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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 -
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Fu Zhu, Rafael Kramann, Sikander Hayat, +1 more
0citations -
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Ping Zhu, Rafael Kramann, Sikander Hayat, +1 more
1citations -
On the benchmarking of clustering algorithms and hyperparameter influence for cell type detection in single-cell RNA sequencing data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Aleksandra Szmigiel, Ivan G. Costa, Ricardo J. G. B. Campello
1citations -
The Cell Ontology in the age of single-cell omics2026 eScholarship (California Digital Library) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian Aevermann, Alida Avola, +29 more
5citations -
The Cell Ontology in the age of single-cell omics2026 Scientific Data data-paper Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian D. Aevermann, Alida Avola, +28 more
0citations -
Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing2020 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent
Patrick S. Stumpf, Haruka Imanishi, Yuya Kunisaki, Yuichiro Semba, Timothy J. Noble, Rosanna C. G. Smith, +8 more
38citations -
Fast model-free standardization and integration of single-cell transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
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 -
scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations
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State of the Art Cell Detection in Bone Marrow Whole Slide Images2021 Journal of Pathology Informatics article Computer Science Digital Imaging for Blood Diseases Open access
Philipp Gräbel, Martina Margrit Crysandt, Reinhild Herwartz, Melanie Baumann, Barbara M. Klinkhammer, Peter Boor, +2 more
7citations -
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 -
Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer-related molecular mechanisms research Open access
Jeffrey Wang, Jung Min Suh, Brian J Woo, Albertas Navickas, Kristle Garcia, Keyi Yin, +10 more
7citations -
2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Sebastian Tiesmeyer, Niklas Müller‐Bötticher, Sergio Marco Salas, Paul Kießling, Paul M. Horn, Adrien Guillot, +7 more
9citations -
MASI enables fast model-free standardization and integration of single-cell transcriptomics data2023 Communications Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
4citations -
Non-Canonical Hedgehog Signaling Mediates Profibrotic Hematopoiesis-Stroma Crosstalk in Myeloproliferative Neoplasms2023 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Hedgehog Signaling Pathway Studies Open access
Jessica Ellen Pritchard, Juliette Pearce, Rebekka K. Schneider
0citations -
Non-Canonical Hedgehog Signaling Mediates Profibrotic Hematopoiesis-Stroma Crosstalk in Myeloproliferative Neoplasms2023 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Hedgehog Signaling Pathway Studies Open access
Jessica Ellen Pritchard, Juliette Pearce, Rebekka K. Schneider
0citations