arXiv:2511. 09026v2 Announce Type: replace-cross Abstract: Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood.
By Pratik Dutta, Matthew Obusan, Rekha Sathian, Max Chao, Pallavi Surana, Nimisha Papineni, Yanrong Ji, Zhihan Zhou, Han Liu, Alisa Yurovsky, Ramana V Davuluri
arXiv:2607. 00931v1 Announce Type: new Abstract: Predicting cancer drug response from transcriptomic profiles is a cornerstone of precision oncology, yet the scientific value of machine learning models hinges not solely on predictive accuracy, but also on their capacity to generate reliable biological insights.
By Martino Ciaperoni, Margherita Lalli, Simone Piaggesi, Martina Varisco, Francesco Carli, Riccardo Guidotti, Dino Pedreschi, Francesco Raimondi, Fosca Giannotti
arXiv:2606. 14734v1 Announce Type: cross Abstract: Motivation: Gene regulatory network inference from single-cell RNA sequencing (scRNA-seq) data is important for uncovering cell-state-specific transcriptional programs.
By Ziyang Dong, Shanwen Tan, Hengchuang Yin, Wei Liu, Yifan Wang, Siyu Yi, Jiancheng Lv, Wei Ju
arXiv:2602. 04901v2 Announce Type: replace-cross Abstract: Predicting transcriptional responses to genetic perturbations is a central problem in functional genomics.
By Jiafa Ruan, Ruijie Quan, Liyang Xu, Zongxin Yang, Yi Yang
arXiv:2602. 17162v3 Announce Type: replace Abstract: Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature".
By Ariel Larey, Elay Dahan, Amit Bleiweiss, Raizy Kellerman, Guy Leib, Omri Nayshool, Dan Ofer, Tal Zinger, Dan Dominissini, Gideon Rechavi, Nicole Bussola, Simon Lee, Shane O'Connell, Dung Hoang, Marissa Wirth, Alexander W. Charney, Nati Daniel, Yoli Shavit
arXiv:2608. 14330v1 Announce Type: new Abstract: Spatial transcriptomics (ST) enables genome-wide gene expression profiling while preserving tissue architecture, but its cost and limited scalability remain major bottlenecks.
By Ruyter Swann, Dorent Reuben, Racoceanu Daniel