P1-01 → けやき / P2-25 → ひめしゃら）
Application of Latent Dirichlet Allocation to imaging-based spatial transcriptomics data
Cross-modality Deep Learning Model for Surface Protein Prediction and Single-Cell Transcriptome Atlas Augmentation
Xenium-Based Spatial Transcriptomic Analysis and CNV Inference in Osteosarcoma
L-Trail: Estimating macroscopic transition directions in scRNA-seq data via outlier-robust L-moments
Recovering causal upstream sources from a single postmortem snRNA-seq snapshot: development of an SPD-manifold Hodge inverse-problem solver(AI collaboration)
Novel AI-powered computational method using tensor decomposition can discover the common optimal bin sizes when integrating multiple Hi-C datasets
Gene and cell line efficiency of CRISPR computed by tensor decomposition in genome-wide CRISPR-Cas9 knockout screens
Multi-Metric QC Scoring of Experimental Conditions in log2FC
MORE-RNAseq: improved references and pipelines for quantifying LINE1 expression based on RNA-seq
ST-CROCK: Spatially Informed Circadian Phase Inference from Spatial Transcriptomics
Multi-scale microenvironment covariance for unsupervised spatial domain identification
Predicting long-term productivity decline in CHO cells using RNA-seq profiles from early passages
Detection of rare T-cell clonotypes using TCR sequence similarity and gene-expression information
Development of a Xenium-Specific Multimodal Framework for Spatial Gene Expression Imputation
Gut Microbial and Metabolic Biomarkers for Early-Onset Colorectal Cancer
Hypothesis testing for inference of cell differentiation structures
Single-Cell Analysis of Age-Related Cell State Changes and Future Application to Geneformer
Drug Response Heterogeneity Analysis in Osteosarcoma using Xenium Spatial Transcriptomics
Graph Neural Networks Integrating Expression Signatures and Gene Knowledge for Perturbation Gene Prediction
SEgene: a super-enhancer analysis framework for prioritizing ERBB2-associated distal H3K27ac candidate loci in lung adenocarcinoma
CisAlign links cellular-state variation in single-cell transcriptomes to promoter-encoded regulatory programs
Pharmacokinetics-Integrated Multi-task ADMET Estimator
Novelty Assessment of Unknown Natural Products via MS/MS–Molecular Representation Alignment
Integrated Network Analysis of DEHP-Associated Alzheimer’s Disease
Deep learning-based single-cell metabolic flux inference
Mathematical modeling of drug response in EML4-ALK lung cancer
Context-specific ceRNA architecture of breast cancer stem cells resolved by single-cell transcriptomics
INGOR Desktop: Bringing Bayesian Network Analysis from Supercomputers to the Researcher’s Desktop
Network-level characterization of the tumor microenvironment in colorectal cancer
Development of an Information-Theoretic Method for Analyzing Enzymatic Reaction Networks
Leveraging binding-site flanking context with RNA language model embeddings for miRNA-mRNA target prediction
Functional Prediction of Microbial Rhodopsins Using a Protein Language Model
Discovery of antibodies with potential therapeutic applications aided by artificial intelligence
Expanding the software repertoire available to AI agents through large-scale automated containerization of bioinformatics software
Evaluating Genomic Language Model Multilinguality Across Nuclear and Organelle Genomes
Database construction for Randomized Controlled Trials on the Human Gut Microbiome
Automatic extraction of cell perturbation effects from biomedical abstracts using LLMs
CHCC-SRTDB: A curated catalogue of human cancer spatially resolved transcriptomics data across public databases
Development of the Cell-IO database integrating cellular-level functions and phenotypes with single-cell gene expression data
Systematic analysis of targets of FDA-approved drugs in 2025 using DISGENET: implications for rational target selection
Release of “Microbial Species Selection Tool” enabling search for microbial species based on phenotypic characteristics
Development of an LLM-based Large-scale Metadata Normalization Support System
CUTD：国際塩基配列データベースに基づくコドン使用頻度リソースの構築と遺伝学的応用の探索
Design and construction of an experimental strategy benchmark for evaluating the scientific decision-making capacity of AI agents
ZBioKit: an open-source bioinformatics toolkit designed for standalone and integrated use
Simple Baseline Superiority without Compound Information in Unseen Chemical Perturbation Prediction
Accelerating Multiple Sequence Alignment Using Quantum Computer
Development of a general-purpose enzyme discovery pipeline using machine learning
An algorithm for centromeric repeat marker selection from ultra-long reads using transitive consistency score
