[ { "pmid": "42771501", "doi": "10.1073/pnas.2611533123", "title": "System-level synchronization and subtype-specific modules govern brain-wide serotonin axon innervation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "published": "2026-Sep-29", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42771501/" }, { "pmid": "42771508", "doi": "10.1073/pnas.2534052123", "title": "Kinetics-seq enables comprehensive profiling of single-cell RNA kinetics in vivo to reveal dynamic tumor heterogeneity.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "published": "2026-Sep-29", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42771508/" }, { "pmid": "42805588", "doi": "10.1016/j.jfp.2026.100933", "title": "Methods to Address Compositional Data Challenges in Clinical Studies for the Safety Assessment of Human Microbiome Perturbations.", "journal": "Journal of food protection", "published": "2026-Sep-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42805588/" }, { "pmid": "42468771", "doi": "10.1016/j.neuroscience.2026.07.027", "title": "Air-Liquid interface midbrain organoids model the pathological features of Parkinson's disease.", "journal": "Neuroscience", "published": "2026-Sep-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42468771/" }, { "pmid": "42565645", "doi": "10.1002/anie.1256471", "title": "Tenfold Expansion Submicrometer MALDI Mass Spectrometry Imaging of Tissues and Cultured Cells.", "journal": "Angewandte Chemie (International ed. in English)", "published": "2026-Sep-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42565645/" }, { "pmid": "42615282", "doi": "10.1002/anie.2990236", "title": "Single-Cell Imaging of Site-Specific RNA-Protein Interactions.", "journal": "Angewandte Chemie (International ed. in English)", "published": "2026-Sep-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42615282/" }, { "pmid": "42803564", "doi": "10.1128/aem.01020-26", "title": "Prospective metagenomic sequencing of wastewater across the United States yields robust viral enrichment and concordance with digital PCR measurements.", "journal": "Applied and environmental microbiology", "published": "2026-Sep-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42803564/" }, { "pmid": "42804522", "doi": "10.1371/journal.pcbi.1014835", "title": "Spatial cell-cell communication inference based on cell-spot-ligand-receptor heterogeneous graphs.", "journal": "PLoS computational biology", "published": "2026-Sep-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42804522/" }, { "pmid": "42802232", "doi": "10.1007/s00011-026-02379-3", "title": "Machine learning-driven M2 macrophage signature for precision prediction of survival and therapy response in acute myeloid leukemia.", "journal": "Inflammation research : official journal of the European Histamine Research Society ... [et al.]", "published": "2026-Sep-27", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42802232/" }, { "pmid": "42802286", "doi": "10.1007/s00011-026-02378-4", "title": "PP4 deficiency drives airway epithelial senescence via the PERK-eIF2α-ATF4-p21 axis in severe asthma.", "journal": "Inflammation research : official journal of the European Histamine Research Society ... [et al.]", "published": "2026-Sep-27", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42802286/" }, { "pmid": "42801568", "doi": "10.1002/advs.77591", "title": "Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "published": "2026-Sep-27", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42801568/" }, { "pmid": "42791187", "doi": "10.1523/ENEURO.0209-26.2026", "title": "Single-Cell and Bulk RNA-Seq Profiling Identifies Cell Adhesion-Related Gene Signatures in Cerebral Ischemia-Reperfusion Injury.", "journal": "eNeuro", "published": "2026-Sep-25", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42791187/" }, { "pmid": "42773672", "doi": "10.13345/j.cjb.260126", "title": "[Stability and viability optimization for filamentous microorganisms in droplet-based microfluidic screening].", "journal": "Sheng wu gong cheng xue bao = Chinese journal of biotechnology", "published": "2026-Sep-25", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42773672/" }, { "pmid": "42788664", "doi": "10.1093/bioinformatics/btag676", "title": "MultiSpaceNet: Graph-based Joint Representation Learning for Paired Spatial Transcriptome-Proteome Data.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Sep-25", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42788664/" }, { "pmid": "42789676", "doi": "10.1371/journal.pcbi.1014801", "title": "Topologically-based parameter inference for agent-based model selection from spatiotemporal cellular data.", "journal": "PLoS computational biology", "published": "2026-Sep-25", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42789676/" }, { "pmid": "42789681", "doi": "10.1371/journal.pcbi.1014779", "title": "Integrating zero-inflation correction and transcriptional kinetics for single-cell transcriptomic analysis.", "journal": "PLoS computational biology", "published": "2026-Sep-25", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42789681/" }, { "pmid": "42781809", "doi": "10.1177/15578666261489802", "title": "Xoublet: An Extreme-Scale Doublet Detection Algorithm for Cardiac Single-Cell Transcriptomics.", "journal": "Journal of computational biology : a journal of computational molecular cell biology", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42781809/" }, { "pmid": "42782096", "doi": "10.1113/JP288988", "title": "Resolution and automated analysis of