A5022750265- Pancreatic and Hepatic Oncology Research
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- RNA and protein synthesis mechanisms
- Pancreatic function and diabetes
- RNA Research and Splicing
- Organ Transplantation Techniques and Outcomes
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Brain Tumor Detection and Classification
- Radiomics and Machine Learning in Medical Imaging
- Genomics and Phylogenetic Studies
- Biochemical and Molecular Research
- Cancer-related Molecular Pathways
- Cancer-related gene regulation
- Amino Acid Enzymes and Metabolism
- Chromosomal and Genetic Variations
- interferon and immune responses
- Gene Regulatory Network Analysis
- Neuroendocrine Tumor Research Advances
- BRCA gene mutations in cancer
- AI in cancer detection
Kyoto University
2022-2025
Cold Spring Harbor Laboratory
2020-2023
Kobe Children's Hospital
2022
National Institute of Advanced Industrial Science and Technology
2015-2021
The University of Tokyo
2015-2019
University of Cincinnati Medical Center
2019
We present a new pair-wise genome alignment method, based on simple concept of finding an optimal set local alignments. It gains accuracy by not masking repeats, and using statistical model to quantify the (un)ambiguity each part. Compared previous animal alignments, it aligns thousands locations differently with much higher similarity, strongly suggesting that alignments are non-orthologous. The methods suffer from overly-strong assumption long un-rearranged blocks. should help find...
Abstract Pancreatic ductal adenocarcinoma (PDAC) is the most lethal common malignancy, with little improvement in patient outcomes over past decades. Recently, subtypes of pancreatic cancer different prognoses have been elaborated; however, inability to model these has precluded mechanistic investigation their origins. Here, we present a xenotransplantation PDAC which neoplasms originate from patient-derived organoids injected directly into murine ducts. Our enables distinction two main...
Machine learning models for automated magnetic resonance image segmentation may be useful in aiding glioma detection. However, the differences among facilities cause performance degradation and impede This study proposes a method to solve this issue. We used data from Multimodal Brain Tumor Image Segmentation Benchmark (BraTS) Japanese cohort (JC) datasets. Three tumor are developed. In our methodology, BraTS JC trained on datasets, respectively, whereas fine-tuning developed model...
Genetic and environmental variation are key contributors during organism development, but the influence of minor perturbations or noise is difficult to assess. This study focuses on stochastic in allele-specific expression that persists through cell divisions nine-banded armadillo (Dasypus novemcinctus). We investigated blood transcriptome five wild monozygotic quadruplets over time explore developmental stochasticity gene expression. identify an enduring signal autosomal allelic variability...
External signals from the thymic microenvironment and activities of lineage-specific transcription factors (TFs) instruct T-cell versus innate lymphoid cell (ILC) fates. However, mechanistic insights into how such as Notch1–Delta-like-4 (Dll4) signaling E-protein TFs collaborate to establish identity remain rudimentary. Using multiple in vivo approaches single-cell multiome analysis, we identified a feedback amplifier circuit that specifies fetal adult In early T progenitors (ETPs) thymus,...
Enhancer RNAs (eRNAs) are transcribed by RNA polymerase II during enhancer activation but typically rapidly degraded in the nucleus. During states of reduced surveillance, however, eRNAs and other similar "noncoding" RNAs, including for example upstream antisense stabilized, some exported to cytoplasm can even be found on polysomes. Here, we report unexpectedly that ∼12% human intergenic contain long open reading frames (>300 nts), many which actively translated, as determined ribosome...
Abstract Background RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing serious experimental and computational limitations, such as low read coverage numerical problems. Results Our novel software, “ParasoR” , designed run on a computer cluster enables exact computation various features long under...
Radiogenomics use non-invasively obtained imaging data, such as magnetic resonance (MRI), to predict critical biomarkers of patients. Developing an accurate machine learning (ML) technique for MRI requires data from hundreds patients, which cannot be gathered any single local hospital. Hence, a model universally applicable multiple cohorts/hospitals is required. We applied various ML and image pre-processing procedures on glioma dataset The Cancer Image Archive (TCIA, n = 159). models that...
Replication of the genome must be coordinated with gene transcription and cellular metabolism, especially following replication stress in presence limiting deoxyribonucleotides. The Saccharomyces cerevisiae Rad53 (CHEK2 mammals) checkpoint kinase plays a major role responses to DNA stress. Cell cycle regulated, genome-wide binding chromatin was examined. Under stress, bound sites active initiation fork progression, but unexpectedly promoters about 20% genes encoding proteins involved...
The influenza A virus genome is segmented into eight viral RNAs (vRNA). Secondary structures of vRNA are known to be involved in the proliferation process. Comprehensive vitro, virio, and cellulo have been analyzed. However, resolution structure map can improved by comparative analysis statistical modeling. Construction a more high-resolution reliable RNA identify uncharacterized functional motifs on virion. Here, we establish global secondary virion using combination dimethyl sulfate...
Recently, next-generation sequencing techniques have been applied for the detection of RNA secondary structures, which is referred to as high-throughput structural (HTS) analyses, and many different protocols used detect comprehensive structures at single-nucleotide resolution. However, existing computational analyses heavily depend on experimental methodology generate data, results in difficulties associated with statistically sound comparisons or combining obtained using HTS methods.Here,...
RAS is the founding member of a superfamily GTPases and regulates signaling pathways involved in cellular growth control. While recent studies have shown that activation state can be controlled by lysine ubiquitylation acetylation, existence methylation remains unexplored. In contrast to does not alter side chain charge it has been challenging deduce its impact on protein structure conventional amino acid substitutions. Herein, we investigate RAS-related GTPases. We developed GoMADScan (Go...
Abstract Motivation RNA-binding proteins (RBPs) play a crucial role in the post-transcriptional regulation of RNA. Given their importance, analyzing specific RNA patterns recognized by RBPs has become significant research focus bioinformatics. Deep Neural Networks have enhanced accuracy prediction for RBP-binding sites, yet understanding structural basis specificity from these models is challenging due to limited interpretability. To address this, we developed RNAelem, which combines profile...
The influenza A virus genome consists of eight RNA segments, each incorporated into a virion. It has been proposed that intersegment interactions bundle these and viral inclusions, which contain ribonucleoproteins (vRNPs) Rab11, facilitate this process. However, the locations mechanisms interaction formation remain unclear. To investigate this, we identified comprehensive in infected cells using customized LIGR-seq. Our results revealed overlapped with those virion were partially formed...
Abstract The influenza A virus genome is segmented into eight viral RNAs (vRNA). Secondary structures on vRNA are thought to be involved in the proliferation process, such as intersegment interactions that necessary for segment bundling. However, functional RNA structure not well known because secondary of virion was partially unwound by binding non-specific proteins a sequence-independent manner. Here, we establish global map using combination dimethyl sulfate (DMS)-seq and selective...
Abstract Replication of the genome must be coordinated with gene transcription and cellular metabolism, especially following replication stress in presence limiting deoxyribonucleotides. The S. cerevisiae Rad53 (CHEK2 mammals) checkpoint kinase plays a major role responses to DNA stress. Cell cycle regulated, genome-wide binding chromatin was examined. Under stress, bound sites active initiation fork progression, but unexpectedly promoters about 20% genes encoding proteins involved multiple...
Abstract Motivation Single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) is a valuable resource to learn cis-regulatory elements such as cell-type specific enhancers and transcription factor binding sites. However, identification of scATAC-seq data known be challenging due the heterogeneity derived from different protocols high dropout rate. Results In this study, we perform systematic comparison 7 datasets mouse brain benchmark efficacy neuronal annotation...