Teemu Kivioja

Sex-specific fish recombination landscapes link recombination and karyotype evolution

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.

Crossover model of Lep-Rec reveals higher heritability of recombination

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.

Sequence determinants of human gene regulatory elements

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.

Identifying critical transcriptional targets of the MYC oncogene using a novel competitive precision genome editing (CGE) assay

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: interpretation of pairwise dependencies and positional preferences learned by deep learning models from sequence data

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

Binding specificities of human RNA binding proteins towards structured and linear RNA sequences

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.

Strong binding activity of few transcription factors is a major determinant of open chromatin

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

CRISPR/Cas9 screening using unique molecular identifiers

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

Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion

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.