single-cell Ca2+ waves within living myocardial tissue slices.", "journal": "The Journal of physiology", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42782096/" }, { "pmid": "42782157", "doi": "10.1128/spectrum.01165-26", "title": "A comparative study of mNGS and tNGS for pathogen detection in paired upper and lower respiratory tract specimens from pediatric pneumonia patients.", "journal": "Microbiology spectrum", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42782157/" }, { "pmid": "42782481", "doi": "10.1007/s10067-026-08436-w", "title": "A mitoxyperiosis-associated gene signature correlates with immune disturbance and provides a potential diagnostic biomarker for systemic lupus erythematosus.", "journal": "Clinical rheumatology", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42782481/" }, { "pmid": "42785586", "doi": "10.1016/j.slasd.2026.100341", "title": "Probing and Painting to Get the Full Picture of Macrophage Polarisation.", "journal": "SLAS discovery : advancing life sciences R & D", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42785586/" }, { "pmid": "42785646", "doi": "10.1016/j.ejps.2026.107676", "title": "A Multiscale Quantitative Systems Pharmacology Platform for Early Screening of MMAE-Based Antibody-Drug Conjugates.", "journal": "European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42785646/" }, { "pmid": "42777131", "doi": "10.1097/CMR.0000000000001141", "title": "Transcriptomic immune subtyping and connectivity mapping nominate DNA methyltransferase inhibitors for immunedepleted melanoma.", "journal": "Melanoma research", "published": "2026-Sep-24", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42777131/" }, { "pmid": "42778526", "doi": "10.1038/s41378-026-01369-z", "title": "Unraveling the dielectric heterogeneity response of cell lines under electroporation: a microfluidic single-cell on-chip system.", "journal": "Microsystems & nanoengineering", "published": "2026-Sep-23", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42778526/" }, { "pmid": "42778538", "doi": "10.1038/s41467-026-75681-7", "title": "Fast, flexible analysis of differences in cellular composition with crumblr.", "journal": "Nature communications", "published": "2026-Sep-23", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42778538/" }, { "pmid": "42778763", "doi": "10.1038/s41591-025-04128-1", "title": "AI-based characterization of Alzheimer's disease phenotypes from population-scale single-cell data.", "journal": "Nature medicine", "published": "2026-Sep-23", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42778763/" }, { "pmid": "42777140", "doi": "10.1021/acssensors.6c02048", "title": "Single-Bacterium Biosensing: A Rapid Electrochemical Strategy to Differentiate Antibacterial Efficacy and Mechanism.", "journal": "ACS sensors", "published": "2026-Sep-23", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42777140/" }, { "pmid": "42777494", "doi": "10.1016/j.forsciint.2026.113146", "title": "Transcriptome-based postmortem interval prediction in the human dorsolateral prefrontal cortex using covariate-aware machine learning.", "journal": "Forensic science international", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42777494/" }, { "pmid": "42779099", "doi": "10.1093/nar/gkag899", "title": "CRYSPER and CUREIPES: two new molecular tools enabling analysis of RNA splicing and C-to-U RNA editing-inducible protein expression at single cell resolution.", "journal": "Nucleic acids research", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42779099/" }, { "pmid": "42772264", "doi": "10.4269/ajtmh.26-0088", "title": "Investigation of Dinga Dinga: A Cluster of Bilateral Lower-Extremity Tremors-Bundibugyo District, Uganda, 2023-2024.", "journal": "The American journal of tropical medicine and hygiene", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42772264/" }, { "pmid": "42772449", "doi": "10.1016/j.kint.2026.07.034", "title": "Large-scale organoid-derived cyst cultures as a drug discovery platform for polycystic kidney disease.", "journal": "Kidney international", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42772449/" }, { "pmid": "42776880", "doi": "10.1109/JBHI.2026.3709624", "title": "Graph Masked Autoencoder With Multi-Head Latent Attention Mechanism for Gene Regulatory Link Prediction.", "journal": "IEEE journal of biomedical and health informatics", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42776880/" }, { "pmid": "42743276", "doi": "10.1073/pnas.2527033123", "title": "Uncovering heterogeneous effects via localized feature selection.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42743276/" }, { "pmid": "42743287", "doi": "10.1073/pnas.2608168123", "title": "Detection and sequencing of Ap2N-capped RNAs in human cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "published": "2026-Sep-22", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42743287/" }, { "pmid": "42794841", "doi": "10.3390/ijms27188416", "title": "Senescent Cell Heterogeneity: Tissue-Dependent Signatures and Age Dynamics Revealed by Human scRNA-Seq Data.", "journal": "International journal of molecular sciences", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42794841/" }, { "pmid": "42777373", "doi": "10.1016/j.psj.2026.107821", "title": "Multi-omics integration and artificial intelligence for the conservation and utilization of local chicken genetic resources.", "journal": "Poultry science", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42777373/" }, { "pmid": "42508407", "doi": "10.1016/j.crmeth.2026.101539", "title": "Trajectory-informed