Fast Gapped Alignment Improves Remote DNA Homology Search
Computational Design of Common-Light-Chain CDR-L3 for Bispecific Antibodies
PATROL: Pareto-Aware Reinforcement Learning for Efficient Antibody CDR Optimization under Limited Oracle Calls
Comparative Evaluation of Boltz-2 Prediction Accuracy for Double-Stranded and Single-Stranded Nucleic Acid–Protein Complexes
Structure-based prediction of aptamer-associated proteins using a geometric graph neural network
AI-driven Discovery of Novel Extremotolerant Proteins of Tardigrades
Equivariant Local Refinement of Transmembrane Helix Packing using Geometric and Biochemical Context
Expanding conformational sampling in diffusion-based protein structure prediction models at inference time
Improving Extended RNA Secondary Structure Prediction Using an Expanded 3D Motif Database and Diverse Candidate Structures
Structural Analysis of CYP2C9 Polymorphisms Associated with Altered Drug Metabolism
De novo Design of Protein for Stable Artificial Bilayers
Estimation of CRISPR-Cas9 R-loop Hybridization Process Using Inverse Optimal Transport and Hidden Markov Models
Exploring Structural Factors Potentially Associated with Bioaccumulation Prediction Errors through Molecular Docking Analysis of CYP Enzymes
Deep Learning Design of Synthetic 5′UTRs for Programmable mRNA Translation
Design of α-amylase Targeting a Specific Optimum pH Using a Conditional Variational Autoencoder
AMP-Atlas: AI-Driven Discovery and Evolutionary Optimization of Medium-Sized Antimicrobial Peptides
Autonomous Genetic Circuit Design Platform
In silico protein design for efficient in vitro circular DNA replication
Evolutionary Perspectives on the Number of Digits in Tetrapods
Interdisciplinary data integration for investigating biological factors behind diversity of Buddha facial morphology
Genome Language Model-Based Cross-Species Enhancer Prediction for Cancer-Resistant and Long-Lived Animals
Testing the distance-dependent class imbalance hypothesis in sequence-based expression models
Nanopore-based DNA modification analysis across eukaryotic species
Transcriptomic Response and Gene Network Analysis of Developmental Neurotoxicants Using VPA-Responsive Genes as Indicators
A Deep Learning Model for Predicting CTCF Binding Occupancy at Single-Nucleotide Resolution
A Comprehensive Freshwater Microalgae Dataset for Deep Learning-based Classification with Transfer Learning Analysis
Weakly Supervised Single-cell Classification in Live-cell Co-cultures from image-level labels
A Human-in-the-Loop Approach for Cell Tracking in Live-Cell Microscopy
Development of a Transformer-Based Model for Predicting Medical Events
Population-Level Sleep Efficiency Prediction in the Tohoku Medical Megabank Fitbit Study
Comprehensive Disproportionality Analysis (DPA) for Drug Repurposing: An Agentic AI Workflow for Systematic Interpretation
HMM-based Dynamic Subphenotyping of Sepsis Using Longitudinal ICU Data
Predicting Aptamer–Protein Binding for Unseen Sequence Pairs
Immune-enhanced machine learning approach for early detection of precancerous colorectal neoplasia: Insights from biomarkers in routine health checkups
cfomics: a unified R workflow for comparing, selecting, and ensembling heterogeneous treatment effect estimators in omics data
Development and Explainable Risk Stratification of MAFLD Using Machine Learning Models Based on Community Health Check-up Data
Emergence of Novel Mycoplasma pneumoniae Macrolide-resistant Sequence type 3 subclades during Post-COVID-19 Resurgence
A Biologically Interpretable Feature Index Improves Machine Learning-based Classification of Neurodegenerative Diseases
A TAD-guided fragmentomics approach for identifying cancer-associated signals in cfDNA
Locus-level analysis of transposable element signals in neuronal WGS from schizophrenia cases using the T2T reference genome
Benchmarking Roche SBX Sequencing Technology across different variant calling pipelines
Gradient-based inference of cancer-associated DNA variants using sequence-to-expression models and expression-based classifiers
Analysis of the Number of Transmembrane Spans and Its Association with Disease-Related Mutations
AI-Driven Discovery of Novel Antimicrobial Peptides from Unexplored Marine Metagenomes
Development of an Analytical Framework for Microbiome Time-Series Data
Soil Microbiome Shifts Following Microbe-Immobilized Biochar Application: A Comparative Assessment Against Conventional Biochar
Global-Scale Microbiome Meta-Analysis Using LLM Empowered Knowledgebase Technology
Isoform Rhapsody: A Novel Long-Read Technology for Single-Cell Full-Length mRNA Profiling
