Vincent Rubinetti
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View article: Scalable data harmonization for single-cell image-based profiling with CytoTable
Scalable data harmonization for single-cell image-based profiling with CytoTable Open
Summary High-content imaging (HCI) involves the automated acquisition and quantitative analysis of cell phenotypes from microscopy images. These studies often rely on screening, which can involve thousands of chemical or genetic perturbati…
View article: Human Microbiome Compendium dataset
Human Microbiome Compendium dataset Open
The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut mic…
View article: STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci Open
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp motifs. TR variants contribute to several d…
View article: Human Microbiome Compendium dataset
Human Microbiome Compendium dataset Open
The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut mic…
View article: The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species Open
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. T…
View article: Reproducible image-based profiling with Pycytominer
Reproducible image-based profiling with Pycytominer Open
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To …
View article: Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome Open
Understanding the factors that shape variation in the human microbiome is a major goal of research in biology. While other genomics fields have used large, pre-compiled compendia to extract systematic insights requiring otherwise impractic…
View article: Human Microbiome Compendium dataset
Human Microbiome Compendium dataset Open
The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut mic…
View article: MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes Open
Gene definitions and identifiers can be painful to manage–more so when trying to include gene function annotations as this can be highly context-dependent. Creating groups of genes or gene sets can help provide such context, but it compoun…
View article: Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Application of Traditional Vaccine Development Strategies to SARS-CoV-2 Open
The development, production, and distribution of vaccines is imperative to saving lives, preventing illness, and reducing the economic and social burdens caused by the COVID-19 pandemic. Vaccines that use cutting-edge biotechnology have pl…
View article: The Coming of Age of Nucleic Acid Vaccines during COVID-19
The Coming of Age of Nucleic Acid Vaccines during COVID-19 Open
The SARS-CoV-2 pandemic has caused untold damage globally, presenting unusual demands on but also unique opportunities for vaccine development. The development, production, and distribution of vaccines are imperative to saving lives, preve…
View article: Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Hetnet connectivity search provides rapid insights into how two biomedical entities are related Open
Hetnets, short for “heterogeneous networks”, contain multiple node and relationship types and offer a way to encode biomedical knowledge. One such example, Hetionet connects 11 types of nodes — including genes, diseases, drugs, pathways, a…
View article: Hetnet connectivity search provides rapid insights into how biomedical entities are related
Hetnet connectivity search provides rapid insights into how biomedical entities are related Open
Background Hetnets, short for “heterogeneous networks,” contain multiple node and relationship types and offer a way to encode biomedical knowledge. One such example, Hetionet, connects 11 types of nodes—including genes, diseases, drugs, p…
View article: Changing word meanings in biomedical literature reveal pandemics and new technologies
Changing word meanings in biomedical literature reveal pandemics and new technologies Open
While we often think of words as having a fixed meaning that we use to describe a changing world, words are also dynamic and changing. Scientific research can also be remarkably fast-moving, with new concepts or approaches rapidly gaining …
View article: MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny Open
Studying proteins through the lens of evolution can reveal features such as conserved domains, lineage-specific variants, and co-occurring domain architectures in phylogenetic context across all superkingdoms. MolEvolvR enables researchers…
View article: Examining linguistic shifts between preprints and publications
Examining linguistic shifts between preprints and publications Open
Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprint…
View article: An Open-Publishing Response to the COVID-19 Infodemic
An Open-Publishing Response to the COVID-19 Infodemic Open
The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of th…
View article: greenelab/BioBombe: Accepted Manuscript - Genome Biology
greenelab/BioBombe: Accepted Manuscript - Genome Biology Open
The repository stores the full analysis pipeline and results for the bioRxiv preprint at https://doi.org/10.1101/573782 Abstract Background Unsupervised compression algorithms applied to gene expression data extract latent or hidden signal…
View article: Additional file 6 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Additional file 6 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations Open
Hetnetpy metaedge summary. Network summary of edge and node counts for each gene set collection.
View article: Additional file 4 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Additional file 4 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations Open
Model coefficients for predicting TP53 loss of function. Using all compressed features in the model implicates compressed features with cancer hallmark signatures. Associated with Fig. 7.
View article: Additional file 3 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Additional file 3 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations Open
Neutrophil and Monocyte Gene Sets. Entrez gene IDs and gene symbols for two xCell gene signatures (Neutrophil_HPCA_2 and Monocyte_FANTOM_2). Associated with Fig. 6.
View article: Additional file 5 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Additional file 5 of Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations Open
Tissue types and counts for TARGET, TCGA, and GTEx.
View article: Open collaborative writing with Manubot
Open collaborative writing with Manubot Open
Open, collaborative research is a powerful paradigm that can immensely strengthen the scientific process by integrating broad and diverse expertise. However, traditional research and multi-author writing processes break down at scale. We p…
View article: Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality Open
Background Unsupervised compression algorithms applied to gene expression data extract latent, or hidden, signals representing technical and biological sources of variation. However, these algorithms require a user to select a biologically…