Dennis A. Sun

Scientist

Scientist at Arcadia Science

0000-0003-1000-7276 mezarque mezarque

All Pubs (14)Attributed Pubs (3)

Comparing gene expression across species based on protein structure

Prachee Avasthi, Jase Gehring, Austin H. Patton, Dennis A. Sun, and Ryan York

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.

Connections

Supplements (2): Code v0.0.1 - GitHub • Related data - Zenodo

ProteinCartography: Comparing proteins with structure-based maps for interactive exploration

Prachee Avasthi, Brae M. Bigge, Feridun Mert Celebi, Keith Cheveralls, Jase Gehring, Erin McGeever, Gilad Mishne, Atanas Radkov, and 1 more

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.

Connections

Supplements (3): ProteinCartography v0.5.0 - GitHub • ProteinCartography v0.4.2 - GitHub • Data - Zenodo

Exploring the actin family: A case study for ProteinCartography

Prachee Avasthi, Brae M. Bigge, Dennis A. Sun, and Ryan York

Published: Feb 14, 2024

We've applied ProteinCartography, a tool for protein family exploration, to the well-studied actin family. We’re able to categorize actins and related proteins into distinguishable functional buckets, and we uncovered some surprising hypotheses that could prompt further study.

Connections

Supplements (2): Code v1.0 - GitHub • Data - Zenodo