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J. Calis · SciRah

Researcher profile · Semantic Scholar

J. Calis

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J. Calis — researcher profile on SciRah

h-index: 16
Works: 39
Citations: 2,945

Most-cited papers

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
J. Calis, Matt Maybeno, Jason A. Greenbaum, D. Weiskopf +4 more
2013PLoS Comput. Biol.867 citations Open access
Semantic Scholar
High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma
Carsten Linnemann, M. V. van Buuren, L. Bies, E. Verdegaal +12 more
2014Nature Medicine659 citations Open access
Semantic Scholar
Human ADAR1 prevents endogenous RNA from triggering translational shutdown
Hachung Chung, J. Calis, Xian-Fang Wu, Tony Sun +7 more
2018Cell484 citations Open access
Semantic Scholar
Characterizing immune repertoires by high throughput sequencing: strategies and applications
J. Calis, Brad R. Rosenberg
2014Trends in immunology163 citations Open access
Semantic Scholar
Predicted indirectly recognizable HLA epitopes presented by HLA-DR correlate with the de novo development of donor-specific HLA IgG antibodies after kidney transplantation.
H. Otten, J. Calis, C. Keşmir, A. V. van Zuilen +1 more
2013Human Immunology112 citations
Semantic Scholar
Cyclin F controls cell cycle transcriptional outputs by directing the degradation of the three activator E2Fs
L. Clijsters, Claire Hoencamp, J. Calis, Antonio Marzio +5 more
2019Molecules and Cells104 citations Open access
Semantic Scholar
High sensitivity of cancer exome-based CD8 T cell neo-antigen identification
M. V. van Buuren, J. Calis, T. Schumacher
2014Oncoimmunology100 citations Open access
Semantic Scholar
Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Kinase Transcriptional and Biochemical Function
C. Gruber, J. Calis, S. Buta, Gilad D. Evrony +14 more
2020Immunity97 citations Open access
Semantic Scholar
Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire
J. Calis, R. D. de Boer, C. Keşmir
2012PLoS Comput. Biol.90 citations Open access
Semantic Scholar
Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23.
Sophie Garnier, M. Harakalova, S. Weiss, M. Mokry +72 more
2021European Heart Journal59 citations Open access
Semantic Scholar
Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs
J. Calis, P. Reinink, C. Keller, P. Kloetzel +1 more
2014Immunogenetics45 citations Open access
Semantic Scholar
Exploratory Study of Predicted Indirectly ReCognizable HLA Epitopes in Mismatched Hematopoietic Cell Transplantations
K. Geneugelijk, K. Thus, H. V. van Deutekom, J. Calis +12 more
2019Frontiers in Immunology25 citations Open access
Semantic Scholar
Recombinant Interleukin‐1 Receptor Antagonist Is an Effective First‐Line Treatment Strategy in New‐Onset Systemic Juvenile Idiopathic Arthritis, Irrespective of HLA‐DRB1 Background and IL1RN Variants
R. Erkens, J. Calis, A. Verwoerd, S. de Roock +15 more
2023Arthritis & Rheumatology23 citations Open access
Semantic Scholar
Transcriptome of airway neutrophils reveals an interferon response in life-threatening respiratory syncytial virus infection.
S. Besteman, A. Callaghan, A. Langedijk, M. Hennus +4 more
2020Clinical Immunology20 citations Open access
Semantic Scholar
Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction
F. Terstappen, J. Calis, N. D. Paauw, J. Joles +4 more
2020Clinical Epigenetics19 citations Open access
Semantic Scholar
MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation
J. Calis, Gabino Sanchez-Perez, C. Keşmir
2010European Journal of Immunology17 citations Open access
Semantic Scholar
Human Plaque Myofibroblasts to Study Mechanisms of Atherosclerosis
M. Buono, E. D. Benavente, L. Slenders, Daisey Methorst +13 more
2023Journal of the American Heart Association : Cardiovascular and Cerebrovascular Disease16 citations Open access
Semantic Scholar
CBP/P300 Inhibition Impairs CD4+ T Cell Activation: Implications for Autoimmune Disorders
L. Picavet, A. A. K. Samat, J. Calis, L. Nijhuis +6 more
2024Biomedicines10 citations Open access
Semantic Scholar
N6-Methyladenosine Directly Regulates CD40L Expression in CD4+ T Lymphocytes
E. V. van Vroonhoven, L. Picavet, R. Scholman, N. V. D. van den Dungen +6 more
2023Biology10 citations Open access
Semantic Scholar
N6-Methyladenosine Promotes TNF mRNA Degradation In CD4+ T Lymphocytes.