gene feature selection in single-cell analysis with SEEK-VFI.", "journal": "Cell reports methods", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42508407/" }, { "pmid": "42767096", "doi": "10.1016/j.tranon.2026.103029", "title": "Multi-omics integration identifies prognostic genes linked to adaptive immunity response and radiosensitivity in cervical cancer.", "journal": "Translational oncology", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42767096/" }, { "pmid": "42767978", "doi": "10.1002/jat.70442", "title": "Sequential Chlorantraniliprole-Bacillus thuringiensis Application Enhances Transcriptomic Reprogramming and Disrupts Detoxification Pathways in Spodoptera frugiperda (Noctuidae: Lepidoptera).", "journal": "Journal of applied toxicology : JAT", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42767978/" }, { "pmid": "42768210", "doi": "10.1038/s41596-026-01416-z", "title": "Trace-n-Seq combines retrograde fluorescent tracing with sorting and single-cell sequencing of innervating peripheral neurons.", "journal": "Nature protocols", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42768210/" }, { "pmid": "42768211", "doi": "10.1038/s41596-026-01427-w", "title": "Tissue expansion mass spectrometry imaging (TEMI) for high-spatial-resolution multiomics molecular mapping.", "journal": "Nature protocols", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42768211/" }, { "pmid": "42768301", "doi": "10.1002/path.70122", "title": "A scalable workflow for sensitive detection and genomic profiling of tumour cells in lymph nodes from FFPE tissue.", "journal": "The Journal of pathology", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42768301/" }, { "pmid": "42764344", "doi": "10.1038/s41378-026-01420-z", "title": "Code-multiplexed multi-frequency impedance cytometry with a unified deep-unfolding network.", "journal": "Microsystems & nanoengineering", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42764344/" }, { "pmid": "42765999", "doi": "10.1021/acssensors.6c01159", "title": "Apollo-IRE1: A Genetically Encoded Sensor for Live Cell and Multiplexed Imaging of Endoplasmic Reticulum Stress.", "journal": "ACS sensors", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42765999/" }, { "pmid": "42766664", "doi": "10.1371/journal.pcbi.1014788", "title": "Mapping a differentiation architecture for hard tissue mineralization with large-scale single-cell atlases.", "journal": "PLoS computational biology", "published": "2026-Sep-21", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42766664/" }, { "pmid": "42795018", "doi": "10.3390/cancers18183050", "title": "STEAP2 Is a Candidate Marker of a 7q/CNA-Associated Iron-Handling Malignant Epithelial State in Lung Adenocarcinoma.", "journal": "Cancers", "published": "2026-Sep-20", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42795018/" }, { "pmid": "42779705", "doi": "10.64898/2026.09.14.751514", "title": "SMORE: joint dimension reduction and cell population discovery on single-cell methylome data.", "journal": "bioRxiv : the preprint server for biology", "published": "2026-Sep-20", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42779705/" }, { "pmid": "42779813", "doi": "10.64898/2026.09.18.752796", "title": "A lifespan single-cell atlas of the human developing hippocampus benchmarks familial Alzheimer's disease brain organoids.", "journal": "bioRxiv : the preprint server for biology", "published": "2026-Sep-20", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42779813/" }, { "pmid": "42781333", "doi": "10.21769/BioProtoc.5821", "title": "Proximity Labeling in Caenorhabditis elegans to Detect Neuronal Proteins During Memory Formation.", "journal": "Bio-protocol", "published": "2026-Sep-20", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42781333/" }, { "pmid": "42764118", "doi": "10.1016/j.jinsphys.2026.105067", "title": "Omics approaches in insect diapause research.", "journal": "Journal of insect physiology", "published": "2026-Sep-20", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42764118/" }, { "pmid": "42764522", "doi": "10.1177/15303667261486623", "title": "Single-Cell Transcriptomic Profiling and Machine Learning Reveal Stage-Specific Gene Dynamics in Brucellosis.", "journal": "Vector borne and zoonotic diseases (Larchmont, N.Y.)", "published": "2026-Sep-20", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42764522/" }, { "pmid": "42779625", "doi": "10.64898/2026.09.12.751186", "title": "Spatially resolved multimodal hallmarks of response to neoadjuvant immunotherapies in the melanoma ecosystem in 2D and 3D.", "journal": "bioRxiv : the preprint server for biology", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42779625/" }, { "pmid": "42779810", "doi": "10.64898/2026.09.16.752238", "title": "In vivo intercellular CRISPR screens using viral proximity barcoding reveal regulators of tumor-immune interactions.", "journal": "bioRxiv : the preprint server for biology", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42779810/" }, { "pmid": "42780042", "doi": "10.64898/2026.09.16.752194", "title": "Joint inference of paired dynamical gene regulatory networks reveals distinct cell-state landscapes of neutrophil reprogramming.", "journal": "bioRxiv : the preprint server for biology", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42780042/" }, { "pmid": "42762141", "doi": "10.3791/71673", "title": "Isolation of Brain Microglia to Study Persistence of Human Immunodeficiency