Development of a drug repurposing workflow using Quartz-Seq2 for high-throughput bulk transcriptomics
Towards the Elucidation of the Molecular Basis of CHD8-Associated ASD Pathogenesis Through Single-Cell Long-Read RNA-seq
AI-assisted spatial omics reveals cold-to-hot immune remodeling in hepatocellular carcinoma
AI Laboratory Assistant Based on Experimental Data Integration: Automated qPCR Protocol Extraction and Experimental Condition Optimization
RepVote: Novel read assigner for repetitive arrays and elements
RHO GTPase by L1 GABAergic neurons in frontal cortex and L6 glutamatergic neurons in prefrontal cortex differentiates states of unconsciousness
Construction of Mamba-based Foundation Model for Mouse Single-cell Analysis
Investigation of methods for predicting cell-surface proteins from single-cell transcriptome data
Counterfactual Spatiotemporal Prediction of Spatial Transcriptomes via Optimal Transport and Conditional Flow Matching
Multicellular gene regulatory network inference by the resampling-based method RCPC
Comprehensive Analysis of Protein Function Changes Based on Alternative TSS Usage
Spatial Transcriptomic Identification of Immune–Stromal Niches Underlying Pre-Fibrotic Atrial Remodeling in Patients with Atrial Fibrillation
Transcription instructs phased chromatin remodelling across seasonal timescales
Prognostic Stratification of Cancer Patients Using Latent Representations Learned from RNA-seq Data by a Deep Survival Model
Detection of Unknown Cell Types and Corresponding Organ Identity in Organoid Spatial Transcriptomics via Human Cell Reference Mapping
Identification of Cancer-Associated Fibroblast Subtypes and Elucidation of Their Differentiation Mechanisms in Liver Cancer
mzTab-M as a HUPO-PSI Standard Format for Reporting of Small Molecule Mass Spectrometry Results: AI-ready Use Case in Japan
Identification and functional analysis of a mitochondria-related molecule at the interface between steatotic liver disease and drug-induced mitochondrial toxicity
Explainable Machine Learning Reveals Disease-associated Gut Microbiome Features and Cross-disease Associations
Metagenomic analysis reveals donor-associated antibiotic resistance gene dynamics after fecal microbiota transplantation
Efficient Fine-Tuning of SMILES Foundation Models: Dense LoRA Outperforms Full Fine-Tuning
Development of an AI platform for predicting functions of natural product biosynthetic enzymes
Uncovering Latent Disease Dynamics in SLE Through Phase-Space Analysis of Transcriptomic Representations
Unraveling metabolic reprogramming across human cardiomyopathies through cell-type-resolved metabolic flux inference
Improved quantification of protein–protein interaction aberrations with application‑based performance evaluation
Minimum Driver Orientation Methods for Control Analysis of Cell-Cell Interaction Networks
TF-Gene Regulatory Networks Dynamics During Early Neural Differentiation in Down Syndrome
Simultaneous quantification of transcription and RNA degradation activities in single-cell level
Information gain-based observation selection for reducing parameter uncertainty in nonlinear metabolic models
Simulation-based inference for switching stochastic differential equation-based models with applications to biological time-series data
Epigenomic and transcriptional networks during neural crest cell differentiation in a human induced pluripotent stem cell model
Color Annotation Compression Based on Monochromatigs in Colored de Bruijn Graphs
AI-gov: An AI Multi-Agent Simulation Platform for Pandemic Response
TipSorter: State-aware workspace reconfiguration via observation and planning for automated liquid handling robots
TogoTV with Today’s Life science Researchers
ViroScape: a Multimodal Database Integrating Viral Genomes, Epidemiological Information, and Host Response Profiles
Improvement of metadata quality in the BioSample database using large language models
Comparative evaluation of ontology mapping methods for tissue names in life science database metadata
MicroGlycoDB and MicroGlycoCurator: Toward a Comprehensive and Scalable Platform for Microbial Glycan Data
RDF Conversion and Reconstruction of the C. elegans GlycoGene DataBase
The Development of a Web-Based Data Submission System for the Proteoglycan Atlas
Development of a haplotype classification tool using the Joint Open Genome and Omics Platform (JoGo)
PathFetch: Pipeline for Automated Extraction of Metabolic Pathway Information from Literatures
Corpus Development and Systematic Model Evaluation for Cell-Cell Relation Extraction
GEMS: a Mealy machine abstraction for adaptive laboratory automation
Joint simulation of robot motion and cell distribution for robotic cell seeding
