The paper introduces a deep learning framework to resolve mechanistic ambiguity in complex signaling networks by learning dynamic signatures from competing models.

bioRxiv · Aug 5, 2026 · PreprintSystems Biology

Allosteric Disordering of eIF2B Regulates the Integrated Stress Response

Udit Dalwadi, Advait Subramanian, Aniliese Deal, Julia E. Conrad, Tamara Nadjsombati, Meera Venkatesh, Morgane Boone, Pascal F. Egea, Ling-jie He, Nimit Jain, D. John Lee, Yuwei Liu, Lucas Charles Reineke, Kazuki Saito, Nathaniel Talledge, , Adam S. Frost

This study identifies an allosteric mechanism in eIF2B that regulates the Integrated Stress Response by showing how eIF2-P binding inhibits eIF2B activity through latch-helix dislocation.

Nature Chemical Biology · Jun 29, 2026Peer-reviewedBiochemistry

IRE1 drives a homeostatic response to reduced protein influx into the endoplasmic reticulum

Francesca Zappa, Advait Subramanian, Benjamin Yang, Julia E. Conrad, Tsan‐Wen Lu, Jing Wang, Nicolas A. DeBeaubien, Rose Yan, Renato Minopoli, Tristan Ian Croll, Stefka Tyanova, Mauro Costa‐Mattioli, Peter Walter, Diego Acosta‐Alvear

The paper identifies a third mode of IRE1 activation called TRES, triggered by reduced protein influx into the ER, leading to a distinct gene expression program to rebalance ER load.

bioRxiv · Mar 9, 2026 · PreprintCell Biology

Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization

Michael S. Costello, Bryan C. Neumann, Bonnie J. Cuthbert, Jana Holubová, Mia W. Raimondi, Fernando Garza‐Sánchez, Abdul Samad, Ladislav Bumba, Jacob A. Torres, Nickolas J. Holznecht, Jessica Mendoza, Ondřej Staněk, Sasiprapa Prombhul, Thomas Weimbs, Meghan A. Morrissey, , Christopher S. Hayes

This study shows that the Bordetella FhaB protein's microtubule-binding domain is delivered into host cells to promote bacterial colonization by interacting with microtubules in cilia.

Science · Feb 19, 2026Peer-reviewedMicrobiology

Intrinsic Molecular Timers and a Biphasic Amplitude Limit Regulate the Integrated Stress Response

Mustafa Ozen, Francesca Zappa, Karolina Kamińska, Daniel N. Itzhak, Stefka Tyanova, Carlos F. Lopez, Diego Acosta‐Alvear

The paper develops a theoretical model of the ISR using time-resolved proteomics data to show molecular timers and a translational cliff limit ISR activation.

bioRxiv · Dec 23, 2025 · PreprintSystems Biology

Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape

Taivan Batjargal, Francesca Zappa, Ryan J. Grant, Robert A. Piscopio, Alex Chialastri, Siddharth S. Dey, Diego Acosta‐Alvear, Maxwell Z. Wilson

This study uses optogenetic control of the ISR to show proportional encoding of stress inputs and reveals a stress memory landscape through an ODE model.

Cell Systems · Jul 1, 2023Peer-reviewedSystems Biology

A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material

Jennifer N. Rauch, Eric Valois, Sabrina C. Solley, Friederike Braig, Ryan S. Lach, Morgane Audouard, José Carlos Ponce‐Rojas, Michael S. Costello, Naomi J. Baxter, Kenneth S. Kosik, Carolina Arias, Diego Acosta‐Alvear, Maxwell Z. Wilson

This paper presents a scalable, easy-to-deploy protocol for detecting SARS-CoV-2 genetic material using Cas13-based technology paired with PCR and low-cost instrumentation.

Journal of Clinical Microbiology · Jan 22, 2021Peer-reviewedMolecular Biology

A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein to Facilitate the Detection of SARS-CoV-2

José Carlos Ponce‐Rojas, Michael S. Costello, Duncan A. Proctor, Kenneth S. Kosik, Maxwell Z. Wilson, Carolina Arias, Diego Acosta‐Alvear

PEARL is a fast, low-cost method for isolating RNA, DNA, and proteins to detect SARS-CoV-2 without commercial kits.

Journal of Clinical Microbiology · Dec 9, 2020Peer-reviewedMolecular Biology