Seemay Chou

CEO

President and CEO of Arcadia Science

www.arcadiascience.com 0000-0002-7271-303X seemaychou

All Pubs (10)Attributed Pubs (9)

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1 pub in other communities.

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Performing mass spectrometry-based proteomics in organisms with minimal reference protein databases

Seemay Chou, Kira E. Poskanzer, and Peter S. Thuy-Boun

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.

Connections

Supplements (1): Protocol - A parallel transcriptomics and proteomics workflow for organisms with minimal reference protein databases - protocols.io

Robust long-read saliva transcriptome and proteome from the lone star tick, Amblyomma americanum

Seemay Chou, Kira E. Poskanzer, and Peter S. Thuy-Boun

Published: May 31, 2022

The way you generate a reference database has a real impact on the completeness and results of proteomics experiments.

Connections

Supplements (3): Transcriptomics Data - SRA • Proteomics Data - PRIDE • Protocol - A parallel transcriptomics and proteomics workflow for organisms with minimal reference protein databases - protocols.io

Creating reproducible workflows for complex computational pipelines

Feridun Mert Celebi, Elizabeth A. McDaniel, and Taylor Reiter

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.

Connections

Supplements (1): Nextflow template v1.1.0 - GitHub

De novo assembly of a long-read Amblyomma americanum tick genome

Seemay Chou, Kira E. Poskanzer, MaryClare Rollins, and Peter S. Thuy-Boun

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.

Connections

Replies (1): Predicted gene models from the Amblyomma americanum tick genome

Supplements (4): Raw Amblyomma americanum genomic data - NCBI • Pseudo-haploid Amblyomma americanum genome - Zenodo • Unphased diploid Amblyomma americanum genome assembly - Zenodo • Code v1.0 - GitHub

A new R package, sourmashconsumr, for analyzing and visualizing the outputs of sourmash

Seemay Chou and Taylor Reiter

Published: Feb 21, 2023

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.

Connections

Supplements (2): sourmashconsumr R package v0.1.0 - GitHub • Code for figures and validation v1.0 - GitHub

Speeding up the quality control of raw sequencing data using seqqc, a Nextflow-based solution

Seemay Chou and Taylor Reiter

Published: Feb 21, 2023

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.

Connections

Supplements (3): seqqc v1.0 - GitHub • seqqc contamination database workflow v1.0 - GitHub • sourmash contamination database - OSF

NovelTree: Highly parallelized phylogenomic inference

Feridun Mert Celebi, Seemay Chou, Erin McGeever, Austin H. Patton, and Ryan York

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.

Connections

Supplements (3): NovelTree workflow v1.0.1-alpha - GitHub • Code for TSAR analysis v1.0.0 - GitHub • Data and workflow outputs from example TSAR analysis - Zenodo

Icebox is a science-sharing strategy designed to encourage risk-taking

Adair L. Borges, Seemay Chou, and Megan L. Hochstrasser

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.

Streamlining microscopy datasets by enriching for in-focus frames

Feridun Mert Celebi, Keith Cheveralls, Seemay Chou, Tara Essock-Burns, and Galo Garcia III

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.

Connections

Supplements (1): Code v1.0 - GitHub

Automated classification of time-course imaging data applied to nematode embryogenesis

Prachee Avasthi, Feridun Mert Celebi, Keith Cheveralls, Seemay Chou, Ilya Kolb, and David Q. Matus

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.

Connections

Supplements (2): Code v1.0 - GitHub • Data- Time-course images of nematode embryos - Zenodo