Jens Keilwagen

Analysis of SpCas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis

The paper analyzes SpCas9 on- and off-target effects in Arabidopsis using high-efficiency multiplex editing and finds high specificity but potential for extensive on-target modifications at complex loci.

Improved reconstruction of transcripts and coding sequences from RNA-seq data

The paper introduces GeMoRNA, a transcript reconstruction method that improves coding sequence prediction in RNA-seq data across multiple species.

High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'

The paper presents a high-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii', revealing detailed gene content and structure.

The structure of the tetraploid sour cherry 'Schattenmorelle' (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature

The paper sequences and analyzes the genome of the sour cherry cultivar Schattenmorelle to reveal its segmental allopolyploid structure and evolutionary history.

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

The paper presents a high-quality chromosome-level genome assembly, DNA methylome, and cranial morphology analysis of an Alpine dingo, supporting its status as an archetype for evolutionary studies.

Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem.

The paper presents a desert dingo genome assembly and compares it to domestic dog genomes, identifying structural variants and physiological differences linked to ecological roles.

The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

The paper presents a chromosome-level genome assembly of tetraploid ground cherry using long-read sequencing technology and reports annotated genes and plastid sequences.

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

The paper presents a chromosome-scale rye genome assembly to study genomic evolution and agronomic traits in Triticeae crops.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

The paper presents two high-quality Basenji genome assemblies and compares structural variations across three dog breeds, highlighting the impact of reference genome choice on variant detection.

Learning from mistakes: Accurate prediction of cell type-specific transcription factor binding

The paper presents a method for predicting cell type-specific transcription factor binding sites using chromatin accessibility and binding motifs, achieving state-of-the-art performance through iterative training and ensemble prediction.

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

The paper extends the GeMoMa gene prediction tool to use RNA-seq data and conservation signals, showing improved performance over existing tools in plants, animals, and fungi.