Martijs J. Jonker

The paper identifies pervasive short hairpin RNA structures in non-encapsidated viruses and shows their association with structural constraints and evolutionary origins.

This study shows that overexpression of the Rob regulator in Yersinia enterocolitica accelerates antibiotic resistance development, but is costly without antibiotic selection.

The paper identifies a novel seaweed virus with extreme GC3 codon bias and pseudoambigrammatic characteristics, suggesting a new RNA virus survival strategy.

This study shows that co-culturing Candida albicans and Staphylococcus aureus increases secretion of virulence factors from both species, with C. albicans Als1p/Als3p playing a key role in this effect.

This study shows that ampC gene amplification drives beta-lactam resistance in E. coli, with resistance gene location affecting amplification targets but not the mechanism.

The paper investigates collateral sensitivity and cross-resistance networks in six bacterial species after induced resistance to six antibiotics, finding specific patterns and genetic mechanisms.

This study investigates de novo antibiotic resistance acquisition in six bacterial species, finding diverse mutational patterns leading to similar resistance outcomes.

This study tracks ampC amplification and promoter mutations during de novo amoxicillin resistance development in E. coli, showing amplification occurs after promoter mutations and is facilitated by IS1 transposition.

The paper identifies new and variant Potyviruses in Asparagales plants from a Dutch urban botanic garden using smallRNA-seq and RNA-seq.

The paper identifies a new Polerovirus species in Asparagaceae plants through RNA-seq and smallRNA-seq, distinguishing it from known viruses by its P0 protein sequence.

This study discovers a new Phenuivirus species in Lachenalia plants and identifies co-evolutionary patterns in RNA sequence motifs.

The paper describes the discovery of a new Betaflexivirus species in Ferraria crispa plants through smallRNA-seq and RNA-seq analysis.

The paper identifies four new viruses in seaweed species through small RNA sequencing, highlighting previously unrecognized viral diversity in seaweeds.

This study determines the genome sequences of three KoMV variants from Zantedeschia cultivars and identifies nucleotide and protein differences compared to the RefSeq sequence.

The paper identifies regulatory factors and mechanisms governing transcriptome dynamics in early zebrafish embryogenesis through computational and small-RNA sequencing analyses.

The paper identifies maternal- and somatic-type snoRNA expression patterns in zebrafish, showing differential regulation through transcription and RNA processing.

The paper identifies embryogenesis-specific spliceosome variants in zebrafish using snRNA gene analysis and PCR-sequencing, revealing distinct snRNA variants with sequence differences in loop structures.