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BB
IK
DM
+5
Published: Mar 06, 2024
We outline a comparative approach to investigate protein function by correlating the presence or absence of a protein with species-level phenotypes. We applied this strategy to a novel actin isoform in fungi but didn’t find an association with any of the phenotypes we considered.
Connections
Supplements (2): Data - Zenodo • Code v1.0 - GitHub
DM
TR
+1
Published: Apr 24, 2024
We’ve developed an easy-to-assemble apparatus and software for the automated collection of visible biological phenotypes such as growth, macroscopic morphology, motion, reflectance, and fluorescence.
BB
TE
+7
Published: May 31, 2024
To test its utility in analyzing biological samples, we built an open-source Raman spectrometer and collected spectra from chilis, beer, and algae. We could stratify samples, classify replicates, and link spectra with quantitative traits of beer (ABV) and chilis (perceived heat).
Connections
Supplements (1): Code and data - GitHub
BB
DS
+2
Published: May 31, 2024
We’re using the well-studied superfamily of small monomeric GTPases, the Ras GTPases, to evaluate our structure-based clustering tool, ProteinCartography. We’re seeking feedback on working with this protein family and determining which individual proteins to study.
Connections
Supplements (1): Data - Zenodo
BB
DS
+2
Published: May 31, 2024
We aim to validate ProteinCartography, a tool for structure-based protein clustering, by evaluating two foundational hypotheses: that proteins within a cluster have similar functions and proteins in different clusters have differing functions.
Connections
How can we biochemically validate protein function predictions with the deoxycytidine kinase family?
BB
DS
+2
Published: May 31, 2024
The human deoxycytidine kinase, a member of the nucleoside salvage pathway, has been studied extensively. We’ll use this family to assess our structure-based protein clustering tool, ProteinCartography. We’d love feedback on how we might work with this protein for validation.
Connections
Supplements (1): Data - Zenodo
SC
Published: Jun 13, 2024
Two years into our publishing experiment, we’ve learned a lot. We built internal processes that worked but inadvertently decreased scientists' agency and creativity. Now, we’re minimizing process in an effort to empower our scientists to share their work how they see fit.
KC
SC
IK
+4
Published: Jul 26, 2024
Sensory disorders are clinically common, debilitating conditions. But mouse behavioral models are often insufficient. We demonstrate that label-free, minimally-invasive brain imaging in mice could be a promising avenue for sensory research or drug discovery efforts.
Connections
Supplements (2): Code v1.0.1 - GitHub • Imaging data - Zenodo
KC
GM
+1
Published: Aug 08, 2024
We explored the use of embeddings from protein language models to distinguish between genuine and putative coding open reading frames (ORFs). We found that an embeddings-based approach (shared as a small Python package called plm-utils) improves identification of short ORFs.
Connections
Supplements (2): Code v1.0.0 - GitHub • Evaluation and training code - GitHub
BB
SC
RD
+5
Published: Aug 09, 2024
Inspired by wasps co-opting viral capsids to deliver genes to the caterpillars they parasitize, we looked for capsid-like proteins in other species. We found capsid homologs in ticks and other parasites, suggesting this phenomenon could be wider spread than previously known.
Connections
Replies (1): Code v1.0 - GitHub
Supplements (2): ProteinCartography run data - Zenodo • Data - Zenodo
KC
SC
+2
Published: Aug 08, 2024
Peptigate predicts bioactive peptides from transcriptomes. It integrates existing tools to predict sORF-encoded peptides, cleavage peptides, and RiPPs, then annotates them for bioactivity and other properties. We welcome feedback on expanding its capabilities.
Connections
Supplements (2): Code v1.0.0 - GitHub • Evaluation code and data v1.0 - GitHub
DM
MM
Published: Aug 22, 2024
We assembled a comprehensive E. coli antimicrobial resistance phenotype-genotype resource. This dataset will aid large-scale genetic studies on anti-microbial resistance and support research in phylogenetics and other fields.
Connections
Supplements (2): Code v1.0 - GitHub • Data - Zenodo
RC
+1
Published: Aug 22, 2024
This workflow lets you find potential circular DNA in your organism of interest using short-read, whole-genome sequencing data and a reference genome. We applied it to parasitoid wasps and some other parasites and found putative circular DNA.
Connections
Supplements (2): Code v1.0 - GitHub • Data - Zenodo
KC
TE
DM
Published: Nov 06, 2024
Live imaging of swimming cells can yield insight into an organism’s viability and responses to environmental stimuli. We developed a microscopy workflow and image analysis pipeline, SwimTracker, to track motility phenotypes from swimming cells in high throughput.
Connections
Supplements (2): Code v1.1 - GitHub • Data - BioImage Archive
