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SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Tamim Abdelaal, Thomas Höllt, Boudewijn P. F. Lelieveldt
2citations -
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain2023 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. F. Lelieveldt, Brian Long, Tamim Abdelaal, +12 more
20citations -
SpaceWalker enables interactive gradient exploration for spatial transcriptomics data2023 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Mitchell M. de Boer, Tamim Abdelaal, Thomas Höllt, +1 more
4citations -
MASI enables fast model-free standardization and integration of single-cell transcriptomics data2023 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
4citations -
962 Single-cell spatial in situ transcriptomics unravels vulvar HSIL composition associated with complete response to therapeutic vaccination2023 Regular and Young Investigator Award Abstracts conference-abstract Medicine Cervical Cancer and HPV Research Open access
Ziena Abdulrahman, Mariëtte I.E. van Poelgeest, Marij J.P. Welters, Sjoerd van der Burg
0citations -
Identification of endothelial-to-mesenchymal transition gene signatures in single-cell transcriptomics of human atherosclerotic tissue2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Marian Wesseling, Arjan Boltjes, Daniek Kapteijn, Marie A.C. Depuydt, Koen H.M. Prange, +8 more
6citations -
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 -
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 -
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 -
Human and murine fibroblast single-cell transcriptomics reveals fibroblast clusters are differentially affected by ageing and serum cholesterol2023 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Kim van Kuijk, Ian R McCracken, Renée J. H. A. Tillie, S. Asselberghs, Dlzar Ali Kheder, Stan Muitjens, +22 more
48citations -
Benchmarking variational AutoEncoders on cancer transcriptomics data2023 PLoS ONE article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Mostafa Eltager, Tamim Abdelaal, Mohammed Charrout, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Stavros Makrodimitris
18citations -
Benchmarking Variational AutoEncoders on cancer transcriptomics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Mostafa Eltager, Tamim Abdelaal, Mohammed Charrout, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Stavros Makrodimitris
4citations -
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Daniel Osorio, Anna Capasso, S. Gail Eckhardt, Uma P. Giri, Alexander J. Somma, Todd M. Pitts, +8 more
2citations -
Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Óscar Lapuente-Santana, Gregor Sturm, Markus Außerhofer, Constantin Zackl, Maria Zopoglou, Nicholas McGranahan, +5 more
0citations -
GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Emily So, Sikander Hayat, Sisira Kadambat Nair, Bo Wang, Benjamin Haibe‐Kains
13citations -
Multiomic profiling of transplant glomerulopathy reveals a novel T-cell dominant subclass2023 Kidney International article Medicine Renal Transplantation Outcomes and Treatments Open access
Iacopo Cristoferi, Hilal Varol, Myrthe van Baardwijk, Layla Rahiem, Karishma A. Lila, Thierry P. P. van den Bosch, +13 more
34citations