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Research Output

  • 27 Article
  • 3 Conference contribution
  • 1 Conference article
2020

GPGPU Linear Complexity t-SNE Optimization

Pezzotti, N., Thijssen, J., Mordvinstev, A., Hollt, T., Van Lew, B., Lelieveldt, B., Eisemann, E. & Vilanova, A., 2020, In : IEEE Transactions on Visualization and Computer Graphics. 26, 1, p. 1172-1181 10 p., 8811606.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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42 Downloads (Pure)

Helminth infections drive heterogeneity in human type 2 and regulatory cells

de Ruiter, K., Jochems, S. P., Tahapary, D. L., Stam, K. A., König, M., van Unen, V., Höllt, T., Mbow, M., Lelieveldt, B. P. F. & More Authors, 2020, In : Science Translational Medicine. 12, 524, 8 p., eaaw3703.

Research output: Contribution to journalArticleScientificpeer-review

3 Citations (Scopus)

ImaCytE: Visual Exploration of Cellular Microenvironments for Imaging Mass

van Unen, V., Hollt, T., Koning, F. & Lelieveldt, B., 2020, In : IEEE Transactions on Visualization and Computer Graphics. p. 1-13 13 p.

Research output: Contribution to journalArticleScientificpeer-review

2019

Conserved cell types with divergent features in human versus mouse cortex

Hodge, R. D., Bakken, T. E., Miller, J. A., Smith, K. A., Barkan, E. R., Graybuck, L. T., Close, J. L., Hollt, T., Mahfouz, A., Lelieveldt, B. & More Authors, 2019, In : Nature. 573, p. 61-68 8 p.

Research output: Contribution to journalArticleScientificpeer-review

99 Citations (Scopus)

CyTOFmerge: integrating mass cytometry data across multiple panels

Abdelaal, T., Hollt, T., van Unen, V., Lelieveldt, B. P. F., Koning, F., Reinders, M. & Mahfouz, A., 2019, In : Bioinformatics. 35, 20, p. 4063-4071 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2 Citations (Scopus)
58 Downloads (Pure)

Cytosplore: Interactive Visual Single-Cell Profiling of the Immune System

Hollt, T., Pezzotti, N., van Unen, V., Koning, F., Eisemann, E., Lelieveldt, B. & Vilanova, A., 2019, Eurographics 2019 : Dirk Bartz Prize. Bruckner, S. & Steffen, O. J. (eds.). The Eurographics Association, p. 1-4 4 p.

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

Focus+context exploration of hierarchical embeddings

Hollt, T., Vilanova, A., Pezzotti, N., Lelieveldt, B. & Hauser, H., 2019, In : Computer Graphics Forum. 38, 3, p. 569-579 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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1 Citation (Scopus)
37 Downloads (Pure)

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Cossarizza, A., Chang, H-D., Radbruch, A., Acs, A., Adam, D., Hollt, T., Adam-Klages, S. & More Authors, 2019, In : European Journal of Immunology. 49, 10, p. 1457-1973 517 p.

Research output: Contribution to journalArticleScientificpeer-review

156 Citations (Scopus)

High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity

De Vries, N. L., Van Unen, V., Ijsselsteijn, M. E., Abdelaal, T., Van Der Breggen, R., Farina Sarasqueta, A., Mahfouz, A., Peeters, K. C. M. J., Höllt, T., Lelieveldt, B. P. F., Koning, F. & De Miranda, N. F. C. C., 2019, In : Gut. p. 1-13 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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10 Citations (Scopus)
24 Downloads (Pure)

Memory CD4+ T cells are generated in the human fetal intestine

Li, N., van Unen, V., Abdelaal, T., Guo, N., Kasatskaya, S. A., Chuva de Sousa Lopes, S. M., Höllt, T., Britanova, O. V., Lelieveldt, B. P. F. & More Authors, 2019, In : Nature Immunology. 20, 3, p. 301-312 12 p.

