An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics

por Makrodimitris, Stavros, Pronk, Bram, Abdelaal, Tamim, Reinders, Marcel
Publicado 2023

SpaGE: Spatial Gene Enhancement using scRNA-seq

por Abdelaal, Tamim, Mourragui, Soufiane, Mahfouz, Ahmed, Reinders, Marcel J T
Publicado 2020

scMoC: single-cell multi-omics clustering

por Eltager, Mostafa, Abdelaal, Tamim, Mahfouz, Ahmed, Reinders, Marcel J T
Publicado 2022

Benchmarking variational AutoEncoders on cancer transcriptomics data

por Eltager, Mostafa, Abdelaal, Tamim, Charrout, Mohammed, Mahfouz, Ahmed, Reinders, Marcel J. T., Makrodimitris, Stavros
Publicado 2023

Predicting Cell Populations in Single Cell Mass Cytometry Data

por Abdelaal, Tamim, van Unen, Vincent, Höllt, Thomas, Koning, Frits, Reinders, Marcel J.T., Mahfouz, Ahmed
Publicado 2019

A comparison of automatic cell identification methods for single-cell RNA sequencing data

por Abdelaal, Tamim, Michielsen, Lieke, Cats, Davy, Hoogduin, Dylan, Mei, Hailiang, Reinders, Marcel J. T., Mahfouz, Ahmed
Publicado 2019

Spondyloarthritis mass cytometry immuno-monitoring: a proof of concept study in the tight-control and treat-to target TiCoSpA trial

por Koppejan, Hester, Beyrend, Guillaume, Hameetman, Marjolijn, Abdelaal, Tamim, Toes, René E.M., van Gaalen, Floris A.
Publicado 2023

CyTOFmerge: integrating mass cytometry data across multiple panels

por Abdelaal, Tamim, Höllt, Thomas, van Unen, Vincent, Lelieveldt, Boudewijn P F, Koning, Frits, Reinders, Marcel J T, Mahfouz, Ahmed
Publicado 2019

Combining Mass Cytometry Data by CyTOFmerge Reveals Additional Cell Phenotypes in the Heterogeneous Ovarian Cancer Tumor Microenvironment: A Pilot Study

por Thomsen, Liv Cecilie Vestrheim, Kleinmanns, Katrin, Anandan, Shamundeeswari, Gullaksen, Stein-Erik, Abdelaal, Tamim, Iversen, Grete Alrek, Akslen, Lars Andreas, McCormack, Emmet, Bjørge, Line
Publicado 2023

Phenotypic Characterization by Mass Cytometry of the Microenvironment in Ovarian Cancer and Impact of Tumor Dissociation Methods

por Anandan, Shamundeeswari, Thomsen, Liv Cecilie V., Gullaksen, Stein-Erik, Abdelaal, Tamim, Kleinmanns, Katrin, Skavland, Jørn, Bredholt, Geir, Gjertsen, Bjørn Tore, McCormack, Emmet, Bjørge, Line
Publicado 2021

Early-Life Compartmentalization of Immune Cells in Human Fetal Tissues Revealed by High-Dimensional Mass Cytometry

por Li, Na, van Unen, Vincent, Guo, Nannan, Abdelaal, Tamim, Somarakis, Antonios, Eggermont, Jeroen, Mahfouz, Ahmed, Chuva de Sousa Lopes, Susana M., Lelieveldt, Boudewijn P. F., Koning, Frits
Publicado 2019

Memory CD8(+) T cell heterogeneity is primarily driven by pathogen-specific cues and additionally shaped by the tissue environment

por van der Gracht, Esmé T.I., Beyrend, Guillaume, Abdelaal, Tamim, Pardieck, Iris N., Wesselink, Thomas H., van Haften, Floortje J., van Duikeren, Suzanne, Koning, Frits, Arens, Ramon
Publicado 2020

High-dimensional analysis reveals an immune atlas and novel neutrophil clusters in the lungs of model animals with Actinobacillus pleuropneumoniae-induced pneumonia

por Li, Na, Zhu, Junhui, Chen, Peiru, Bao, Chuntong, Wang, Jun, Abdelaal, Tamim, Chen, Dexi, Zhu, Sibo, Wang, Wenjing, Mao, Jiangnan, Scicluna, Brendon P., Koning, Frits, Li, Fengyang, Lei, Liancheng
Publicado 2023

