PETAL
PETAL is an end-to-end machine learning platform for predictive modeling of regulatory DNA sequences. It combines model prediction, interpretation and sequence evolution workflows in a web-accessible format.
Computational biology · Gene regulation · Plant genomics
Sebastian Triesch
I work where plant genomics and machine learning meet experimental discovery.
- Institute of Synthetic Biology
- Heinrich Heine University Düsseldorf
- CEPLAS
- Germany
About
I am a computational biologist and quantitative geneticist interested in how genomes encode biological function. My work combines plant genomics, biostatistics, regulatory sequence analysis and machine learning to connect genetic variation with gene regulation and complex traits.
I am a biochemist by training and began my scientific career in experimental biology. During my PhD, I moved from the bench into computational genomics, generating and analyzing multi-omics, epigenomic and single-cell datasets for non-model plant systems.
In my current postdoctoral work, I use machine learning as one quantitative tool to model regulatory DNA, interpret genetic variation and understand how plant genomes shape complex traits.
Software
SEPAL
SEPAL is a low-cost, modular plant environment monitoring system built on a Raspberry Pi. It provides a user-friendly interface for monitoring environmental parameters such as temperature, humidity and light in plant growth chambers or greenhouses.
Helixer
Helixer is a deep learning-based gene annotation tool for eukaryotic genomes. It combines deep neural networks with a hidden Markov model to predict primary gene models from genomic DNA sequences.
I contributed to Helixer as a co-author involved in the biological validation and interpretation of the model.
Predmoter
Predmoter is a deep learning-based tool for predicting plant promoter and enhancer regions across species.
I contributed to Predmoter as a co-author involved in project conceptualization, data analysis and interpretation of the model.
Publications
- , Reichel-Deland, V., Valderrama Martín, J.M., Melzer, M., Schlüter, U., Weber, A.P.M. Single-nuclei sequencing of Moricandia arvensis reveals bundle-sheath cell function in the photorespiratory shuttle of C3–C4 intermediate Brassicaceae.
- Dickinson, P.J., , Schlüter, U., Weber, A.P.M., Hibberd, J.M. A transcription factor module mediating C2 photosynthesis in the Brassicaceae.
- Holst, F., Bolger, A., Günther, C., Maß, J., , Kindel, F., Kiel, N., Saadat, N., Ebenhöh, O., Usadel, B., Schwacke, R., Bolger, M., Weber, A.P.M., Denton, A.K. Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model.
- , Denton, A.K., Bouvier, J.W., Buchmann, J.P., Reichel-Deland, V., Guerreiro, R.N.F.M., Busch, N., Schlüter, U., Stich, B., Kelly, S., Weber, A.P.M. Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species.
- Kindel, F., , Schlüter, U., Randarevitch, L.A., Reichel-Deland, V., Weber, A.P.M., Denton, A.K. Predmoter: cross-species prediction of plant promoter and enhancer regions.
- Germann, A.T., Nakielski, A., Dietsch, M., Petzel, T., Moser, D., , Westhoff, P., Axmann, I.M. A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803.
- Segura Broncano, L., Pukacz, K.R., Reichel-Deland, V., Schlüter, U., , Weber, A.P.M. Photorespiration is the solution, not the problem.
- Guerreiro, R., Bonthala, V.S., Schlüter, U., Hoang, N.V., , Schranz, M.E., Weber, A.P.M., Stich, B. A genomic panel for studying C3–C4 intermediate photosynthesis in the Brassiceae tribe.