Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model.

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Title: Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model.
Authors: Holst F; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany., Bolger AM; IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany., Kindel F; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany.; IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany., Günther C; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany., Maß J; Institute of Quantitative and Theoretical Biology, Heinrich Heine University, Düsseldorf, Germany., Triesch S; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany., Kiel N; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany., Saadat N; Institute of Quantitative and Theoretical Biology, Heinrich Heine University, Düsseldorf, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany., Ebenhöh O; Institute of Quantitative and Theoretical Biology, Heinrich Heine University, Düsseldorf, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany., Usadel B; IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany.; Institute for Biological Data Science, Heinrich Heine University, Düsseldorf, Germany., Schwacke R; IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany., Weber APM; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany., Bolger ME; IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany. m.bolger@fz-juelich.de., Denton AK; Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany.; Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany.; Recursion, Valence Labs, Montreal, Quebec, Canada.
Source: Nature methods [Nat Methods] 2026 Apr; Vol. 23 (4), pp. 732-739. Date of Electronic Publication: 2025 Nov 24.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
Database: MEDLINE Ultimate
Description
ISSN:1548-7105
DOI:10.1038/s41592-025-02939-1