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Single-cell immune profiling reveals novel thymus-seeding populations, T cell commitment, and multi-lineage development in the human thymus2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology T-cell and B-cell Immunology Open access
Martijn Cordes, Kirsten Canté-Barrett, Erik B. van den Akker, Federico A. Moretti, Szymon M. Kiełbasa, Sandra A. Vloemans, +6 more
5citations -
Combi-Seq: Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Lukas Mathur, Bence Szalai, Ramesh Utharala, Martine Ballinger, Jonathan J. M. Landry, Michaël Ryckelynck, +3 more
4citations -
Single-Cell Integration and Multi-Modal Profiling Reveals Phenotypes and Spatial Organization of Neutrophils in Colorectal Cancer2025 SSRN Electronic Journal preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Valentin Marteau, Niloofar Nemati, Kristina Handler, Deeksha Raju, Alexander Kirchmair, Dietmar Rieder, +37 more
0citations -
Integrative single-cell and genetic profiling of human heart failure identifies targets for cardiomyocyte restoration2025 medRxiv preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tore Bleckwehl, David Schumacher, Charlotte Heymanns, Sidrah Maryam, Sean Joseph Jurgens, Junedh Amrute, +13 more
1citations -
Multimodal single-cell profiling reveals cancer crosstalk between macrophages and stromal cells in poor prognostic cholangiocarcinoma patients2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cholangiocarcinoma and Gallbladder Cancer Studies Open access
Lara Rosaline Heij, Sikander Hayat, Konrad Reichel, Sidrah Maryam, Colm J. O’Rourke, Xiuxiang Tan, +22 more
0citations -
Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mina Shaigan, Deepika Puri, Giulia Fornero, René Krüger, Mara Steiger, Hannes Klump, +4 more
0citations -
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing2021 Genome Research preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Mohamed Keshk, Trygve E. Bakken, Jeremy A. Miller, +4 more
96citations -
WALDO: community-Wide Annotation of γδ Lymphocytes in single-cell Data, Openly benchmarked2026 Zenodo (CERN European Organization for Nuclear Research) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Farid Keramati, Moosa Rezwani, Likai Tan, David Hamilton, Zheng Song, Tao Yang, +10 more
0citations -
scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa
0citations -
Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Joana B. Nunes, Marieke E. Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Bart Everts, +3 more
3citations -
An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and functional types2023 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
0citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
1citations -
Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access
Daniel Osorio, Parastoo Shahrouzi, Xavier Tekpli, Vessela Nedelcheva Kristensen, Marieke L. Kuijjer
4citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
3citations -
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 -
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 -
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, +5 more
4citations -
Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Colorectal Cancer Treatments and Studies Open access
Christina Plattner, Giorgia Lamberti, Peter Blattmann, Alexander Kirchmair, Dietmar Rieder, Zuzana Loncová, +23 more
0citations