This study identifies sequence elements that enable dual localization of mitochondrial proteins, showing how combinatorial features regulate import and function across compartments.

bioRxiv · Aug 1, 2026 · PreprintBiochemistry

In Vivo Massively Parallel Reporter Assay Reveals Sequence Determinants of mRNA Localization in Astrocytes

Sarah K. Koester, Kristina Sakers, Gareth M. Rurak, Stephen P. Plassmeyer, Kelli McFarland White, Sebastian Alves Ferreira Dias, Peter Baird, D.J. Kornbluth, Joseph D. Dougherty

The paper develops an in vivo MPRA method to identify sequence determinants of mRNA localization in astrocytes and finds diverse regulatory mechanisms are used.

bioRxiv · Apr 30, 2026 · PreprintNeuroscience

Direct prediction of intermolecular interactions driven by disordered regions

Garrett M. Ginell, Ryan J. Emenecker, Jeffrey M. Lotthammer, Alex T. Keeley, Stephen P. Plassmeyer, Nicholas J. Razo, Emery T. Usher, Jacqueline F. Pelham, Alex S. Holehouse

The paper develops a method to predict intermolecular interactions between intrinsically disordered regions and partner proteins using chemical physics principles.

Science · May 22, 2025Peer-reviewedBiophysics

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Luke Lambourne, Kaia Mattioli, Clarissa Stephanie Santoso, Gloria Sheynkman, Sachi Inukai, Babita Kaundal, Anna Berenson, Kerstin Spirohn, Anukana Bhattacharjee, Elisabeth Rothman, Shaleen Shrestha, Florent Laval, Brent S. Carroll, Stephen P. Plassmeyer, Ryan J. Emenecker, , Juan I. Fuxman Bass

The paper identifies two categories of transcription factor isoforms with distinct molecular functions and shows they contribute to gene regulatory complexity.

Molecular Cell · Mar 27, 2025Peer-reviewedSystems Biology

Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

James L. Shepherdson, David M. Granas, Jie Li, Zara Shariff, Stephen P. Plassmeyer, Alex S. Holehouse, Michael A. White, Barak A. Cohen

The paper performs a deep mutational scan of CRX variants to classify clinical variants and reveals biochemical properties of the transcriptional effector domain.

Genome Research · Oct 1, 2024Peer-reviewedGenomics

A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

Tomás Lagunas, Stephen P. Plassmeyer, Anthony D. Fischer, Ryan Z. Friedman, Michael A. Rieger, Din Selmanovic, Simona Sarafinovska, Yvette K Sol, Michael J. Kasper, Stuart B. Fass, Alessandra F. Aguilar Lucero, Joon‐Yong An, Stephan Sanders, Barak A. Cohen, Joseph D. Dougherty

The paper develops a method to assess the functional effects of non-coding elements in specific cell types in vivo using a Cre-dependent MPRA approach.

Communications Biology · Nov 12, 2023Peer-reviewedGenetics

A Massively Parallel Screen of 5'UTR Mutations Identifies Variants Impacting Translation and Protein Production in Neurodevelopmental Disorder Genes

Stephen P. Plassmeyer, Colin P. Florian, Michael J. Kasper, Rebecca Chase, Shayna Mueller, Yating Liu, Kelli McFarland White, Courtney F. Jungers, Slavica Pavlovic Djuranovic, Sergej Djuranović, Joseph D. Dougherty

The paper screens 5'UTR mutations in neurodevelopmental disorder genes to identify functional variants impacting translation and protein production, finding some mutations affect known syndromic autism genes in neurons.

medRxiv · Nov 2, 2023 · PreprintGenetic & Genomic Medicine