E. V. van Vroonhoven, L. Picavet, R. Scholman, Lyanne J. P. M. Sijbers +10 more
2024Journal of Leukocyte Biology6 citations Open access
Semantic Scholar
Nicotinamide Inhibits CD4+ T-Cell Activation and Function
L. Nijhuis, Alejandra Bodelόn, R. Scholman, Isabelle Houtzager +7 more
2025Cells5 citations Open access
Semantic Scholar
Transcriptional regulation profiling reveals disrupted lipid metabolism in failing hearts with a pathogenic phospholamban mutation
J. Pei, R. Maas, E. Nagyova, J. M. I. H. Gho +28 more
2020bioRxiv5 citations Open access
Semantic Scholar
Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Transcriptional and Biochemical Function
C. Gruber, J. Calis, S. Buta, Gilad D. Evrony +14 more
2019bioRxiv4 citations Open access
Semantic Scholar
Get Spliced: Uniting Alternative Splicing and Arthritis
Maurice J. H. van Haaren, Levina Bertina Steller, S. Vastert, J. Calis +1 more
2024International Journal of Molecular Sciences3 citations Open access
Semantic Scholar
Regulation of CLK1 Isoform Expression by Alternative Splicing in Activated Human Monocytes Contributes to Activation-Associated TNF Production
Maurice J. H. van Haaren, A. Bodelón, Lyanne J. P. M. Sijbers, R. Scholman +4 more
2025Cells2 citations
Semantic Scholar
Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms
A. Bodelón, Maurice J. H. van Haaren, Paula Sobrevals Alcaraz, Lyanne J. P. M. Sijbers +9 more
2026Nature Communications1 citations Open access
Semantic Scholar
Prenatal Sildenafil and Fetal-placental Programming in Human Pregnancies Complicated by Fetal Growth Restriction: A Retrospective Gene Expression Analysis
F. Terstappen, T. Plösch, J. Calis, W. Ganzevoort +6 more
2023Journal of Trial and Error1 citations Open access
Semantic Scholar
A Cross-Study Multi-Organ Cell Atlas of Macaca fascicularis Informed by Human Foundation Model Annotation: A Resource for Translational Target Assessment
Terezinha M. Souza, J. Gamse, Leandro Moreno, Marilijn van Rumpt +14 more
2026bioRxiv0 citations Open access
Semantic Scholar
Gene regulatory networks define human airway epithelial cell types and their distinct responses to type I interferon
A. Bejjani, A. Pankow, Ava R. Lamberty, J. Calis +25 more
2026bioRxiv0 citations
Semantic Scholar
Transcriptional Regulation of WTAP Isoforms by NF-κB Signaling in Human Monocytes
L. Picavet, Hisham I. Abu-Tawil, Lyanne J. P. M. Sijbers, J. Calis +4 more
2025International Journal of Molecular Sciences0 citations Open access
Semantic Scholar
Human primary plaque cell cultures to study mechanisms of atherosclerosis
M. Buono, E. D. Benavente, L. Slenders, D. Methorst +13 more
2023bioRxiv0 citations Open access
Semantic Scholar
P0278 / #842: OUTCOME AND PREDICTORS OF MORTALITY IN CHILDREN ADMITTED TO A RECENTLY OPENED PEDIATRIC INTENSIVE CARE UNIT IN MALAWI.
M. de Visser, D. Kululanga, S. Chikumbanje, E. Thomson +6 more
20210 citations Open access
Semantic Scholar
Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction
F. Terstappen, J. Calis, N. D. Paauw, J. Joles +4 more
2020Clinical Epigenetics0 citations Open access
Semantic Scholar
Benchmarking the Foreign Antigen Space of Human Malignancies
M. Slagter, Lorenzo F. Fanchi, M. V. van Buuren, A. Velds +9 more
20180 citations Open access
Semantic Scholar
Identifying Permissible HLA-Mismatches in Unrelated-Donor Hematopoietic Stem-Cell Transplantation Using Predicted Indirectly Recognizable HLA Epitopes
K. Thus, K. Geneugelijk, H. W. V. van Deutekom, J. Calis +12 more
20170 citations Open access
Semantic Scholar
High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4(+) T cells in human melanoma (vol 21, pg 81, 2015)
Carsten Linnemann, M. V. van Buuren, L. Bies, E. Verdegaal +12 more
20160 citations
Semantic Scholar
Abstract A009: Benchmarking the foreign antigen space of human malignancies
M. Slagter, Lorenzo F. Fanchi, M. V. van Buuren, J. Calis +11 more
20160 citations
Semantic Scholar
A Universal Approach to Identify Permissible HLA-Mismatches in HSCT: Predicted Indirectly Recognizable HLA Epitopes
K. Thus, D. Fürst, H. V. van Deutekom, J. Calis +5 more
20140 citations Open access
Semantic Scholar
Bound to be an Epitope: Determinants of the T-cell response to MHC-I presented peptides
J. Calis
20120 citations
Semantic Scholar

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