We are pleased to announce that Dr. Julien Gagneur will be the guest speaker of our upcoming Sven Furberg Webinar in Bioinformatics and Statistical Genomics on Thursday May 4th at 14:30 on Zoom (see details below and at https://www.mn.uio.no/sbi/english/furberg-seminars/dr.-julien-gagneur.html).
Dr. Julien Gagneur, Professor in Computational Molecular Medicine at the Technical University of Munich, Germany, will present his research on "Detecting and predicting aberrant splicing in human and Species-aware DNA language modeling."
Abstract
The first part of my talk covers a series of studies concerned with the detection aberrant splicing from RNA-seq data [1-2] and their predictions from genomics sequence [3-4]. This work has translational relevance for pinpointing the genetic cause of individuals affected with a genetically undiagnosed rare disorders [5]. The algorithms developed could also help for interpreting mutations found in tumours.
In the second part of my talk, I will present recent results using language models to identify conserved genomic sequences in an alignment-free fashion [6]. We train a masked language model on 3’ regions of ORFs across more than 800 fungal species spanning over 500 million years of evolution. We show that explicitly modeling species is instrumental in capturing conserved yet evolving regulatory elements. We demonstrate the utility of the resulting sequence embedding for range of regulatory genomics prediction tasks.
References: 1. Mertes, Scheller, et al. Detection of aberrant splicing events in RNA-Seq data with FRASER. Nature Communications, 2021; 2. Scheller et al. Improved detection of aberrant splicing using the Intron Jaccard Index. medRxiv 2023; 3. Cheng, et al., MMSplice: Modular modeling improves the predictions of genetic variant effects on splicing, Genome Biology. 2019; 4. Celik, Wagner, et al. Aberrant splicing prediction across human tissues. bioRxiv, 2022 (now in press Nat genet.); 5. Yépez, Gusic, et al. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Medicine, 2022; 6. Gankin, Karollus, et al. Species-aware DNA language modeling. bioRxiv 2023
Looking forward to seeing you all at the webinar.
Zoom info:
Join Zoom Meeting at https://uio.zoom.us/j/65895596084?pwd=b29ubjQ2VEtCNE1vM0NPRkluMGFKdz09.
Meeting ID: 658 9559 6084; Passcode: 505310
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Anthony Mathelier, PhD
Associate Director - Centre for Molecular Medicine Norway (NCMM)
Group Leader - Computational Biology & Gene Regulation Group, NCMM
Adjunct Professor - Centre for Bioinformatics, University of Oslo
Adjunct Researcher - Dept. of Medical Genetics, Oslo University Hospital
http://mathelierlab.com
anthony.mathelier@ncmm.uio.no
(+47) 22840561