Virus-1.", "journal": "Journal of visualized experiments : JoVE", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42762141/" }, { "pmid": "42763279", "doi": "10.1016/j.jmii.2026.09.004", "title": "Rapid and accurate diagnosis of bloodstream infections: A multiplex real-time PCR assay with selective microbial enrichment for direct whole-blood detection and positive blood culture confirmation.", "journal": "Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42763279/" }, { "pmid": "42759521", "doi": "10.1016/j.crmeth.2026.101604", "title": "Revealing therapeutic single-cell transcriptomic signatures using a simple classifier.", "journal": "Cell reports methods", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42759521/" }, { "pmid": "42760285", "doi": "10.1038/s41467-026-77360-z", "title": "ConvexGating infers gating strategies from clusters in single cell cytometry data.", "journal": "Nature communications", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42760285/" }, { "pmid": "42699773", "doi": "10.1016/j.isci.2026.117314", "title": "Community: Component based differential cell communication analysis in large multi-sample case-control scRNAseq datasets.", "journal": "iScience", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42699773/" }, { "pmid": "42755294", "doi": "10.1093/nar/gkag909", "title": "iPscDB: a comprehensive platform for plant single-cell transcriptomic data integration and analysis.", "journal": "Nucleic acids research", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42755294/" }, { "pmid": "42758797", "doi": "10.1126/sciimmunol.aeg5223", "title": "In vitro induction of human germinal center B cells.", "journal": "Science immunology", "published": "2026-Sep-18", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42758797/" }, { "pmid": "42780032", "doi": "10.64898/2026.09.15.751821", "title": "Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia.", "journal": "bioRxiv : the preprint server for biology", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42780032/" }, { "pmid": "42462710", "doi": "10.1016/j.cell.2026.06.027", "title": "Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues.", "journal": "Cell", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42462710/" }, { "pmid": "42752543", "doi": "10.1093/bioinformatics/btag671", "title": "CoSAG-nf: A Scalable Nextflow Pipeline for Co-assembly, Optimization, and Interactive Visualization of High-Throughput Single-Cell Genomes.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42752543/" }, { "pmid": "42754122", "doi": "10.1016/j.biortech.2026.135849", "title": "Novel insight into diversity of active tetracycline-resistant bacteria and genes in sludge by in situ microcapsule-entrapped cultivation.", "journal": "Bioresource technology", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42754122/" }, { "pmid": "42755034", "doi": "10.1002/advs.77756", "title": "A Real-Data-Driven Framework for Evaluating Differential Transcript Usage Methods Across Long-Read Bulk, Single-Cell, and Spatial Transcriptomics.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42755034/" }, { "pmid": "42520338", "doi": "10.1016/j.bbrc.2026.154303", "title": "Key genes identified in ammonia-induced cell death during pediatric sepsis: Machine learning, single-cell, and virtual gene knockout approaches.", "journal": "Biochemical and biophysical research communications", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42520338/" }, { "pmid": "42752934", "doi": "10.1007/s00011-026-02370-y", "title": "STAT1: a central hub linking ferroptosis and inflammation in hepatic ischemia-reperfusion injury.", "journal": "Inflammation research : official journal of the European Histamine Research Society ... [et al.]", "published": "2026-Sep-17", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42752934/" }, { "pmid": "42527318", "doi": "10.1261/rna.080852.125", "title": "A systematic evaluation of the sources of nonuniform coverage in RNA-seq and limitations of current practices.", "journal": "RNA (New York, N.Y.)", "published": "2026-Sep-16", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42527318/" }, { "pmid": "42749802", "doi": "10.1038/s41586-026-11055-9", "title": "Identification of broadly tumour-reactive γδ TCRs from multiple myeloma.", "journal": "Nature", "published": "2026-Sep-16", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42749802/" }, { "pmid": "42598968", "doi": "10.1039/d6an00700g", "title": "A dual-mode nano-microelectrode for PTH detection at the single-cell level.", "journal": "The Analyst", "published": "2026-Sep-16", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42598968/" }, { "pmid": "42745609", "doi": "10.1039/d6cc01207h", "title": "Synthesis of Pt-Pd bimetallic nanorods and nanoparticles supported on single-walled carbon nanotubes via a solvothermal approach.", "journal": "Chemical communications (Cambridge, England)", "published": "2026-Sep-16", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42745609/" }, { "pmid": "42746902", "doi": "10.1039/d6tb01298a", "title": "Intracellular gelation technology: frontier exploration in biomaterials and biomedical applications.", "journal": "Journal of materials chemistry. B", "published": "2026-Sep-16", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42746902/" }, { "pmid": "42762696", "doi": "10.1016/j.compbiolchem.2026.109370", "title": "Benchmarking reference-based cellular deconvolution algorithms to predict cell proportions.", "journal": "Computational biology and