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A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing2021 Genome Research preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Mohamed Keshk, Trygve E. Bakken, Jeremy A. Miller, +4 more
96citations -
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
2citations -
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 -
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 -
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 -
Benchmarking Imputation Methods for Single-Cell RNA Sequencing Data Using Peripheral Blood Mononuclear Cells from Acute Myocardial Infarction Patients0citations
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Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Boudewijn P. F. Lelieveldt
2citations -
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 -
Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tommaso Andreani, Linda M. Slot, Samuel Gabillard, Carsten Struebing, Claus Reimertz, Yaligara Veeranagouda, +6 more
4citations -
GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Emily So, Sikander Hayat, Sisira Kadambat Nair, Bo Wang, Benjamin Haibe‐Kains
13citations -
Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Daniel Dimitrov, Dénes Türei, Charlotte Boys, James Shiniti Nagai, Ricardo O. Ramirez Flores, Hyojin Kim, +5 more
23citations -
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 -
Cell-cell Communication Inference from Single-cell RNA-Seq Data: a Comparison of Methods and Resources2021 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Daniel Dimitrov, Dénes Türei, Charlotte Boys, James Shiniti Nagai, Ricardo Ramirez Flores, Hyojin Kim, +5 more
3citations -
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 -
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Daniel Osorio, Anna Capasso, S. Gail Eckhardt, Uma P. Giri, Alexander J. Somma, Todd M. Pitts, +8 more
2citations -
NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, +3 more
12citations -
Post-transcriptional regulatory mechanisms in human islets inferred from cell type-specific eQTLs detected by single-cell RNA-seq2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Twan J. J. de Winter, Miha Sovrovic, Han Sun, James D. Johnson, Patrick Edward MacDonald, Anna L. Gloyn, +3 more
0citations -
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 -
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 -
mcBERT: Patient-Level Single-cell Transcriptomics Data Representation2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Benedikt von Querfurth, Johannes Lohmöller, Jan Pennekamp, Tore Bleckwehl, Rafael Kramann, Klaus Wehrle, +1 more
3citations