AI-based TCR-pMHC binding prediction for interpreting T-cell responses in autoimmune diseases
RNA Representation Learning via Knowledge Graph Integration
Predicting transcription direction using genome language models and validating sequence conservation across mammals
RNA Sequence Design Using a Pseudoknot-Aware Sampling-Based Differentiable Folding Model
Artificial peptide nanopore design by directed evolution using structure prediction
Development of a global refinement method for RNA 3D structures
Computational Design of β-Hairpin Peptide Nanopores toward Reduced Structural Heterogeneity
Neuronal ArhGAP21 function and pathological effects of a intellectual disability-associated mutation in the GAP domain
Prediction of Binding Molecules from Protein Structures Using a Graph of Residue-Sized Probe Spheres and Amino Acid Residues
Chemically Constrained Diffusion-Based Prediction of Cyclic Peptide–Protein Complex Structures
Refinement of AI-Predicted RNA Structures Using a Distance Geometry Transformer
Enhancing Ligand Pose Prediction Accuracy with Confidence Metrics and Target-Specific Fine-Tuning
Quantum-Chemical and Conformation-Aware Foundation Model for Middle-Molecule Drug Discovery
Solvent-Dependent Conformational Sampling of Cyclic Peptides Toward Membrane Permeability Prediction
De Novo Design of EGFR Tyrosine Kinase Inhibitors Using Deep Reinforcement Learning
Machine Learning-Guided Engineering of FqzB for Enhanced Production of Spirotryprostatin A
Protein language model-based binary AutoEncoder for enabling Quantum Computing-driven protein design
Distribution-Constrained Optimization for Reliable ML-Guided 5'UTR Sequence Design
General-purpose protein property prediction by multimodal integration of pLMs and LLMs
Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA
Establishment of transposon subfamily classification methods
Evolutionary Patterns of DNA Base Substitutions Across Eukaryotes
Evolutionary Neofunctionalization of Praja1 and Its Impact on Tau Proteostasis Network Rewiring
Toward Controllable mRNA Design through Functional and Sequence Constraints
ChIP-Atlas 2025 Update: 10-year anniversary of a data-mining platform for exploring epigenomic landscape
Spatially Resolved Enhancer Activity in Breast Cancer Reveals Subtype Specific Spatial Niches of Gene Regulation
Development of a Bayesian RNA Velocity Model for Comprehensive Characterization of Qualitative and Quantitative Changes in Transcription Factor Activity
Pathway redistribution across cellular states reveals a shared signaling backbone and context-dependent regulatory modules in RNA-binding protein networks
A Web-Accessible Database of Sialidase Activity Images
Quantitative cell imaging analysis for modeling cellular senescence
Development of a Point-Cloud-Based Erythrocyte Information Integration Framework for Biological State Characterization
がん組織の生物学的年齢に基づく患者の予後予測
Analysis of Confirmed and Suspected SFTS Cases Based on the Vectorization of Unstructured Electronic Health Record Text
Extracting 3D Spatial Features from ECG Temporal Data toward Screening of Structural Heart Disease
External validation and target-label adaptation of ICU delirium prediction models across eICU and MIMIC-IV
Antibody Language Model-Based Construction of Antigen-Specific Reference Sequence Databases for QASAS-Based Immune State Estimation from BCR Repertoires
AI-Guided Precision Combination Therapy from Tumor Transcriptomes
Integrated Serum Metabolomic Profiling and Machine Learning for Liquid Biopsy-Based Pancreatic Cancer Diagnosis
Multimodal Analysis of Disease Risk Structure Using Genomic and Lifestyle Data
Discovery of genes related to atopic dermatitis and psoriasis
Plant pathogenicity prediction model using genetic diversity data
Comprehensive analysis of Japanese-specific multiple-nucleotide variants and their potential regulatory effects
Coalescent Distortion Index: A simple statistic for evaluating the relative level of heterozygosity in diploid individuals with respect to a reference genome
Evidence-guided ranking of candidate variants by integrating genomic language model embeddings and MAVE functional scores: a PTEN case study
Screening Candidate Amino Acid Variant Pairs for Pathogenicity Reassessment Using ClinVar
Comprehensive Mutational Analysis of Cell Surface and Mitochondria in Cancer Metastasis
Incorporating rich biological features in phage-host infection prediction models
PlanDyO: A long-read metagenomic platform for elucidating adaptive mechanisms in coastal marine ecosystems
GeoAI-Enabled Environmental Annotation of Metagenomic Data for Microbial Ecology
Metagenomic Latent Space Mapping for Environmental Source Tracking