We address biological questions by combining molecular biology and computational methods. Our focus is on the genetic basis of plant specialized metabolism and the evolution of biosynthetic capabilities. To elucidate biosynthetic networks, we combine data from our own sequencing with public datasets. Bioinformatics tools are developed to answer specific questions through the analysis of large datasets, often employing methods of artificial intelligence. We investigate the regulation of biosynthetic networks through transcriptomics. Phylogenetic analyses assist in selecting candidate genes for specific molecular functions. Identified genes and biosynthetic pathways serve as a basis for experiments using synthetic biology methods. The results from the various approaches culminate in biotechnological applications.
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Sep 16, 2026
Nowak, Melina Sophie; Harder, Benjamin; Meckoni, Samuel Nestor; Friedhoff, Ronja; Wolff, Katharina; Pucker, Boas, 2025, "Genome sequence and annotation of Victoria cruziana", https://doi.org/10.60507/FK2/5DS0JZ, bonndata, V2
The genome of a Victoria cruziana plant was sequenced with nanopore long reads. The genome sequence was assembled with Verkko2, scaffolding was conducted with CPhasing and the gene models were predicted by BRAKER3 and GeMoMa. The functional annotation was predicted based on sequence similarity to well characterized Arabidopsis thaliana sequences.
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Aug 29, 2026
Natarajan, Shakunthala; Sterling, Claudia; Choudhary, Nancy; Khatun, Najnin; Brieske, Mia-Sophie; Busch, Hannah Elisa; Pucker, Boas, 2026, "PanXpresso - comprehensive collection of gene expression data across domains of life", https://doi.org/10.60507/FK2/OBIGQH, bonndata, V1
This is a comprehensive collection of gene expression count tables in transcripts per million (TPMs) encompassing species from five domains of life - plants, fungi, animals, bacteria and archaea. This data publication is referenced and discussed in detail in the manuscript - “XpBrew and PanXpresso - automatic RNA-seq processing workflow and compreh...
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