Local and systemic immune profiles of human pancreatic ductal adenocarcinoma revealed by single-cell mass cytometry

por Brouwer, Thomas P, de Vries, Natasja L, Abdelaal, Tamim, Krog, Ricki T, Li, Zheng, Ruano, Dina, Fariña, Arantza, Lelieveldt, Boudewijn P F, Morreau, Hans, Bonsing, Bert A, Vahrmeijer, Alexander L, Koning, Frits, de Miranda, Noel F C C
Publicado 2022

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

por de Vries, Natasja L, van Unen, Vincent, Ijsselsteijn, Marieke E, Abdelaal, Tamim, van der Breggen, Ruud, Farina Sarasqueta, Arantza, Mahfouz, Ahmed, Peeters, Koen C M J, Höllt, Thomas, Lelieveldt, Boudewijn P F, Koning, Frits, de Miranda, Noel F C C
Publicado 2020

Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

por Zhang, Yun, Miller, Jeremy A., Park, Jeongbin, Lelieveldt, Boudewijn P., Long, Brian, Abdelaal, Tamim, Aevermann, Brian D., Biancalani, Tommaso, Comiter, Charles, Dzyubachyk, Oleh, Eggermont, Jeroen, Langseth, Christoffer Mattsson, Petukhov, Viktor, Scalia, Gabriele, Vaishnav, Eeshit Dhaval, Zhao, Yilin, Lein, Ed S., Scheuermann, Richard H.
Publicado 2023

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

por Li, Na, van Unen, Vincent, Abdelaal, Tamim, Guo, Nannan, Kasatskaya, Sofya A., Ladell, Kristin, McLaren, James E., Egorov, Evgeny S., Izraelson, Mark, Chuva de Sousa Lopes, Susana M., Höllt, Thomas, Britanova, Olga V, Eggermont, Jeroen, de Miranda, Noel F.C.C., Chudakov, Dmitriy M., Price, David A., Lelieveldt, Boudewijn P.F., Koning, Frits
Publicado 2019

Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease

por van Unen, Vincent, Ouboter, Laura F., Li, Na, Schreurs, Mette, Abdelaal, Tamim, Kooy-Winkelaar, Yvonne, Beyrend, Guillaume, Höllt, Thomas, Maljaars, P. W. Jeroen, Mearin, M. Luisa, Mahfouz, Ahmed, Witte, Anne M. C., Clemens, Cornelis H. M., Abraham, Sunje, Escher, Johanna C., Lelieveldt, Boudewijn P. F., Pascutti, M. Fernanda, van der Meulen – de Jong, Andrea E., Koning, Frits
Publicado 2022

OX40 agonism enhances PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum

por van der Sluis, Tetje C., Beyrend, Guillaume, van der Gracht, Esmé T.I., Abdelaal, Tamim, Jochems, Simon P., Belderbos, Robert A., Wesselink, Thomas H., van Duikeren, Suzanne, van Haften, Floortje J., Redeker, Anke, Ouboter, Laura F., Beyranvand Nejad, Elham, Camps, Marcel, Franken, Kees L.M.C., Linssen, Margot M., Hohenstein, Peter, de Miranda, Noel F.C.C., Mei, Hailiang, Bins, Adriaan D., Haanen, John B.A.G., Aerts, Joachim G., Ossendorp, Ferry, Arens, Ramon
Publicado 2023

A third vaccination with a single T cell epitope confers protection in a murine model of SARS-CoV-2 infection

por Pardieck, Iris N., van der Sluis, Tetje C., van der Gracht, Esmé T. I., Veerkamp, Dominique M. B., Behr, Felix M., van Duikeren, Suzanne, Beyrend, Guillaume, Rip, Jasper, Nadafi, Reza, Beyranvand Nejad, Elham, Mülling, Nils, Brasem, Dena J., Camps, Marcel G. M., Myeni, Sebenzile K., Bredenbeek, Peter J., Kikkert, Marjolein, Kim, Yeonsu, Cicin-Sain, Luka, Abdelaal, Tamim, van Gisbergen, Klaas P. J. M., Franken, Kees L. M. C., Drijfhout, Jan Wouter, Melief, Cornelis J. M., Zondag, Gerben C. M., Ossendorp, Ferry, Arens, Ramon
Publicado 2022