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SIRV: Spatial inference of RNA velocity at the single-cell resolution2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens M. Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
12citations -
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 -
scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations
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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 -
SIRV: Spatial inference of RNA velocity at the single-cell resolution2022 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
1citations -
SIRV: Spatial inference of RNA velocity at the single-cell resolution2022 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
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, Hyojin Kim, Rafael Kramann, Sikander Hayat
0citations -
Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics2020 Circulation Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Marie A.C. Depuydt, Koen H.M. Prange, Lotte Slenders, Tiit Örd, D. Elbersen, Arjan Boltjes, +17 more
619citations -
Peer Review Report For: Community-driven ELIXIR activities in single-cell omics [version 1; peer review: 2 approved with reservations]2023 peer-review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Paulo Czarnewski, Ahmed Essam Mahfouz, Raffaele Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez‐Uriarte, +21 more
0citations -
Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets2026 Computational and Structural Biotechnology Journal article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Dorien J.M. Peters, Ahmed Essam Mahfouz
1citations -
Integrative learning of disentangled representations from single-cell RNA-sequencing datasets2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Dorien J.M. Peters, Ahmed Essam Mahfouz
0citations -
scRIPT: a rapid, high-coverage single-cell lineage-tracing method applied to the hematoendothelial differentiation of embryonic stem cells2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Rıdvan Çeti̇n, Eric M. Bindels, Jente van Staalduinen, Lucas Kuijpers, Giulia Picco, Mathijs Arnoud Sanders, +6 more
0citations -
Longitudinal dynamics of human B-cell response at single-cell level in response to Tdap vaccination2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology T-cell and B-cell Immunology Open access
Indu Khatri, Annieck M. Diks, Erik B. van den Akker, Liesbeth E.M. Oosten, Jaap Jan Zwaginga, Marcel J. T. Reinders, +2 more
0citations -
Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis2023 Frontiers in Microbiology article Engineering Microfluidic and Capillary Electrophoresis Applications Open access
Keitaro Kasahara, Markus Leygeber, Johannes Seiffarth, Karina Ruzaeva, Thomas Drepper, Katharina Nöh, +1 more
16citations -
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 -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
12citations -
Development of an untargeted peak confidence index for noise filtering in high-resolution mass spectrometry for single-cell metabolomics0citations
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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 -
Single-cell reference mapping to construct and extend cell-type hierarchies2023 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Lieke Michielsen, Mohammad Lotfollahi, Daniel C. Strobl, Lisa Sikkema, Marcel J. T. Reinders, Fabian Joachim Theis, +1 more
43citations -
Comparison of Liquid Chromatography- and Nano-Electrospray Ionization-Mass Spectrometry Approaches for Single-Cell Metabolomics2026 Analytical Chemistry article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Abigail Cook, Claire Davison, Jordan Pascoe, Harpreet Atwal, George Mayson, Dany J. V. Beste, +1 more
3citations