Papers matching “single-cell spatial transcriptomics” 358
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SCHNEL: scalable clustering of high dimensional single-cell data2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Paul de Raadt, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
9citations -
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 -
Single-cell, whole-embryo phenotyping of mammalian developmental disorders2023 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Oana Veronica Amarie, +35 more
41citations -
Single‐cell omics: Overview, analysis, and application in biomedical science2021 Journal of Cellular Biochemistry article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Catarina M. Stein, Ralf Weiskirchen, Frédérik Damm, Paulina M. Strzelecka
43citations -
GraphHDBSCAN*: Graph-based Hierarchical Clustering on High Dimensional Single-cell RNA Sequencing Data2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Seyed Ardalan Ghoreishi, Aleksandra Szmigiel, James Shiniti Nagai, Ivan G. Costa, Arthur Zimek, Ricardo J. G. B. Campello
1citations -
SCHNEL: Scalable clustering of high dimensional single-cell data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Paul de Raadt, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
2citations -
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 -
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 -
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 -
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 -
Differential analysis of binarized single-cell RNA sequencing data captures biological variation2021 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
29citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Kirti Biharie, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
6citations -
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 -
scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations
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Community-driven ELIXIR activities in single-cell omics2022 F1000Research article 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
11citations -
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 -
Differential dropout analysis captures biological variation in single-cell RNA sequencing data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Gerard A. Bouland, Ahmed Essam Mahfouz, Marcel J. T. Reinders
3citations -
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 -
Single-cell reference mapping to construct and extend cell-type hierarchies2022 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
7citations -
MACA: Marker-based automatic cell-type annotation for single cell expression data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Simon J. Baumgart, Christian M. Stegmann, Sikander Hayat
2citations -
Multimodal single-cell profiling reveals crosstalk between macrophages and stromal cells in poor prognostic cholangiocarcinoma patients2026 npj Precision Oncology article Medicine Cholangiocarcinoma and Gallbladder Cancer Studies Open access
Lara Rosaline Heij, Sikander Hayat, Konrad Reichel, Sidrah Maryam, Colm J. O’Rourke, Xiuxiang Tan, +27 more
3citations -
Hierarchical progressive learning of cell identities in single-cell data2020 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Lieke Michielsen, Marcel J. T. Reinders, Ahmed Essam Mahfouz
0citations