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Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 medRxiv preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
4citations -
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 -
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 -
Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer2026 Cancer Cell article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Valentin Marteau, Niloofar Nemati, Kristina Handler, Deeksha Raju, Alexander Kirchmair, Dietmar Rieder, +40 more
37citations -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +3 more
0citations -
scDecorr: feature decorrelation based representation learning enables self-supervised alignment of multiple single-cell experiments2026 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ritabrata Sanyal, Yang Xu, Hyojin Kim, Rafael Kramann, Sikander Hayat
0citations -
Abstract 4366465: Integrative Single-Cell and Genetic Profiling of Human Heart Failure for Therapeutic Target Discovery2025 Circulation conference-abstract Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Tore Bleckwehl, David Schumacher, Junedh Amrute, Konrad Hoeft, Vivek Das, Simon J. Baumgart, +2 more
0citations -
PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
0citations -
OP0243 SINGLE-CELL RNA SEQUENCING OF ACPA-ENRICHED B CELLS REVEALED A CD11c+ ATYPICAL B CELL GENE SIGNATURE IN RHEUMATOID ARTHRITIS2025 Annals of the Rheumatic Diseases conference-abstract Medicine Rheumatoid Arthritis Research and Therapies Open access
Yasuo Nagafuchi, Linda M. Slot, Deimantė Šimaitė, Aleida M. Bakker, Erik B. van den Akker, Tom W. J. Huizinga, +3 more
0citations -
scACCorDiON: a clustering approach for explainable patient level cell–cell communication graph analysis2025 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
James Shiniti Nagai, Tiago Maié, Michael T. Schaub, Ivan G. Costa
3citations -
Benchmarking Imputation Methods for Single-Cell RNA Sequencing Data Using Peripheral Blood Mononuclear Cells from Acute Myocardial Infarction Patients0citations
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scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations
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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 -
Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen2021 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Zhijian Li, Christoph Kuppe, Susanne Maria Ziegler, Mingbo Cheng, Nazanin Kabgani, Sylvia Menzel, +3 more
141citations -
A single-cell atlas of mouse central nervous system immune cells reveals unique infection-stage immune signatures during the progression of meningitis caused by Streptococcus suis2025 Communications Biology article Immunology and Microbiology Bacterial Infections and Vaccines Open access
Xuan Jade Jiang, Jikun Mei, Junhui Zhu, Yanyan Tian, Ziheng Li, Zengshuai Wu, +4 more
5citations -
Single-cell RNA sequencing of human fetal epicardium reveals novel markers and regulators of EMT2020 European Heart Journal article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
T J Streef, Tessa van Herwaarden, Anke M. Smits, Marie‐José Goumans
0citations -
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 -
Single-cell characterization of human periodontal ligament (PDL) cells reveals uniformly mesenchymal populations in matched maxilla and mandible pairs from four donors2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Periodontal Regeneration and Treatments Open access
Chloé Radermacher, Robert Dzhanaev, Christian Hasberg, Sabine Neuß-Stein, Andrea Gorgels, Julia Moellmann, +8 more
0citations -
Unraveling Divergent Transcriptomic Profiles: A Comparative Single-Cell RNA Sequencing Study of Epithelium, Gingiva, and Periodontal Ligament Tissues12citations
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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
1citations -
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