chemistry", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42762696/" }, { "pmid": "41981916", "doi": "10.1016/j.bpj.2026.04.010", "title": "TopClust: Topological-based analysis of scRNA-seq data for data-driven identification of clusters and core cluster cells.", "journal": "Biophysical journal", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41981916/" }, { "pmid": "42744928", "doi": "10.1038/s41596-026-01432-z", "title": "Quantitative imaging of dynamic processes in intestinal organoids.", "journal": "Nature protocols", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42744928/" }, { "pmid": "42745263", "doi": "10.1186/s40164-026-00825-w", "title": "Multimodal AI and single-cell transcriptomics integrate to construct a histopathological prognostic model for bladder cancer, revealing the RTN3-glycolysis axis in chemoresistance.", "journal": "Experimental hematology & oncology", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42745263/" }, { "pmid": "42747099", "doi": "10.3791/72246", "title": "Integrated Visualization of Neutrophil Recruitment and Inflammatory Cytokine Profiling in Bronchoalveolar Lavage Fluid.", "journal": "Journal of visualized experiments : JoVE", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42747099/" }, { "pmid": "41887362", "doi": "10.1016/j.jmb.2026.169766", "title": "Paean: A Unified and Efficient Transcriptome Quantification System Using Heterogeneous Computing.", "journal": "Journal of molecular biology", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41887362/" }, { "pmid": "41997213", "doi": "10.1016/j.jmb.2026.169810", "title": "ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.", "journal": "Journal of molecular biology", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41997213/" }, { "pmid": "41999938", "doi": "10.1016/j.jmb.2026.169815", "title": "Deeptosis: A Deep Learning-Based Platform for Label-Free Discrimination of Apoptosis and Pyroptosis from Brightfield Microscopy.", "journal": "Journal of molecular biology", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41999938/" }, { "pmid": "42013531", "doi": "10.1016/j.jcis.2026.140538", "title": "A surface enhanced Raman scattering nanotag library based on cucurbit[7]uril controlled nanoparticle aggregates for fast cell imaging.", "journal": "Journal of colloid and interface science", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42013531/" }, { "pmid": "42127674", "doi": "10.1016/j.bios.2026.118757", "title": "Fast fourteen-frequency impedance spectroscopy of single erythrocytes and yeast cells in flow.", "journal": "Biosensors & bioelectronics", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42127674/" }, { "pmid": "42476392", "doi": "10.1016/j.envres.2026.125284", "title": "Function-driven analytical strategies for identifying contaminants of emerging concern-degrading bacteria: From enrichment cultures to single-cell technologies.", "journal": "Environmental research", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42476392/" }, { "pmid": "42740657", "doi": "10.1093/plcell/koag282", "title": "Unlocking the Full Potential of Spatial Omics in Plants: Practical Challenges, Solutions, and a Path Forward.", "journal": "The Plant cell", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42740657/" }, { "pmid": "42741932", "doi": "10.1177/15578666261477771", "title": "Unique Molecular Identifiers Don't Need to be Unique: A Collision-Aware Estimator for RNA-Seq Quantification.", "journal": "Journal of computational biology : a journal of computational molecular cell biology", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42741932/" }, { "pmid": "42742076", "doi": "10.1002/anie.1708018", "title": "BrIS: Visualizing Internal Standards at the MS1 Level via Bromine Fingerprint for Sensitive and Robust Proteomics Quality Control.", "journal": "Angewandte Chemie (International ed. in English)", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42742076/" }, { "pmid": "42742387", "doi": "10.1093/neuonc/noag209", "title": "The Spatiotemporal Evolution of Radiation Resistance in Glioblastoma.", "journal": "Neuro-oncology", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42742387/" }, { "pmid": "42743026", "doi": "10.1109/TPAMI.2026.3733393", "title": "Domain Elastic Transform: Bayesian Function Registration for High-Dimensional Scientific Data.", "journal": "IEEE transactions on pattern analysis and machine intelligence", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42743026/" }, { "pmid": "42709819", "doi": "10.1073/pnas.2619143123", "title": "Cell-type-specific circadian and light-responsive transcriptional dynamics in adult Drosophila neurons.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "published": "2026-Sep-15", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42709819/" }, { "pmid": "42756771", "doi": "10.1039/d6eb00156d", "title": "Revalidating KCrPDTA for aqueous redox flow batteries.", "journal": "EES batteries", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42756771/" }, { "pmid": "42735479", "doi": "10.1016/j.ecoenv.2026.120794", "title": "Machine learning-based identification of core regulatory targets in 1-nitropyrene-induced placental trophoblast dysfunction and FGR.", "journal": "Ecotoxicology and environmental safety", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42735479/" }, { "pmid": "42735562", "doi": "10.1016/j.tranon.2026.102987", "title": "An immune related cell death index for prognostic stratification and immunotherapy response prediction in oral cancer.", "journal": "Translational