Jussi Taipale

This paper designs sequence-specific DNA binding proteins using deep learning, achieving a 100-fold improvement in success rates over previous methods.

The paper identifies reduced IFN-I pathway activity as a driver of chemo-refractory ovarian cancer using multi-omics analysis in a clinical trial cohort.

This study reveals how ELF2, a pioneer transcription factor, remodels nucleosomes near transcription start sites by unwrapping DNA and exposing chromatin, facilitating transcription initiation.

The paper shows how DNA motifs guide transcription factor cooperativity in embryonic face and limb mesenchyme, shaping cell identity and morphology.

The paper proposes a roadmap to solve the cis-regulatory code by training models on synthetic DNA sequences instead of genomic sequences to improve predictive accuracy.

The paper investigates how chromosome size affects transcriptional activity and finds that gene expression scales with the surface-area-to-volume ratio, suggesting active genes are located at chromosomal surfaces.

The paper identifies T1D risk genes and regulatory elements that influence beta cell survival under proinflammatory cytokine exposure using functional genomics and genetics.

The paper identifies DNA methylation patterns at TF binding sites across species, linking them to functional roles and evolutionary changes.

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.

The paper evaluates DNA repair protein-Cas9 fusions for improving CRISPR editing efficiency, finding that most require optimization for specific cell types and genomic loci.

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.

This study shows that combining oncogenes with lineage reprogramming can transform human cells into tumorigenic liver-like cells.

The paper investigates how transcription factors interact with nucleosomal DNA, finding that most have less access to it than free DNA and that nucleosome structure affects motif positioning and orientation.

Cas9-induced double-strand breaks trigger p53/p21/RB1-dependent G1 arrest in RPE-1 cells; transient p53 inhibition via MDM2 markedly raises homologous recombination precision editing efficiency.

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.