Seemay Chou, Kira E. Poskanzer, and Peter S. Thuy-Boun
SC
TD
BF
WH
KP
+6
Published: May 31, 2022
If you’re interested in generating proteomics data but your organism of interest doesn’t have a sequenced genome to use as a reference database, it is straightforward and useful to collect a transcriptome instead.
Feridun Mert Celebi, Elizabeth A. McDaniel, and Taylor Reiter
SC
+2
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.
Seemay Chou, Kira E. Poskanzer, MaryClare Rollins, and Peter S. Thuy-Boun
SC
TD
BF
KP
TR
+2
Published: Mar 30, 2023
We generated a whole-genome assembly for the lone star tick to serve as a reference for downstream efforts where whole-genome maps are required. We created our assembly using pooled DNA from salivary glands of 50 adult female ticks that we sequenced using PacBio HiFi reads.
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.
seqqc is a Nextflow pipeline for quality control of short- or long-read sequencing data. It quickly assesses the quality of sequencing data so that it can be posted to a public repository before analysis for biological insights. Faster open data, faster knowledge for everyone.
Feridun Mert Celebi, Seemay Chou, Erin McGeever, Austin H. Patton, and Ryan York
SC
+4
Published: Sep 29, 2023
We want to find and use evolutionary innovations to solve present-day problems. We developed NovelTree, an efficient phylogenomic workflow that will empower us to decode the evolutionary traces of these innovations across the tree of life.
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.
Feridun Mert Celebi, Keith Cheveralls, Seemay Chou, Tara Essock-Burns, and Galo Garcia III
KC
SC
TE
Published: Nov 17, 2023
We distilled label-free microscopy data by comparing and implementing feature-detection algorithms. Sobel and Laplacian methods outperformed pixel intensity variance in accuracy.
Prachee Avasthi, Feridun Mert Celebi, Keith Cheveralls, Seemay Chou, Ilya Kolb, and David Q. Matus
PA
KC
SC
AH
+5
Published: Dec 02, 2023
Machine learning is a powerful tool for classifying images in a time series, such as the developmental stages of embryos. We built a classifier using only bright-field microscopy images to infer nematode embryonic stages at high throughput.