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Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Giulia Cesaro, James Shiniti Nagai, Nicolò Gnoato, Alice Chiodi, Gaia Tussardi, Vanessa Klöker, +6 more
39citations -
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 -
GraphComm predicts cell cell communication using a graph based deep learning method in single cell RNA sequencing data2025 Scientific Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Emily So, Sikander Hayat, Sisira Kadambat Nair, Bo Wang, Benjamin Haibe‐Kains
6citations -
OmniPath: integrated knowledgebase for multi-omics analysis2025 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Dénes Türei, Jonathan Schaul, Nicolàs Palacio‐Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, +26 more
22citations -
OmniPath: integrated knowledgebase for multi-omics analysis2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Dénes Türei, Jonathan Schaul, Nicolàs Palacio‐Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, +26 more
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
Detection of cell markers from single cell RNA-seq with sc2marker2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ronghui Li, Bella Benjamin, Rebekka K. Schneider, Ivan G. Costa
0citations -
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 -
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 -
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 -
Application of 3D MAPs pipeline identifies the morphological sequence chondrocytes undergo and the regulatory role of GDF5 in this process2021 Nature Communications article Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Sarah Rubin, Ankit Agrawal, Johannes Stegmaier, Sharon Krief, Neta Felsenthal, Jonathan Svorai, +4 more
20citations -
The limits of mtDNA analysis for determining the provenance of invasive species: a midwife toad example2022 Amphibia-Reptilia article Biochemistry, Genetics and Molecular Biology Genetic diversity and population structure Open access
Chris Vliegenthart, Maurits van de Vrede, Ingrid den Boer, Maarten J. Gilbert, Pim Lemmers, James France, +3 more
11citations
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