The paper develops GENBAIT, a genetic algorithm-based tool to optimize bait selection for BioID experiments, reducing bait numbers while maintaining dataset coverage and structure.

Nature Communications · Oct 22, 2025Peer-reviewedBioinformatics

Benchmarking of proximity-dependent biotinylation enzymes across cellular compartments and time windows

Saya Sedighi, Kosar Vafaee, William Rod Hardy, Vesal Kasmaeifar, Zhen‐Yuan Lin, Rawan M. Kalloush, Julia Kitaygorodsky, Brendon Seale, Queenie Hu, Monica Hasegan, Anne‐Claude Gingras

This study benchmarks ten proximity ligases across cellular compartments and time windows, finding variations in activity, background, and spatial specificity, with ultraID showing the best balance.

bioRxiv · Aug 29, 2025 · PreprintSystems Biology

Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts

Yi-Cheng Tsai, Hiroyuki Uechi, Sean R. Millar, Eileigh Kadijk, Alon Minkovich, John Paul Tsu Ouyang, Karl J. Schreiber, Jie Qi Huang, Carina A. Lyons, Vesal Kasmaeifar, Zhixin Zhang, Rico Barsacchi, Claudia Möbius, Antje Janosch, Jonathan C. Savage, , Ji‐Young Youn

The paper shows that stress granules sequester the CCR4-NOT complex, leading to poly(A) tail lengthening and increased survival transcript abundance under stress.

bioRxiv · Feb 4, 2025 · PreprintCell Biology

Spatial proteomic mapping of human nuclear bodies reveals new functional insights into RNA regulation

Boris J.A. Dyakov, Simon Kobelke, B. Raktan Ahmed, Mingkun Wu, Jonathan F. Roth, Vesal Kasmaeifar, Zhen‐Yuan Lin, Ji‐Young Youn, Caroline Thivierge, Kieran R. Campbell, Thomas F. Duchaîne, Benjamin J. Blencowe, Archa H. Fox, Anne‐Claude Gingras

The paper maps human nuclear bodies using proximity proteomics, identifying new components and regulatory functions in RNA regulation.

bioRxiv · Jul 3, 2024 · PreprintCell Biology

Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component

Rasha Al Mismar, Payman Samavarchi‐Tehrani, Brendon Seale, Vesal Kasmaeifar, Claire Emilie Martin, Anne‐Claude Gingras

The paper introduces ecTurboID, a method to profile extracellular protein interactions, identifying LDLR as a new EGF-dependent EGFR partner.

bioRxiv · Nov 9, 2023 · PreprintMolecular Biology