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Deciphering the signaling network of breast cancer improves drug sensitivity prediction2021 Cell Systems article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Marco Tognetti, Attila Gábor, Mi Yang, Valentina Cappelletti, Jonas Windhager, Oscar M. Rueda, +9 more
45citations -
Distinct morphological features of malignant cells in large B-cell lymphoma identified by soft-segmentation in imaging-based spatial proteomics2025 Blood conference-abstract Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Troy Noordenbos, Marieke E. Ijsselsteijn, Noel de Miranda, Joost S.P. Vermaat, Mohammad Shahrokh Esfahani
1citations -
Protocol for multispectral imaging on cryosections to map myeloid cell heterogeneity in its spatial context2023 STAR Protocols article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Elias B Wieland, Laura JAP Kempen, Chang Wei Lu, Marjo M. P. C. Donners, Erik A.L. Biessen, Pieter Goossens
2citations -
SpatialCOC: an integrative framework for spatial continuous mapping and cross-omics correction in spatial multi-omics data2026 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingxuan Li, Peisen Sun, Yisi Luo, Guancheng Zhou, Xiaofei Yang, Deyu Meng, +1 more
3citations -
AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kai Peng, Mayra L. Ruiz Tejada Segura, Barthélémy Caron, Christoph Kuppe, James Shiniti Nagai, Ivan G. Costa
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 -
Semi-automated background removal limits loss of data and normalises the images for downstream analysis of imaging mass cytometry data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Marieke E. Ijsselsteijn, Antonios Somarakis, Boudewijn P. F. Lelieveldt, Thomas Höllt, Noel F.C.C. de Miranda
2citations -
Targeting modulated vascular smooth muscle cells in atherosclerosis via FAP-directed immunotherapy2026 Science article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Junedh Amrute, In‐Hyuk Jung, Tracy Yamawaki, Wen-Ling Lin, Andrea L. Bredemeyer, Johanna Diekmann, +32 more
38citations -
Practical observations on the use of fluorescent reporter systems in Clostridioides difficile2022 Antonie van Leeuwenhoek article Biochemistry, Genetics and Molecular Biology Advanced Fluorescence Microscopy Techniques Open access
Ana M. Oliveira Paiva, Annemieke H. Friggen, Roxanne Douwes, Bert Wittekoek, Wiep Klaas Smits
15citations -
Age-associated B cells predict coronary events in humans and aggravate murine atherosclerosis2026 Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Jill de Mol, Pernilla Katra, Virginia Smit, Anna Witteveen, Lukas Tomas, Linda Andersson, +10 more
0citations -
Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Junedh Amrute, In‐Hyuk Jung, Tracy Yamawaki, Andrea L. Bredemeyer, Johanna Diekmann, Sikander Hayat, +28 more
5citations -
microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation2022 PLoS ONE article Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Tim Scherr, Johannes Seiffarth, Bastian Wollenhaupt, Oliver Neumann, Marcel P. Schilling, Dietrich Kohlheyer, +3 more
11citations -
microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Tim Scherr, Johannes Seiffarth, Bastian Wollenhaupt, Oliver Neumann, Marcel P. Schilling, Dietrich Kohlheyer, +3 more
1citations -
The proteomic landscape of proteotoxic stress in a fibrogenic liver disease2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Chemistry Advanced Proteomics Techniques and Applications Open access
Florian A. Rosenberger, Sophia Clara Mädler, Katrine Holtz Thorhauge, Sophia Steigerwald, Malin Fromme, Caroline A M Weiss, +13 more
2citations -
A 34-Marker Panel for Imaging Mass Cytometric Analysis of Human Snap-Frozen Tissue2020 Frontiers in Immunology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Nannan Guo, Vincent van Unen, Marieke E. Ijsselsteijn, Laura F. Ouboter, Andrea E. van der Meulen‐de Jong, Susana M. Chuva de Sousa Lopes, +3 more
45citations -
Infiltrative classical monocyte-derived and SPP1 lipid-associated macrophages mediate inflammation and fibrosis in ANCA-associated glomerulonephritis2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Vasculitis and related conditions Open access
Yosta Vegting, Aldo Jongejan, Annette E. Neele, Nike Claessen, Gal Sela, Koen H.M. Prange, +10 more
2citations