oncology", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42735562/" }, { "pmid": "42735857", "doi": "10.1016/j.biortech.2026.135851", "title": "Elucidating how calcium inhibits anammox systems and a novel recovery strategy using cation exchange resin: Performance and mechanisms.", "journal": "Bioresource technology", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42735857/" }, { "pmid": "42736018", "doi": "10.1101/gr.282250.126", "title": "k-mer-based Upstream Preprocessing of long reads for Isoform Discovery.", "journal": "Genome research", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42736018/" }, { "pmid": "42736370", "doi": "10.1038/s44320-026-00241-6", "title": "Cell cycle-dependent protein dynamics in budding yeast resolved by deconvolution of bulk proteomics.", "journal": "Molecular systems biology", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42736370/" }, { "pmid": "42740305", "doi": "10.1111/pce.70888", "title": "ScLRR Identified From BSR-seq Inhibits Sugarcane Yellow Leaf Virus Accumulation by Interacting With Its Coat Protein in the Nucleus.", "journal": "Plant, cell & environment", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42740305/" }, { "pmid": "42561109", "doi": "10.1021/acsbiomaterials.6c00717", "title": "Steady Cone-Jet Mode of Electrospray for Single-Cell Deposition.", "journal": "ACS biomaterials science & engineering", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42561109/" }, { "pmid": "42734361", "doi": "10.1128/msystems.00897-26", "title": "Library strategies differentially shape microbial, functional, and host signals in clinical metagenomic sequencing.", "journal": "mSystems", "published": "2026-Sep-14", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42734361/" }, { "pmid": "42730546", "doi": "10.1177/15578666261485334", "title": "Using Mapping-Profiles to Refine Strain-Level Metagenomic Classification.", "journal": "Journal of computational biology : a journal of computational molecular cell biology", "published": "2026-Sep-12", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42730546/" }, { "pmid": "42731626", "doi": "10.1016/j.cmi.2026.09.010", "title": "Detection of antibiotic heteroresistance in clinical microbiology: current and emerging methodologies.", "journal": "Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases", "published": "2026-Sep-12", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42731626/" }, { "pmid": "42731980", "doi": "10.1080/08869634.2026.2733451", "title": "Associations between brain phenotypes and temporomandibular disorders: An integrative multi-omics investigation.", "journal": "Cranio : the journal of craniomandibular practice", "published": "2026-Sep-12", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42731980/" }, { "pmid": "42746303", "doi": "10.1016/j.patter.2026.101612", "title": "OscillomeR infers ultradian oscillations and targets of the Hes family.", "journal": "Patterns (New York, N.Y.)", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42746303/" }, { "pmid": "42746519", "doi": "10.1016/j.patter.2026.101589", "title": "Disentangling covariate effects on single-cell-resolved epigenomes with DeepDive.", "journal": "Patterns (New York, N.Y.)", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42746519/" }, { "pmid": "42730668", "doi": "10.3791/73225", "title": "Genetic Deletion of Cis-Regulatory Elements to Dissect the Function of the Non-coding Genome in human Preimplantation Models.", "journal": "Journal of visualized experiments : JoVE", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42730668/" }, { "pmid": "42727577", "doi": "10.1016/j.ajhg.2026.08.018", "title": "Distinct cochlear cell types associated with genetic susceptibility to sensory and metabolic hearing loss in older adults.", "journal": "American journal of human genetics", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42727577/" }, { "pmid": "42727749", "doi": "10.1016/j.biosystems.2026.105937", "title": "Disagreement-Informed Arbitration for Gene Regulatory Network Inference: A Score-Level Meta-Classifier and a Diagnostic Typology of Inter-Method Conflict.", "journal": "Bio Systems", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42727749/" }, { "pmid": "42728314", "doi": "10.1038/s44385-026-00111-8", "title": "Evaluating and comparing the signalling and functional landscape of hiPSC-CMs derived from patients with dilated cardiomyopathy.", "journal": "npj biomedical innovations", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42728314/" }, { "pmid": "42725652", "doi": "10.1093/genetics/iyag228", "title": "Estimating cis and trans contributions to differences in gene regulation.", "journal": "Genetics", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42725652/" }, { "pmid": "42725726", "doi": "10.1128/mra.00612-26", "title": "VISTA: a classifier for metagenomic subspecies and community state typing of the vaginal microbiome.", "journal": "Microbiology resource announcements", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42725726/" }, { "pmid": "42726433", "doi": "10.1007/s13679-026-00759-8", "title": "Obesity-Related Tendon Pathology: Cardiometabolic Mechanisms, Clinical Implications, and Management.", "journal": "Current obesity reports", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42726433/" }, { "pmid": "42726615", "doi": "10.1109/JBHI.2026.3733404", "title": "Multiview Transformer-Based Hierarchical Fusion Model for Cell Type Identification.", "journal": "IEEE journal of biomedical and