{"year":"2026","release_number":11,"doi":"10.1093/nar/gkaf1209","citation":"Baydar Ovek D, Rauluseviciute I, Aronsen DR, Blanc-Mathieu R, Bonthuis I, de Beukelaer H, Ferenc K, Jegou A, Kumar V, Lemma RB, Lucas J, Pochon M, Yun CM, Ramalingam V, Deshpande SS, Patel A, Marinov GK, Wang AT, Aguirre A, Castro-Mondragon JA, Baranasic D, Chèneby J, Gundersen S, Johansen M, Khan A, Kuijjer ML, Hovig E, Lenhard B, Sandelin A, Vandepoele K, Wasserman WW, Parcy F, Kundaje A, Mathelier A JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models Nucleic Acids Res. 2026 Jan 6;54(D1):D184-D193.","release_date":"2025-12-31","pubmed_id":"41325984","abstract":"JASPAR (https://jaspar.elixir.no/) is an open-access database that has provided high-quality, manually curated, and non-redundant DNA binding profiles for transcription factors (TFs) as position frequency matrices (PFMs) for over 20 years. We expanded the CORE (306 new profiles, 12% increase) and UNVALIDATED (433, 60% increase) collections with new PFMs and updated 13 existing profiles. We updated the TF binding site predictions and genome tracks for eight species. TF binding profile clusters and familial TF binding sites were updated accordingly. We integrate the inMOTIFin software into JASPAR to easily simulate regulatory sequences using JASPAR PFMs. To enrich TFs’ annotations, we provide scientific literature-based human TF target information. Notably, this release features a Deep Learning (DL) collection, providing a paradigm shift in modeling and characterizing TF-DNA interactions with 1,304 BPNet models trained on Homo sapiens ENCODE ChIP-seq datasets from 264 TFs and interpreted to reveal predictive binding profiles for the models. The profiles associated with the same TF were clustered to provide a non-redundant summary of the binding properties, resulting in 266 primary motifs in the DL collection. The JASPAR 2026 collections lay a foundation for future endeavors in genomic research, serving the scientific community in uncovering the mechanisms of gene regulation.","website":"https://jaspar.elixir.no","active":"Yes"}