The paper introduces Capiti, an edge-deployed system that detects pathogenic protein function during DNA synthesis by analyzing valve control signals, outperforming existing sequence-based screening tools.

bioRxiv · Oct 20, 2026 · PreprintBioinformatics

Global Evaluation of Congenital Heart Disease-Associated Non-Coding Variants

Edwin G. Peña-Martínez, Edwin Peña-Martínez, Shreya Sharma, Joshua Medina-Feliciano, Elise Root, Lois Parks, Marissa Granitto, Diego Pomales-Matos, Jean Messon- Bird, Adriana Barreiro-Rosario, Leandro Sanabria-Alberto, Alejandro Rivera-Madera, Jessica Rodríguez-Ríos, Rosalba Velázquez-Roig, Juan Figueroa- Rosado, , Devesh Bhimsaria

This study evaluates over 3,000 congenital heart disease-risk variants using SNP Bind-n-Seq and MPRA to identify variants with allelic TF binding and regulatory activity.

bioRxiv · Dec 10, 2025 · PreprintGenomics

Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays

John C. Butts, Stephen Rong, Sager J. Gosai, Rodrigo I. Castro, Mackenzie Noon, Kehinde Adeniran, Rohit Ghosh, Pardis Christine Sabeti, Ryan Tewhey, Steven K. Reilly

This study introduces MPAC, a machine learning model that predicts the cis-regulatory impact of non-coding variants, demonstrating its accuracy across diverse applications and datasets.

bioRxiv · Apr 16, 2025 · PreprintGenomics

A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development

Andrew J. Modzelewski, Wanqing Shao, Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy Tjokro, Gabriele Sales, Anne Biton, Aparna Anand, Terence Paul Speed, Zhenyu Xuan, Ting Wang, Davide Risso, Lin He

The paper identifies a species-specific retrotransposon promoter that generates a conserved Cdk2ap1 isoform essential for preimplantation development across mammals.

Cell · Oct 1, 2021Peer-reviewedDevelopmental Biology