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Jase Gehring
Scientist
I love to explore biology with new technologies. I work at Arcadia to develop new experiments, generate large datasets, and understand complex systems like cells and proteins.
Published: May 31, 2022
Researchers studying any organism with genomic data can follow this simple walkthrough to create sets of barcoded probes for the multiplexed FISH technique called MERFISH. We’re sharing interactive code notebooks that can be adapted to design barcoded FISH probes for any species.
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Published: Mar 07, 2023
A workflow orchestration framework can streamline repeatable tasks and make workflows broadly usable. From several options, we chose Nextflow due to the ease of deploying across platforms, vibrant nf-core community, and ability to manage and monitor workflows with Nextflow Tower.
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Supplements (1): Nextflow template v1.1.0 - GitHub
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Published: May 03, 2023
Constraining motile microorganisms for live imaging often requires costly microfluidics or optical traps to keep them in view. We used patterned stamps and agar to make versatile, inexpensive “microchambers” and offer a way to predict the right chamber size for a given organism.
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Published: Sep 29, 2023
We investigated protein structure predictions as an alternative to protein sequence homology for comparing single-cell RNA-seq data across species.
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Supplements (2): Code v0.0.1 - GitHub • Related data - Zenodo
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Published: Sep 29, 2023
The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.
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Supplements (3): ProteinCartography v0.5.0 - GitHub • ProteinCartography v0.4.2 - GitHub • Data - Zenodo
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Published: Oct 06, 2023
Only some bacteria accumulate substantial amounts of polyphosphate (polyP). We thought that despite sequence divergence, polyP synthesis enzymes in these bacteria might have similar structures. We found this is sometimes true but doesn’t fully explain the phenomenon.
Connections
Replies (1): How can we identify the common molecular signatures underlying polyphosphate accumulation?
Supplements (2): Data - Zenodo • Code - GitHub
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Published: Dec 02, 2023
Oligo pools can contain millions of unique sequences, but they’re limited by length, error rate, and bias. We propose methods to scalably screen synthetic DNA libraries, so an individual researcher can obtain thousands of error-free synthetic DNA assemblies at low cost.
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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
