Ricardo O. Ramirez Flores

European Bioinformatics Institute — United Kingdom

Biochemistry, Genetics and Molecular Biology · Life Sciences

20h-index3.8kcitations56works20.12yr avg
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Research Topics

Single-cell and spatial transcriptomics(24), Bioinformatics and Genomic Networks(18), Gene Regulatory Network Analysis(10), Gene expression and cancer classification(9), Health, Environment, Cognitive Aging(9)

Publications56 total

Processed bulk and snRNA-seq data: Multicellular signaling and partial recovery define reverse cardiac remodeling
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
Processed bulk and snRNA-seq data: Multicellular signaling and partial recovery define reverse cardiac remodeling
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
Author Reply to Peer Reviews of ParTIpy: A Scalable Framework for Archetypal Analysis and Pareto Task Inference
2025
A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling
Nature Communications·2025· 2 citedOpen Access
ParTIpy: A Scalable Framework for Archetypal Analysis and Pareto Task Inference
2025Open Access
Cold and hot fibrosis define clinically distinct cardiac pathologies
Cell Systems·2025· 16 citedOpen Access
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data
2024· 15 citedOpen Access
A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling
2024· 3 citedOpen Access
Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions
Nature Neuroscience·2024· 36 citedOpen Access
Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction
Basic Research in Cardiology·2024· 27 citedOpen Access
LIANA+ provides an all-in-one framework for cell–cell communication inference
Nature Cell Biology·2024· 149 citedOpen Access
Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results
Nucleic Acids Research·2024· 7 citedOpen Access
Complementing Cell Taxonomies with a Multicellular Analysis of Tissues
Physiology·2024· 6 citedOpen Access
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
eLife·2023· 41 citedOpen Access
Author response: Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
2023Open Access
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
Nucleic Acids Research·2023· 269 citedOpen Access
Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results
2023· 3 citedOpen Access
LIANA+: an all-in-one cell-cell communication framework
2023· 34 citedOpen Access
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
2023Open Access
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
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Frequent Co-authors

Julio Sáez-Rodríguez(46), Jovan Tanevski(16), Pau Badia-i-Mompel(14), Denis Schapiro(12), Rebecca T. Levinson(11), Ivan G. Costa(11), Florian Wünnemann(10), James S. Nagai(10), Jan D. Lanzer(10), Daniel Dimitrov(9), Sophia Müller‐Dott(9), Christoph Kuppe(9), Zhijian Li(9), Monica T. Hannani(9), Maurice Halder(9), Mingbo Cheng(9), Susanne Ziegler(9), Nadine Kaesler(9), Remco M. Hoogenboezem(9), Eric M. Bindels(9)