health informatics", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42726615/" }, { "pmid": "42715312", "doi": "10.1126/sciadv.aed3414", "title": "A systematic comparison of single-cell perturbation response prediction models.", "journal": "Science advances", "published": "2026-Sep-11", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42715312/" }, { "pmid": "42733658", "doi": "10.1016/j.omta.2026.201836", "title": "Single-cell vector copy number analysis of phenotypically defined long-term hematopoietic stem cells for gene therapy safety assessment.", "journal": "Molecular therapy. Advances", "published": "2026-Sep-10", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42733658/" }, { "pmid": "42584226", "doi": "10.1039/d6nr01349j", "title": "Photonic fingerprint barcodes mediated by microsphere WGM lasing.", "journal": "Nanoscale", "published": "2026-Sep-10", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42584226/" }, { "pmid": "42720181", "doi": "10.1002/cyto.a.70066", "title": "Velociraptor Machine Learning Quantifies Similarity to Known Cell Types and Matches Cells Across Flow and Imaging Cytometry Platforms.", "journal": "Cytometry. Part A : the journal of the International Society for Analytical Cytology", "published": "2026-Sep-10", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42720181/" }, { "pmid": "42720611", "doi": "10.1093/bioinformatics/btag675", "title": "Partaker: deep-learning-based single-cell-resolution analysis of multi-dimensional, long-term, microfluidic-based time-lapse microscopy data.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Sep-10", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42720611/" }, { "pmid": "42721176", "doi": "10.1109/TCBBIO.2026.3731227", "title": "DMGRN: Enhancing Diffusion Models for Gene Regulatory Network Inference.", "journal": "IEEE transactions on computational biology and bioinformatics", "published": "2026-Sep-10", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42721176/" }, { "pmid": "42722723", "doi": "10.1038/s41417-026-01080-1", "title": "Clinical translation of senescence-related pan-cancer multi-omics: tools for assessment and immunotherapy prediction.", "journal": "Cancer gene therapy", "published": "2026-Sep-10", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42722723/" }, { "pmid": "42729941", "doi": "10.1021/acsmaterialsau.5c00231", "title": "DNA/RNA Hybrid Hairpin Gold Nanobeacons Targeting miR-31 Reprogram Invasion in Lung Cancer and Remodel Tumor Histo-Architecture In Vivo.", "journal": "ACS materials Au", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42729941/" }, { "pmid": "42716018", "doi": "10.1016/j.crmeth.2026.101580", "title": "Causal assessment of Bayesian gene regulatory networks from single-cell transcriptomics.", "journal": "Cell reports methods", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42716018/" }, { "pmid": "42717051", "doi": "10.1038/s41589-026-02322-x", "title": "Plasma membrane order maps functional diversity in immune cells.", "journal": "Nature chemical biology", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42717051/" }, { "pmid": "42711459", "doi": "10.1007/s00438-026-02516-x", "title": "Circular RNAs orchestrate integrated post-transcriptional responses to combined heat and drought stress in rice.", "journal": "Molecular genetics and genomics : MGG", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42711459/" }, { "pmid": "42714077", "doi": "10.1093/brain/awag303", "title": "Multimodal discovery of a pathogenic B cell-dependent T cell state in multiple sclerosis.", "journal": "Brain : a journal of neurology", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42714077/" }, { "pmid": "42714164", "doi": "10.1128/jvi.00630-26", "title": "MADCAP: isolation of novel nAb-naïve AAV capsids from metagenomic data.", "journal": "Journal of virology", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42714164/" }, { "pmid": "42714221", "doi": "10.1242/dev.205715", "title": "A Protoplast-based method to visualize early cell biological events in plant cellular reprogramming and regeneration.", "journal": "Development (Cambridge, England)", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42714221/" }, { "pmid": "42714244", "doi": "10.1093/jaoacint/qsag085", "title": "STRATUM-Structured Framework for Reporting, Assessment, and Translational Utility of Metagenomics.", "journal": "Journal of AOAC International", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42714244/" }, { "pmid": "42715043", "doi": "10.1021/acs.nanolett.6c02449", "title": "Spatiotemporal Sequential Fluorescence and Electrochemistry Bimodal Quantitation of Enzyme Activity in a Living Cell.", "journal": "Nano letters", "published": "2026-Sep-09", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42715043/" }, { "pmid": "42721651", "doi": "10.1016/j.legalmed.2026.102991", "title": "Development of a novel universal primer set with high sensitivity and specificity for detection of diatom.", "journal": "Legal medicine (Tokyo, Japan)", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42721651/" }, { "pmid": "42624101", "doi": "10.1016/j.stemcr.2026.103053", "title": "Development and validation of a long-term co-maturation protocol for human stem cell-derived microglia and neuronal networks.", "journal": "Stem cell reports", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42624101/" }, { "pmid": "42714000", "doi": "10.3791/72156", "title": "LINC01871-Mediated Sensitivity to Cyclin-Dependent Kinase 4/6 Inhibitors in Human