Itoshi Nikaido

GenPerturb: sequence-grounded interpretation of perturbation transcriptomes using pretrained genomic models

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

Cycling persister clones with elevated NR2F1-mediated cholesterol biosynthesis cause chemotherapy resistance

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

Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure

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: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data

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.

Elucidation of the mechanism of byproduct DNA synthesis in whole-transcript amplification by poly-A tagging and development of its specific suppression

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

Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation

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 detects many-to-many cell-cell interactions from single cell RNA-sequencing data

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

Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of thalamus

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.

A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads

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.

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

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.

Local states of chromatin compaction at transcription start sites control transcription levels

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.

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

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

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

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

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

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

A NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data

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.

Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

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

Uncovering hypergraphs of cell-cell interaction from single cell RNA-sequencing data

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: an ultrafast and scalable cell search method for single-cell RNA-sequencing

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

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

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.

An efficient gene regulatory network inference algorithm for early Drosophila melanogaster embryogenesis

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: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

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