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161 Single-cell spatial in situ transcriptomics unravels vulvar HSIL composition associated with complete response to therapeutic vaccination2022 Regular and Young Investigator Award Abstracts conference-abstract Medicine Cervical Cancer and HPV Research Open access
Ziena Abdulrahman, Mariette I. van Poelgeest, Marij JP Welters, Sjoerd H. van der Burg
0citations -
Evaluating exon-skipping therapies targeting the central nervous system in Duchenne muscular dystrophy using high-resolution spatial transcriptomics2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Sharon I. de Vries, Laura G.M. Heezen, Ophélie Vacca, Mathilde Doisy, Annemieke M Aartsma-Rus, Maaike van Putten, +3 more
0citations -
D18-09 The Multiorgan Multicenter Spatial Transcriptomics Atlas Reveals Layered Granuloma Architecture and Cellular Programs Driving Sarcoidosis2026 American Journal of Respiratory and Critical Care Medicine article Medicine Sarcoidosis and Beryllium Toxicity Research
Jannik Ruwisch, Leonard Christian, Stephan Traidl, J Dietrich, J-C Kamp, Janis Casper, +19 more
0citations -
Spatial transcriptomics defines the mechanisms of hiPSC-derived stem cell-mediated repair in human articular cartilage2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Osteoarthritis Treatment and Mechanisms Open access
Y.F. Ramos, Sayedeh Sana Sayedipour, Georgina Shaw, Margo Tuerlings, Timo Schomann, H. Eka D. Suchiman, +7 more
0citations -
Evaluating exon skipping in the central nervous system in Duchenne muscular dystrophy using spatial transcriptomics2026 iScience article Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Sharon I. de Vries, Laura G.M. Heezen, Ophélie Vacca, Mathilde Doisy, Annemieke M Aartsma-Rus, Maaike van Putten, +3 more
0citations -
Comparative transcriptomics reveals human-specific cortical features2023 Science article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nikolas L. Jorstad, Janet H. T. Song, David Exposito-Alonso, Hamsini Suresh, Nathan Castro-Pacheco, Fenna M. Krienen, +37 more
209citations -
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data2020 Life Science Alliance article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Thin Nguyen, Buu Minh Thanh Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, +32 more
25citations -
Comparative transcriptomics reveals human-specific cortical features2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nikolas L. Jorstad, Janet H. T. Song, David Exposito-Alonso, Hamsini Suresh, Fenna M. Krienen, Anna Marie Yanny, +35 more
24citations -
Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations2022 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli, Stefan Semrau
19citations -
Spatial transcriptomics reveals molecular cues underlying the site specificity of the adult mouse oral mucosa and its stem cell niches2024 Stem Cell Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Anna C. Seubert, Marion Krafft, Moutaz Helal, Pranjali Bhandare, Elmar Wolf, Anna Alemany, +2 more
11citations -
A clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli, Stefan Semrau
0citations -
Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models2023 Nature Communications article Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Laura G.M. Heezen, Tamim Abdelaal, Maaike van Putten, Annemieke M Aartsma-Rus, Ahmed Essam Mahfouz, Pietro Spitali
55citations -
Characterization of the human fetal gonad and reproductive tract by single-cell transcriptomics2024 Developmental Cell article Biochemistry, Genetics and Molecular Biology Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities Open access
Jasin Taelman, Sylwia M. Czukiewska, Ioannis Moustakas, Yolanda W. Chang, Sanne Hillenius, Talia van der Helm, +4 more
31citations -
Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Laura G.M. Heezen, Tamim Abdelaal, Maaike van Putten, Annemieke M Aartsma-Rus, Ahmed Essam Mahfouz, Pietro Spitali
5citations -
A collaborative network analysis for the interpretation of transcriptomics data in Huntington’s disease2025 Scientific Reports article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ozan Özışık, Nazli Sila Kara, Tooba Abbassi‐Daloii, Morgane Térézol, Elsa C. Kuijper, Núria Queralt-Rosiñach, +7 more
1citations -
The landscape of tertiary lymphoid structures in endometrial cancer revealed through harmonized multi-level transcriptomics2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Marta Requesens, Koen Brummel, Arkajyoti Bhattacharya, Feija Somefun, Nienke van Rooij, Annechien Plat, +10 more
0citations -
Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington’s disease2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ozan Özışık, Tooba Abbassi‐Daloii, Morgane Térézol, Núria Queralt-Rosiñach, Annika Jacobsen, Osman Uğur Sezerman, +5 more
0citations -
Single-cell and spatial transcriptomics resolve airway obliteration in bronchiolitis obliterans syndrome2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Transplantation: Methods and Outcomes Open access
Jannik Ruwisch, Hande Yilmaz, Leonard Christian, Lavinia Neubert, Lena Maureen Leiber, Annalea Brüggemann, +29 more
0citations -
Single-Cell Transcriptomics Indicate That CD163+ Kidney Macrophages Are Pro-Inflammatory and May Orchestrate Further Immune Cell Recruitment to Kidney Lesions in ANCA-Associated Glomerulonephritis2022 Journal of the American Society of Nephrology conference-abstract Medicine Vasculitis and related conditions
Yosta Vegting, Aldo Jongejan, Ester B. M. Remmerswaal, Perry D. Moerland, Jesper Kers, Liffert Vogt, +2 more
0citations -
GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Boudewijn P. F. Lelieveldt
2citations