Itoshi Nikaido

GenPerturb links Perturb-seq expression changes to cis-regulatory elements and transcription factor motifs without needing chromatin data.

The paper identifies cycling persisters (CPs) in cancer organoids and shows that elevated NR2F1-mediated cholesterol biosynthesis contributes to chemotherapy resistance.

The paper investigates retinal spheroid layer formation by analyzing Rax::GFP-positive retinal progenitor cells, revealing sequential WNT signaling and environmental factors in retinal development.

MitoDelta detects mitochondrial DNA deletions at cell-type resolution using single-cell RNA sequencing data, revealing distinct deletion burdens across neuronal subtypes in Parkinson's disease.

This paper elucidates the mechanism of byproduct DNA synthesis in poly-A tagging and develops SupTag to suppress it, improving transcriptomic analysis accuracy.

This study uses single-cell RNA sequencing to analyze WNT signaling's role in granulosa cell-oocyte interactions during primordial follicle activation, revealing transcriptomic changes and their impact on fertility.

scTensor identifies many-to-many cell-cell interactions from single-cell RNA-seq data by detecting triadic relationships not captured by conventional methods.

This study identifies four cell types in the mouse PVT using single-cell RNA sequencing and shows their transcriptomic continuity along the anterior-posterior axis, with distinct axon projection patterns and functional responses to neuropeptides.

This paper introduces a centrifugation-based method for high-throughput separation of supernatant from magnetic microbeads, offering a faster, cheaper, and more efficient alternative to manual pipetting and robotic systems.

The paper investigates NF-κB super-enhancers in B cells, finding they enhance transcriptional variability and gene expression through cis-regulatory interactions and NF-κB binding sites.

The paper identifies local chromatin compaction states at transcription start sites (TSSs) as determinants of transcription levels by correlating weak compaction with RNA polymerase binding.

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

Millefy visualizes cell-to-cell heterogeneity in read coverage of scRNA-seq data using heat maps and dynamic reordering to highlight genomic variations.

This study benchmarks PCA implementations for large-scale scRNA-seq, finding variations in speed, memory efficiency, and accuracy across algorithms and providing selection guidelines.

The paper introduces an NMF-based method to identify overlooked differentially expressed gene regions in single-cell RNA-seq data, finding novel transcripts related to neural stem/progenitor cell differentiation.

This study investigates transcriptional bursting kinetics in mESCs using scRNA-seq and identifies regulatory factors and pathways influencing gene expression noise.

scTensor stacks ligand-receptor coexpression across cell-type pairs into a tensor and applies non-negative Tucker decomposition, recovering many-to-many cell-cell interactions that a label-permutation test missed in simulation.

CellFishing.jl efficiently searches large scRNA-seq datasets to find similar cells and identify notable genes with high accuracy and speed.

Quartz-Seq2 improves single-cell RNA-seq by increasing UMI conversion efficiency and gene detection from limited reads using in vitro and in vivo samples.

The paper develops an efficient algorithm to infer gene regulatory networks in Drosophila melanogaster embryogenesis, identifying key regulatory interactions and demonstrating its computational efficiency.

SCODE infers gene regulatory networks from single-cell RNA-Seq data during differentiation, showing improved performance and efficiency compared to existing methods.