Research output: Contribution to journalArticleScientificpeer-review

32 Citations (Scopus)

Multidimensional analyses of proinsulin peptide-specific regulatory T cells induced by tolerogenic dendritic cells

Suwandi, J. S., Laban, S., Vass, K., Joosten, A., van Unen, V., Lelieveldt, B., Höllt, T., Zwaginga, J. J., Nikolic, T. & Roep, B. O., 2019, In : Journal of Autoimmunity. 107 (2020), p. 1-11 11 p., 102361.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Downloads (Pure)

PD-L1 blockade engages tumor-infiltrating lymphocytes to co-express targetable activating and inhibitory receptors

Beyrend, G., van der Gracht, E., Yilmaz, A., van Duikeren, S., Camps, M., Hollt, T., Vilanova, A., van Unen, V., Koning, F., de Miranda, N. F. C. C., Arens, R. & Ossendorp, F., 2019, In : Journal for ImmunoTherapy of Cancer. 7, 1, p. 1-14 14 p., 217.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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8 Citations (Scopus)
49 Downloads (Pure)

Predicting Cell Populations in Single Cell Mass Cytometry Data

Abdelaal, T., van Unen, V., Höllt, T., Koning, F., Reinders, M. J. T. & Mahfouz, A., 2019, In : Cytometry Part A. 95, 7, p. 769-781 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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5 Citations (Scopus)
55 Downloads (Pure)

The anatomical location shapes the immune infiltrate in tumors of same etiology and affects survival

Santegoets, S. J., van Ham, V. J., Ehsan, I., Charoentong, P., Duurland, C. L., van Unen, V., Hollt, T., van der Velden, L. A., van der Burg, S. H. & More Authors, 2019, In : Clinical Cancer Research. 25, 1, p. 240-252 13 p.

Research output: Contribution to journalArticleScientificpeer-review

13 Citations (Scopus)
2018

CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis

Hollt, T., Pezzotti, N., van Unen, V., Koning, F., Lelieveldt, B. P. F. & Vilanova, A., 2018, In : IEEE Transactions on Visualization and Computer Graphics. 24, 1, p. 739-748 10 p., 8017575.

Research output: Contribution to journalArticleScientificpeer-review

12 Citations (Scopus)

Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations

Beyrend, G., Stam, K., Hollt, T., Ossendorp, F. & Arens, R., 2018, In : Computational and Structural Biotechnology Journal. 16, p. 435-442 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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9 Citations (Scopus)
24 Downloads (Pure)

DeepEyes: Progressive Visual Analytics for Designing Deep Neural Networks

Pezzotti, N., Hollt, T., van Gemert, J., Lelieveldt, B., Eisemann, E. & Vilanova Bartroli, A., 2018, In : IEEE Transactions on Visualization and Computer Graphics. 24, 1, p. 98-108 11 p., 8019872.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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57 Citations (Scopus)
52 Downloads (Pure)

Heterogeneity of circulating CD8 T-cells specific to islet, neo-antigen and virus in patients with type 1 diabetes mellitus

Laban, S., Suwandi, J. S., van Unen, V., Pool, J., Wesselius, J., Hollt, T., Pezzotti, N., Vilanova, A., Lelieveldt, B. P. F. & Roep, B. O., 2018, In : PLoS ONE. 13, 8, p. 1-15 15 p., e0200818.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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7 Citations (Scopus)
13 Downloads (Pure)

Interactive Visual Exploration of 3D Mass Spectrometry Imaging Data Using Hierarchical Stochastic Neighbor Embedding Reveals Spatiomolecular Structures at Full Data Resolution

Abdelmoula, W. M., Pezzotti, N., Hollt, T., Dijkstra, J., Vilanova, A., McDonnell, L. A. & Lelieveldt, B., 2018, In : Journal of Proteome Research. 17, 3, p. 1054-1064 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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9 Citations (Scopus)
29 Downloads (Pure)

Mass cytometry reveals innate lymphoid cell differentiation pathways in the human fetal intestine

Li, N., van Unen, V., Hollt, T., Thompson, A., van Bergen, J., Pezzotti, N., Eisemann, E., Vilanova, A., Chuva de Sousa Lopes, S. M., Lelieveldt, B. & Koning, F., 2018, In : Journal of Experimental Medicine. 215, 5, p. 1383-1396 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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23 Citations (Scopus)
13 Downloads (Pure)

Multiscale Visualization and Exploration of Large Bipartite Graphs

Pezzotti, N., Fekete, J-D., Hollt, T., Lelieveldt, B., Eisemann, E. & Vilanova, A., 2018, In : Computer Graphics Forum: the international journal of the Eurographics Association. 37, 3, p. 549-560 12 p.

