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Hodge Laplacians and Trajectory Inference with PHLOWER accepted in Nature Methods
Thrilled to share PHLOWER, which uses Hodge Laplacians to build trajectory-level embedding for inferring complex cellular differentiation trees from multimodal (RNA+ATAC) single-cell data (https://www.nature.com/articles/s41592-025-02870-5). Hodge Laplacian (HL) is a generalisation of a graph Laplacian used for clustering/pseudo-time estimation. Spectral decomposition …
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Commentary on the value of multimodal single cell sequencing for inference of gene regulatory networks out in Nature Methods
A short take on how computational approaches leverage multimodal single cell (RNA+ATAC) for inference of regulatory networks and a brief review of recent ground-breaking work by Dictys, SCENIC+ and MIRA at https://rdcu.be/disS3
Paper on computational method for the detection of small DNA methylation signatures out in Genome Biology
In a study lead by Tiago Maié, we present a computational pipeline for the detection of accurate DNA methylation signatures for cell type identification and cell deconvolution. Check the manuscript here!
Paper on spatial map of the myocardial infarction published in Nature!
We are delighted to have our manuscript co-lead by Zhijian Li being published in Nature! Great collaboration with R. Kramann and Saez lab! Check our our pre-print on a novel computational framework for computing gene regulatory networks from single cell …
Paper on spatial map of the myocardial infarction published in Nature! Read more »
Congratulations Zhijian Li and Ronghui Li for theirs successful Ph.D. defenses
We are happy to have two fresh PhDs from the lab! We wish you all the luck to Li & Li on their future work on Broad Institute and Shandong University Hospital!
Integration of Multimodal single cell data with MOJITOO – Accepted at ISMB/Bioinformatics
Our manuscript describing a fast and universal integration approach for multiome protocols was accepted as a paper at ISMB 2022 and will soon appears in Bioinformatics Journal. A pre-print is found here.
Area Under the Curve for Clustering @ ECML/PKDD 2022
The paper “The area under the ROC curve as a measure of clustering quality” was published in a special issue in “Data Mining and Knowledge Discovery” and accepted for a talk at ECML/PKDD 2022. Congrats to Pablo!
Kidney Fibrosis after COVID Infection / Study published in Cell Stem Cell
In a recently published work, we were able to show that there is increased scarring of the kidneys in patients who died after intensive care treatment for COVID19. Our data with kidney organoids from human induced pluripotent stem cells showed …
Kidney Fibrosis after COVID Infection / Study published in Cell Stem Cell Read more »