillé, Laure ; Cropp, Daniela ; Charmoy, Mélanie ; Reichenbach, Patrick ; Andreatta, Massimo ; Wyss, Tania ; Bodley, Gabrielle ; Crespo, Isaac ; Nassiri, Sina ; Lourenco, Joao ; Leblond, Marine M. ; Lopez-Rodriguez, Cristina ; Speiser, Daniel E. ; Coukos, George ; Irving, Melita ; Carmona, Santiago J. ; Held, Werner ; Verdeil, Grégory
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2023-10, Vol.24 (10), p.1645-1653
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Orthogonal Gene Engineering Enables CD8+ T Cells to Control Tumors through a Novel PD-1+ TOX-indifferent Synthetic Effector State
Author / Creator:Corria-Osorio, Jesus ; Carmona, Santiago J ; Stefanidis, Evangelos ; Andreatta, Massimo J ; Muller, Tania ; Ortiz, Yaquelin ; Seijo, Bili ; Castro, Wilson ; Jimenez-Luna, Cristina ; Scarpellino, Leonardo ; Ronet, Catherine ; Spill, Aodrenn ; Lanitis, Evripidis ; Luther, Sanjiv A ; Romero, Pedro ; Irving, Melita ; Coukos, George
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2022-02
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ArticlesPeer ReviewedFull Text
In Silico Prediction of Human Pathogenicity in the [gamma]-Proteobacteria
Author / Creator:Andreatta, Massimo ; Nielsen, Morten ; Møller Aarestrup, Frank ; Lund, Ole
Publisher:Public Library of Science
Journal title:PloS one, 2010-10, Vol.5 (10), p.e13680
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Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts: e1002141
Author / Creator:Roque, Francisco S ; Jensen, Peter B ; Schmock, Henriette ; Dalgaard, Marlene ; Andreatta, Massimo ; Hansen, Thomas ; Søeby, Karen ; Bredkjær, Søren ; Juul, Anders ; Werge, Thomas ; Jensen, Lars J ; Brunak, Søren
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2011-08, Vol.7 (8)
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Wounding triggers invasive progression in human basal cell carcinoma
Author / Creator:Yerly, Laura ; Andreatta, Massimo ; Garnica, Josep ; Jeremy Di Domizio ; Gilliet, Michel ; Carmona, Santiago J ; Kuonen, Francois
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2025-02
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UCell: robust and scalable single-cell gene signature scoring
Author / Creator:Andreatta, Massimo ; Carmona, Santiago J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2021-04
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STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data
Author / Creator:Andreatta, Massimo ; Carmona, Santiago J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-06
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Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses
Author / Creator:Andreatta, Massimo ; Corria-Osorio, Jesus ; Müller, Sören ; Cubas, Rafael ; Coukos, George ; Carmona, Santiago J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-10
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Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes
Author / Creator:Alvarez, Bruno ; Barra, Carolina ; Nielsen, Morten ; Andreatta, Massimo
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2017-10
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NNAlign_MA; MHC peptidome deconvolution for accurate MHC binding motif characterization and improved T cell epitope predictions
Author / Creator:Alvarez, Bruno ; Reynisson, Birkir ; Barra, Carolina ; Buus, Søren ; Ternette, Nicola ; Connelley, Tim ; Andreatta, Massimo ; Nielsen, Morten
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2019-06
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Showing 1 to 20 of 24 results

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NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

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Interpretation of T cell states from single-cell transcriptomics data using reference atlases

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A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections

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Semi-supervised integration of single-cell transcriptomics data

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Footprints of antigen processing boost MHC class II natural ligand predictions

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Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

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NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

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In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria

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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

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Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8+ T cells

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Activation of the transcription factor NFAT5 in the tumor microenvironment enforces CD8+ T cell exhaustion

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Orthogonal Gene Engineering Enables CD8+ T Cells to Control Tumors through a Novel PD-1+ TOX-indifferent Synthetic Effector State

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In Silico Prediction of Human Pathogenicity in the [gamma]-Proteobacteria

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Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts: e1002141

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Wounding triggers invasive progression in human basal cell carcinoma

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UCell: robust and scalable single-cell gene signature scoring

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STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data

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Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses

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Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes

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NNAlign_MA; MHC peptidome deconvolution for accurate MHC binding motif characterization and improved T cell epitope predictions

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