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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ZIP Archive - 26.8 MB - MD5: 7477e293c76fe034016b59140acfced2
ZIP Archive - 27.2 MB - MD5: c206316d0f27116d3ddf87c1e16769a4
ZIP Archive - 37.8 MB - MD5: c42afd00c867156755c967c1a83fa283
ZIP Archive - 26.6 MB - MD5: f78edbcdc08b895baec520de5561965b
Plain Text - 4.6 KB - MD5: 31e1673d51f7645fdbae8a21d3a0388f
Sep 18, 2026
Here, we present the genome annotation of 11 Manihot esculenta (cassava) cultivars retrieved from the NCBI genome database. We predicted gene models using the homology-based annotation tool GeMoMa, using Jatropha curcas and Hevea brasiliensis, both close relatives of cassava within the Euphorbiaceae, as reference gene models. This annotation resour...
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.
Markdown Text - 6.4 KB - MD5: 97ce03291194df59dd8558a9b970b35a
Gzip Archive - 1.0 GB - MD5: ac504019e11f5d4e5133fbae25a97011
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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