Devin P. Sullivan
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View article: SBML level 3 package: spatial processes, version 1, release 1
SBML level 3 package: spatial processes, version 1, release 1 Open
While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed…
View article: Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics Open
View article: Author Correction: Analysis of the Human Protein Atlas Image Classification competition
Author Correction: Analysis of the Human Protein Atlas Image Classification competition Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Spatial Characterization of the Human Centrosome Proteome Opens Up New Horizons for a Small but Versatile Organelle
Spatial Characterization of the Human Centrosome Proteome Opens Up New Horizons for a Small but Versatile Organelle Open
After a century of research, the human centrosome continues to fascinate. Based on immunofluorescence and confocal microscopy, an extensive inventory of the protein components of the human centrosome, and the centriolar satellites, with th…
View article: Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition
Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition
Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition Open
View article: Analysis of the Human Protein Atlas Image Classification competition
Analysis of the Human Protein Atlas Image Classification competition Open
Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to s…
View article: The human secretome
The human secretome Open
A database provides information on the relative abundances and locations of human proteins that are predicted to be secreted.
View article: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics Open
Cellular division is a fundamental source of cell-to-cell variability, and studies of transcript and protein abundances have revealed several hundred genes that are regulated by the cell cycle 1–8 . However, none of these studies provide s…
View article: Deep learning is combined with massive-scale citizen science to improve large-scale image classification
Deep learning is combined with massive-scale citizen science to improve large-scale image classification Open
View article: Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia
Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia Open
In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing their surrounding vasculature network. Transformed cancer cells are known to exhibit phenotypic alterations, enabling con…
View article: Seeing More: A Future of Augmented Microscopy
Seeing More: A Future of Augmented Microscopy Open
View article: Vitamin D-deficient mice have more invasive urinary tract infection
Vitamin D-deficient mice have more invasive urinary tract infection Open
Vitamin D deficiency is a common health problem with consequences not limited to bone and calcium hemostasis. Low levels have also been linked to tuberculosis and other respiratory infections as well as autoimmune diseases. We have previou…
View article: Spatiotemporal characterization of the human proteome.
Spatiotemporal characterization of the human proteome. Open
Characterizing the molecular components of the basic unit of life; the cell, is crucial for a complete understanding of human biology. The cell is divided into compartments to create a suitable environment for the resident proteins to fulf…
View article: Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories Open
The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to s…
View article: Active machine learning-driven experimentation to determine compound effects on protein patterns
Active machine learning-driven experimentation to determine compound effects on protein patterns Open
High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among …
View article: Author response: Active machine learning-driven experimentation to determine compound effects on protein patterns
Author response: Active machine learning-driven experimentation to determine compound effects on protein patterns Open
Full text Figures and data Side by side Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract High throughpu…
View article: Joint modeling of cell and nuclear shape variation
Joint modeling of cell and nuclear shape variation Open
Modeling cell shape variation is critical to our understanding of cell biology. Previous work has demonstrated the utility of nonrigid image registration methods for the construction of nonparametric nuclear shape models in which pairwise …