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De-novoreconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters2023 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Mhaned Oubounyt, Maria L. Elkjaer, Tanja Laske, Alexander G. B. Grønning, Marcus Johannes Moeller, Jan Baumbach
8citations -
A clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli, Stefan Semrau
0citations -
SciViewer- An interactive browser for visualizing single cell datasets2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Dhawal S. Jain, Sikander Hayat, Joydeep Charkaborty, Pooja Srinivasa, Michael H. Cho, Edwin K. Silverman, +2 more
1citations -
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 -
An m / z - and Intensity-Based HRMS Clustering Algorithm Targeted toward Single-Cell Metabolomics2026 Journal of the American Society for Mass Spectrometry article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Dirk Wevers, Laura Koldenhof, Laura Ann Hetzel, Anouschka van der Zeeuw, Hellen Fass, Thomas Hankemeier, +1 more
1citations -
An m/z- and intensity-based HRMS clustering algorithm targeted toward single-cell metabolomics2026 Leiden Repository (Leiden University) article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
L.D. Wevers, Laura Koldenhof, L. Castaneda, A. van der Zeeuw, H. Fass, Thomas Hankemeier, +2 more
0citations -
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 -
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 -
Single-cell transcriptional diversity is a hallmark of developmental potential2020 Science article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 4 patents
Gunsagar Singh Gulati, Shaheen S. Sikandar, Daniel J. Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J. Berger, +12 more
1,715citations -
Single-cell analysis reveals chemokine-mediated differential regulation of monocyte mechanics2021 iScience article Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access cited by 1 patent
Tom M. J. Evers, Vahid Sheikhhassani, Mariëlle C. Haks, Cornelis Storm, Tom H. M. Ottenhoff, Alireza Mashaghi
30citations -
Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access
Anoushka Joglekar, Andrey D. Prjibelski, Ahmed Essam Mahfouz, Paul G. Collier, Susan Lin, Anna Katharina Schlusche, +22 more
5citations -
Endothelial Recovery in Bare Metal Stents and Drug-Eluting Stents on a Single-Cell Level2021 Arteriosclerosis Thrombosis and Vascular Biology article Medicine Coronary Interventions and Diagnostics Open access
Anne Cornelissen, Liang Guo, Raquel Fernandez, Michael C. Kelly, Christine Janifer, Salome H. Kuntz, +9 more
20citations -
Tracking One-in-a-Million: Large-Scale Benchmark for Microbial Single-Cell Tracking with Experiment-Aware Robustness Metrics2025 Lecture notes in computer science conference-paper Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Johannes Seiffarth, Luisa Blöbaum, Richard Dominik Paul, Nils Friederich, Angelo Jovin Yamachui Sitcheu, Ralf Mikut, +3 more
3citations -
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing2022 Bioinformatics article Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access cited by 1 patent
Hana Rozhoňová, Daniel Danciu, Stefan G. Stark, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann
9citations -
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 -
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access
Hana Rozhoňová, Daniel Danciu, Stefan G. Stark, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann
1citations -
Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping2021 Zenodo (CERN European Organization for Nuclear Research) dataset Medicine SARS-CoV-2 and COVID-19 Research Open access
Felix Schreibing, Monica Toft Hannani, Fabio Ticconi, Eleanor Fewings, James Shiniti Nagai, Matthias Begemann, +18 more
0citations -
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 -
High-dimensional single-cell analysis of human natural killer cell heterogeneity2024 Nature Immunology article Immunology and Microbiology Immune Cell Function and Interaction Open access
Lucas Rebuffet, Janine E. Melsen, Bertrand Escalière, Daniela Basurto-Lozada, Avinash Bhandoola, Niklas K. Björkström, +21 more
278citations -
Single-cell analysis of human fetal epicardium reveals its cellular composition and identifies CRIP1 as a modulator of EMT2023 Stem Cell Reports article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Thomas J. Streef, Esmee J. Groeneveld, Tessa van Herwaarden, Jesper Hjortnaes, Marie‐José Goumans, Anke M. Smits
16citations