Teemu Kivioja

This study presents the first collection of sex-specific recombination maps across 40 fish species, revealing links between recombination rates, karyotype, and sex-specific crossover positioning.

The paper introduces Lep-Rec, a software tool to compute local recombination rates and estimate tetrad crossover distributions, showing improved performance over existing tools and better heritability estimates of recombination.

The paper identifies sequence determinants of human gene regulatory elements by analyzing transcriptional activity of long DNA sequences in three cell types, revealing distinct enhancer types and TF subtypes based on motif content and activity patterns.

This study uses a novel competitive genome editing assay to identify MYC oncogene transcriptional targets by analyzing the effects of E-box mutations on cellular fitness.

PlotMI visualizes positional preferences and pairwise dependencies learned by sequence models, enabling comparison across models and datasets.

The paper identifies binding specificities of human RNA-binding proteins using HTR-SELEX, revealing that 70% bind linear sequences and 30% bind structured motifs, with novel roles for ZC3H12A/B/C in viral transcript degradation.

The paper introduces ATI, a method to measure TF DNA-binding activity, and finds that few TFs with strong binding activity determine open chromatin.

This paper introduces RSLs as UMIs to improve CRISPR/Cas9 screening reproducibility by enhancing precision and reducing required cells and sequencing reads.

The paper identifies CASP8AP2 as a cell-cycle regulator with differential effects on DNA replication in normal and tumor cells, leading to distinct outcomes in S-phase progression and cell survival.