Publications
Here you can find our recent publications.
Selected
![Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets](https://www.embopress.org/cms/10.15252/msb.20178124/asset/38d5fe53-2af9-469a-a44c-399133a490df/assets/graphic/msb178124-abs-0001-m.png)
Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets
Molecular Systems Biology
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18 Jun 2018
·
doi:10.15252/msb.20178124
MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in an unsupervised fashion
![Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO](https://biofam.github.io/MOFA2/images/mefisto.png)
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
Nature Methods
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13 Jan 2022
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doi:10.1038/s41592-021-01343-9
MEFISTO is a unsupervised method to integrate multi-modal data with continuous structures among the samples, e.g. in spatial or temporal data.
![FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution](https://github.com/bioFAM/FISHFactor/raw/master/model.png)
FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution
Bioinformatics
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11 Apr 2023
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doi:10.1093/bioinformatics/btad183
FISHFactor identifies spatial gene expression patterns at subcellular resolution
Guide assignment in single-cell CRISPR screens using crispat
Cold Spring Harbor Laboratory
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10 May 2024
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doi:10.1101/2024.05.06.592692
All
2024
Guide assignment in single-cell CRISPR screens using crispat
Cold Spring Harbor Laboratory
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10 May 2024
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doi:10.1101/2024.05.06.592692
In situ analysis of osmolyte mechanisms of proteome thermal stabilization
Nature Chemical Biology
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29 Feb 2024
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doi:10.1038/s41589-024-01568-7
2023
The changing career paths of PhDs and postdocs trained at EMBL
eLife
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23 Nov 2023
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doi:10.7554/elife.78706
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease
eLife
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22 Nov 2023
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doi:10.7554/elife.93161
Principles and challenges of modeling temporal and spatial omics data
Nature Methods
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14 Sep 2023
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doi:10.1038/s41592-023-01992-y
![FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution](https://github.com/bioFAM/FISHFactor/raw/master/model.png)
FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution
Bioinformatics
·
11 Apr 2023
·
doi:10.1093/bioinformatics/btad183
FISHFactor identifies spatial gene expression patterns at subcellular resolution
Spatial multiomics map of trophoblast development in early pregnancy
Nature
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29 Mar 2023
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doi:10.1038/s41586-023-05869-0
2022
![Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO](https://biofam.github.io/MOFA2/images/mefisto.png)
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
Nature Methods
·
13 Jan 2022
·
doi:10.1038/s41592-021-01343-9
MEFISTO is a unsupervised method to integrate multi-modal data with continuous structures among the samples, e.g. in spatial or temporal data.
2020
Developmental Gene Expression Differences between Humans and Mammalian Models
Cell Reports
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01 Oct 2020
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doi:10.1016/j.celrep.2020.108308
Survey of ex vivo drug combination effects in chronic lymphocytic leukemia reveals synergistic drug effects and genetic dependencies
Leukemia
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13 May 2020
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doi:10.1038/s41375-020-0846-5
MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data
Genome Biology
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11 May 2020
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doi:10.1186/s13059-020-02015-1
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions
Nature Communications
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08 Jan 2020
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doi:10.1038/s41467-019-13888-7
2019
Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
Biostatistics
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09 Oct 2019
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doi:10.1093/biostatistics/kxz034
Gene expression across mammalian organ development
Nature
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26 Jun 2019
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doi:10.1038/s41586-019-1338-5
2018
![Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets](https://www.embopress.org/cms/10.15252/msb.20178124/asset/38d5fe53-2af9-469a-a44c-399133a490df/assets/graphic/msb178124-abs-0001-m.png)
Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets
Molecular Systems Biology
·
18 Jun 2018
·
doi:10.15252/msb.20178124
MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in an unsupervised fashion
2017
Drug-perturbation-based stratification of blood cancer
Journal of Clinical Investigation
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11 Dec 2017
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doi:10.1172/jci93801