FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. - Huanying Ge; Kejun Liu; Todd Juan; Fang Fang; Matthew Newman; Wolfgang Hoeck (Bioinform., 2011)

OSA: a fast and accurate alignment tool for RNA-Seq. - Jun Hu; Huanying Ge; Matthew Newman; Kejun Liu (Bioinform., 2012)

RNA-Seq Analysis Pipeline Based on Oshell Environment. - Jing Li; Jun Hu; Matthew Newman; Kejun Liu; Huanying Ge (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Using Deep Learning to Identify Initial Error Sensitivity of ENSO Forecasts. - Kinya Toride; Matthew Newman; Andrew Hoell; Antonietta Capotondi; Jakob Schlör; Dillon Amaya (CoRR, 2024)

A Hybrid Deep-Learning Model for El Niño Southern Oscillation in the Low-Data Regime. - Jakob Schlör; Matthew Newman; Jannik Thümmel; Antonietta Capotondi; Bedartha Goswami (CoRR, 2024)

FRAME BY FRAME: The Development and Integration of a Community Stop-motion Animation Area at Mount Holyoke College. - Matthew Newman (SIGUCCS, 2025)

AI-Informed Model Analogs for Subseasonal-to-Seasonal Prediction. - Jacob B. Landsberg; Elizabeth A. Barnes; Matthew Newman (CoRR, 2025)