Scientist @ArcadiaScience. @Harvard, @ucdavis, @CUAnschutz alum. Computational biologist and sequencing data enthusiast.
Philadelphia, PA
Joined October 2012
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Introducing peptigate (peptide+investigate), a workflow that predicts and annotates peptides from transcriptome assemblies. It predicts small ORF-encoded peptides, cleavage peptides, and ribosomally synthesized and posttranslationally modified peptides.🧵
github.com/Arcadia-Science/p…
If you want to learn more about peptigate, read our pub or take a look at the GitHub repo.
research.arcadiascience.com/…
github.com/Arcadia-Science/p…
Thank you to all of my colleagues @ArcadiaScience who helped put this project together – @emilycpierce, @seemaychou, @AdairLBorges, @mertcelebi_, @kchev, Audrey Bell, @thecrispress, and @RobertRoth57.
Have you ever wondered whether a transcript is coding or noncoding? Or whether a predicted open reading frame encodes a functional protein? We recently had this question for very short open reading frames (sORFs). Enter the Python package plmutils 🧵
research.arcadiascience.com/…
This was a combined effort between many scientists @ArcadiaScience. @Gilad had the initial idea to use ESM embeddings to improve prediction accuracy, while @kchev implemented the code and performed some of the validation.
Learn more about plm-utils by reading our pub, “Using protein language models to predict coding and noncoding transcripts,” or see the GitHub repository.
research.arcadiascience.com/…
github.com/Arcadia-Science/2…
Taylor Reiter retweeted
🚨Another new job alert @ArcadiaScience! I know some of you have been waiting for this kind of role and there are openings on both the discovery and translation side of the org! Apply now!
New open search! We are looking for project scientists to help us pilot high-risk, high-reward ideas:
jobs.lever.co/arcadiascience…