Publications

Here you can find our recent publications.

Selected

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle

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

multi-modal-data-integration probabilistic-factor-models

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle

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.

multi-modal-data-integration probabilistic-factor-models spatio-temporal-models

FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution

Florin C Walter, Oliver Stegle, Britta Velten

Bioinformatics · 11 Apr 2023 · doi:10.1093/bioinformatics/btad183

FISHFactor identifies spatial gene expression patterns at subcellular resolution

probabilistic-factor-models spatial-models

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All

2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Tim E Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P Rubinetti, Faisal S Alquaddoomi, …, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres

Nucleic Acids Research · 24 Nov 2023 · doi:10.1093/nar/gkad1082

Integration of 168,000 samples reveals global patterns of the human gut microbiome

Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman

Cold Spring Harbor Laboratory · 11 Oct 2023 · doi:10.1101/2023.10.11.560955

MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes

Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu

Nucleic Acids Research · 18 Apr 2023 · doi:10.1093/nar/gkad289

FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution

Florin C Walter, Oliver Stegle, Britta Velten

Bioinformatics · 11 Apr 2023 · doi:10.1093/bioinformatics/btad183

FISHFactor identifies spatial gene expression patterns at subcellular resolution

probabilistic-factor-models spatial-models

Hetnet connectivity search provides rapid insights into how two biomedical entities are related

Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, …, David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene

Cold Spring Harbor Laboratory · 07 Jan 2023 · doi:10.1101/2023.01.05.522941

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related

Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene

GigaScience · 28 Dec 2022 · doi:10.1093/gigascience/giad047

MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny

Jacob D Krol, Joseph T Burke, Samuel Z Chen, Lo M Sosinski, Faisal S Alquaddoomi, …, Vincent P Rubinetti, Shaddai Amolitos, Kellen M Reason, John B Johnston, Janani Ravi

Cold Spring Harbor Laboratory · 22 Feb 2022 · doi:10.1101/2022.02.18.461833

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle

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.

multi-modal-data-integration probabilistic-factor-models spatio-temporal-models

2020

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene

Genome Biology · 11 May 2020 · doi:10.1186/s13059-020-02021-3

2019

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology · 24 Jun 2019 · doi:10.1371/journal.pcbi.1007128

Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality