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Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
0citations -
Abstract 4141516: Cross-species single-cell RNA sequencing reveals divergent phenotypes and activation states of adaptive immunity in human carotid and experimental murine atherosclerosis2024 Circulation conference-abstract Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases
Hauke Horstmann, Nathaly Anto-Michel, Holger Winkels, Ingo Hilgendorf, Teresa Gerhardt, Alma Zernecke, +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 -
Batch-effect correction improves downstream imaging mass cytometry data quality and facilitates robust cell type identification in the liver and hepatocellular carcinoma microenvironment2025 Zeitschrift für Gastroenterologie conference-paper Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Henrike Salié, Ana Marta Sequeira, Marieke E. Ijsselsteijn, Felix Röttele, Yuan Suo, Lara Wischer, +4 more
0citations -
Reference-based cell type matching of spatial transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
5citations -
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 -
Single-cell RNA sequencing analysis of the human fetal epicardium results in novel epicardial-specific markers and reveals a role for CRIP1 in epicardial EMT2023 European Heart Journal article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Anke M. Smits, T J Streef, Els Groeneveld, Tessa van Herwaarden, Marie‐José Goumans
0citations -
Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms2024 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Adam Tisch, Siddharth Madapoosi, Jan Rosa, Sean F. Eddy, Laura H. Mariani, Abhijit S. Naik, +8 more
2citations -
A guide to the BRAIN Initiative Cell Census Network data ecosystem2023 PLoS Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Michael Hawrylycz, Maryann Elizabeth Martone, Giorgio A. Ascoli, Jan Gunnar Bjaalie, Hong‐Wei Dong, Satrajit Ghosh, +92 more
53citations -
Identifying commonalities between cell lines and tumors at the single cell level using Sobolev Alignment of deep generative models2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Soufiane M. C. Mourragui, Joseph C. Siefert, Marcel J. T. Reinders, Marco Loog, Lodewyk F.A. Wessels
2citations -
NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, +3 more
12citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
PHLOWER - Single cell trajectory analysis using Hodge Decomposition2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingbo Cheng, Jitske Jansen, Katharina C. Reimer, James Shiniti Nagai, Zhijian Li, Paul Kießling, +5 more
0citations -
scAGG: Sample-level embedding and classification of Alzheimer's disease from single-nucleus data2025 Computational and Structural Biotechnology Journal article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Timo Verlaan, Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
2citations -
PathwayFinder enables linked exploration of cell types and gene modules in spatially resolved transcriptomics data2026 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Lisa Koorneef, Thomas Höllt, Louise van der Weerd, +1 more
0citations -
Random forest and live single‐cell metabolomics reveal metabolic profiles of human macrophages upon polarization2023 Biotechnology and Bioengineering article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Huaqi Tang, Ahmed Ali, Eman Muhammad Abdelazem, Tom H. M. Ottenhoff, Ron M. A. Heeren, Alireza Mashaghi
13citations -
An integrated single‐cell RNA ‐seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptomic and functional types2024 Journal of Neuroendocrinology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jari B. Berkhout, Delaram Poormoghadam, Chun‐Xia Yi, Andries Kalsbeek, Onno Cornelis Meijer, Ahmed Essam Mahfouz
38citations -
QUAS-R: Glutamine (Q) Uptake Assay with Single cell Resolution reveals metabolic heterogeneity with immune populations2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Amino Acid Enzymes and Metabolism Open access
Leonard R. Pelgrom, Simon O’Shoughnessy, Sander van Kasteren, David K. Finlay, Linda V. Sinclair
5citations