Research output: Contribution to journalConference articleScientificpeer-review

4 Citations (Scopus)

The contribution of cytomegalovirus infection to immune senescence is set by the infectious dose

Redeker, A., Remmerswaal, E. B. M., van der Gracht, E. T. I., Welten, S. P. M., Hollt, T., Koning, F., Cicin-Sain, L., Nikolich-Žugich, J., ten Berge, I. J. M., van Lier, R. A. W., van Unen, V. & Arens, R., 2018, In : Frontiers in Immunology. 8, p. 1-15 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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18 Citations (Scopus)
16 Downloads (Pure)
2017

BrainScope: Interactive visual exploration of the spatial and temporal human brain transcriptome

Huisman, S. M. H., Van Lew, B., Mahfouz, A., Pezzotti, N., Höllt, T., Michielsen, L., Vilanova, A., Reinders, M. J. T. & Lelieveldt, B. P. F., 2017, In : Nucleic Acids Research. 45, 10, e83.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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14 Citations (Scopus)
42 Downloads (Pure)

Comparative Visualization for Diffusion Tensor Imaging Group Study at Multiple Levels of Detail

Zhang, C., Höllt, T., Caan, M. W. A., Eisemann, E. & Vilanova, A., 2017, Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM). Bruckner, S., Hennemuth, A. & Kainz, B. (eds.). Eurographics Association, p. 1-10 10 p.

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

Overview + Detail Visualization for Ensembles of Diffusion Tensors

Zhang, C., Caan, M. W. A., Höllt, T., Eisemann, E. & Vilanova, A., 2017, In : Computer Graphics Forum (online). 36, 3, p. 121-132 12 p.

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types

van Unen, V., Höllt, T., Pezzotti, N., Li, N., Reinders, M. J. T., Eisemann, E., Koning, F., Vilanova, A. & Lelieveldt, B. P. F., 2017, In : Nature Communications. 8, p. 1-10 10 p., 1740.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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60 Citations (Scopus)
47 Downloads (Pure)
2016

Approximated and User Steerable tSNE for Progressive Visual Analytics

Pezzotti, N., Lelieveldt, B. P. F., van der Maaten, L., Höllt, T., Eisemann, E. & Vilanova, A., 2016, In : IEEE Transactions on Visualization and Computer Graphics. 23, 7, p. 1739-1752 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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76 Citations (Scopus)
32 Downloads (Pure)

Cytosplore: Interactive Immune Cell Phenotyping for Large Single-Cell Datasets

Hollt, T., Pezzotti, N., van Unen, V., Koning, F., Eisemann, E., Lelieveldt, B. P. F. & Vilanova Bartroli, A., 2016, In : Computer Graphics Forum (online). 35, 3, p. 171-180 10 p.

Research output: Contribution to journalArticleScientificpeer-review

37 Citations (Scopus)

Hierarchical Stochastic Neighbor Embedding

Pezzotti, N., Hollt, T., Lelieveldt, B. P. F., Eisemann, E. & Vilanova Bartroli, A., 2016, In : Computer Graphics Forum (online). 35, 3, p. 21-30 10 p.

Research output: Contribution to journalArticleScientificpeer-review

52 Citations (Scopus)

Mass Cytometry of the Human Mucosal Immune System Identifies Tissue- and Disease-Associated Immune Subsets

van Unen, V., Li, N., Molendijk, I., Temurhan, M., Hollt, T., van der Meulen-de Jong, A. E., Verspaget, H. W., Mearin, M. L., Mulder, C. J., van Bergen, J., Lelieveldt, B. P. F. & Koning, F., 2016, In : Immunity. 44, 5, p. 1227-1239 13 p.

Research output: Contribution to journalArticleScientificpeer-review

58 Citations (Scopus)

Visual Analysis of Reservoir Simulation Ensembles

Hollt, T., de Matos Ravanelli, F. M., Hadwiger, M. & Hoteit, I., 2016, Workshop on Visualisation in Environmental Sciences (EnvirVis 2016). Middel, A., Rink, K. & Zeckzer, D. (eds.). The Eurographics Association, p. 1-4 4 p.

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review