Adair L. Borges, Atanas Radkov, and Peter S. Thuy-Boun
TR
+1
Published: Dec 19, 2022
This pub details a process for phage amplification and concentration, DNA extraction, and HPLC and MS analysis of phage nucleosides. We optimized the approach with model phages known to use non-canonical nucleosides in their DNA, but plan to apply it for other phages.
The sourmash Python package produces many outputs that describe the content and similarity of sequencing data. We developed a new R package, sourmashconsumr, that lets a wider range of users easily load, analyze, and visualize those outputs in R.
Adair L. Borges, Rachel J. Dutton, Elizabeth A. McDaniel, Taylor Reiter, and Emily C.P. Weiss
RD
TR
Published: Mar 11, 2023
How do you approach getting a microbiome set up in a new lab? We’re sharing protocols for how we collected, stocked, and sequenced a set of cheese rind microbiomes and generated a high-quality metagenomics resource for future computational studies.
Januka Athukoralage, Adair L. Borges, and Taylor Reiter
TR
Published: Mar 14, 2023
We struggled to isolate enough phage mRNA for HPLC as we searched for new nucleoside chemistries. Ribodepleting the abundant extracted rRNA introduced contaminating DNA, and we were still left with more bacterial mRNA than phage transcripts. We suggest an alternative approach.
We want to seamlessly process and summarize metagenomics data from Illumina or Nanopore technologies. We built a Nextflow workflow that handles common metagenomics tasks and produces useful outputs and intuitive visualizations.
Horizontal gene transfer (HGT) is the exchange of DNA between species. It can lead to the acquisition of new gene functions, so finding HGT events can reveal genome novelty. preHGT is a pipeline that uses multiple existing methods to quickly screen for transferred genes.
Adair L. Borges, Rachel J. Dutton, Elizabeth A. McDaniel, Atanas Radkov, Taylor Reiter, and Emily C.P. Weiss
RD
+4
Published: Jul 19, 2023
We sampled cheese microbial communities to discover bacteriophages with unusual genome chemistries. We isolated 114 bacterial host strains and 17 phages, and identified one phage with a probable arabinose hypermodification of hydroxymethylcytosine.
Rachel J. Dutton, Elizabeth A. McDaniel, and Manon Morin
RD
MM
DS
Published: Aug 15, 2023
Hoping to find proteins that alter physiology in useful ways, we screened venom data sets for toxins fused to domains with additional functionality. We identified candidates, but struggled to infer any novel functions, and none seem well-conserved across venomous species.
Adair L. Borges, Feridun Mert Celebi, Kira E. Poskanzer, and Taylor Reiter
RD
KP
TR
Published: Aug 25, 2023
We implemented a lightweight method to identify viruses in 342 human brain bulk and single-cell sequencing data sets, and identified two glioblastoma cells from a single patient that contained deltapolyomavirus sequences.
Prachee Avasthi, Brae M. Bigge, Feridun Mert Celebi, Keith Cheveralls, Jase Gehring, Erin McGeever, Gilad Mishne, Atanas Radkov, and 1 more
BB
KC
RD
+14
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.
Adair L. Borges, Seemay Chou, and Megan L. Hochstrasser
SC
Published: Nov 02, 2023
Our "icebox" is where we share the projects that we've decided not to continue. We surveyed our company to understand resulting cultural shifts and how others are carrying our iced work forward.
Adair L. Borges, Seemay Chou, Ilya Kolb, Ryan Lane, David G. Mets, and Kira E. Poskanzer
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.
Adair L. Borges, Feridun Mert Celebi, Keith Cheveralls, and Taylor Reiter
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.
Brae M. Bigge, Adair L. Borges, Seemay Chou, Elizabeth A. McDaniel, Kira E. Poskanzer, and Ryan York
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.
Adair L. Borges, Feridun Mert Celebi, Keith Cheveralls, Seemay Chou, Taylor Reiter, and Emily C.P. Weiss
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.
Adair L. Borges, Feridun Mert Celebi, Reilly O. Cooper, and Elizabeth A. McDaniel
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.