Breast Cancer.", "journal": "Journal of visualized experiments : JoVE", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42714000/" }, { "pmid": "42708591", "doi": "10.1128/spectrum.02027-26", "title": "Divergent avian strains drive an off-season influenza A peak in municipal wastewater.", "journal": "Microbiology spectrum", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42708591/" }, { "pmid": "42708762", "doi": "10.1021/acs.analchem.6c02686", "title": "An Instrumental Optimization of a Label-Free Proteomic Method for Trace Protein Input.", "journal": "Analytical chemistry", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42708762/" }, { "pmid": "42709526", "doi": "10.1109/TCBBIO.2026.3731145", "title": "scCGC2T: Curriculum-Guided Contrastive Co-Training Framework for scRNA-Seq Data Clustering.", "journal": "IEEE transactions on computational biology and bioinformatics", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42709526/" }, { "pmid": "42709908", "doi": "10.1371/journal.pcbi.1014728", "title": "Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.", "journal": "PLoS computational biology", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42709908/" }, { "pmid": "42673453", "doi": "10.1073/pnas.2531151123", "title": "Single-cell profiling of mitochondrial phenotyping-coupled mtDNA genotyping.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "published": "2026-Sep-08", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42673453/" }, { "pmid": "42705211", "doi": "10.1016/j.tranon.2026.103028", "title": "Integrated single-cell and bulk transcriptomic analysis reveals an epithelial cell-derived prognostic and immunotherapeutic signature with ADAM12 as a key functional regulator in non-small cell lung cancer.", "journal": "Translational oncology", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42705211/" }, { "pmid": "42705234", "doi": "10.1016/j.crmeth.2026.101593", "title": "ON-Time enables rapid microbiome sequencing and analysis for precision medicine.", "journal": "Cell reports methods", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42705234/" }, { "pmid": "42706481", "doi": "10.1007/s11626-026-01240-5", "title": "Site-specific gene integration by recombinase-mediated cassette exchange in anhydrobiotic Pv11 cells.", "journal": "In vitro cellular & developmental biology. Animal", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42706481/" }, { "pmid": "42704489", "doi": "10.1007/s10142-026-02040-6", "title": "NFS1 activates PI3K/AKT/mTOR signaling to upregulate GPX4 expression and enhance ferroptosis resistance in osteosarcoma.", "journal": "Functional & integrative genomics", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42704489/" }, { "pmid": "42704667", "doi": "10.1093/bioinformatics/btag662", "title": "DECANT: Decoupling mechanism from context in single-cell drug perturbation representation.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42704667/" }, { "pmid": "42704692", "doi": "10.1093/reprod/xaag114", "title": "Automated Sperm Tracking Using Deep Learning for High-Resolution Analysis of Motility.", "journal": "Reproduction (Cambridge, England)", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42704692/" }, { "pmid": "42704804", "doi": "10.1109/TCBBIO.2026.3731206", "title": "Graph-Attentional Deep Sparse Subspace Clustering for Single-Cell Transcriptomics.", "journal": "IEEE transactions on computational biology and bioinformatics", "published": "2026-Sep-07", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42704804/" }, { "pmid": "42727380", "doi": "10.1016/j.placenta.2026.09.001", "title": "Single-cell transcriptomics on FFPE placenta: A novel method for comprehensive exploration of an entire placental section.", "journal": "Placenta", "published": "2026-Sep-05", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42727380/" }, { "pmid": "42715797", "doi": "10.1016/j.jphotobiol.2026.113561", "title": "When light colour matters: Spectral quality is associated with distinct small RNA candidates in Arabidopsis thaliana.", "journal": "Journal of photochemistry and photobiology. B, Biology", "published": "2026-Sep-05", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42715797/" }, { "pmid": "42725359", "doi": "10.21769/BioProtoc.5813", "title": "Determining the Age of Every Cell Within Each Budding Yeast Microcolony Combining Single-Cell Microencapsulation With Confocal Microscopy.", "journal": "Bio-protocol", "published": "2026-Sep-05", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42725359/" }, { "pmid": "42700855", "doi": "10.1016/j.envres.2026.125593", "title": "Cable Bacteria Accelerate Nitrogen Removal in Freshwater Sediments by Mitigating Diffusion Limitation via Long-Distance Electron Transport.", "journal": "Environmental research", "published": "2026-Sep-05", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42700855/" }, { "pmid": "42696959", "doi": "10.1016/j.tranon.2026.103018", "title": "A chemoresistance-associated proliferation gene signature identified by single-cell and machine learning analysis predicts prognosis in high-grade serous ovarian carcinoma.", "journal": "Translational oncology", "published": "2026-Sep-04", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42696959/" }, { "pmid": "42697413", "doi": "10.1016/j.jcmgh.2026.101872", "title": "Comparative Analysis of Primary and Liver Fibroblasts Reveals MET as a Potent Target in Pancreatic Cancer Metastasis.", "journal": "Cellular and molecular gastroenterology and hepatology", "published": "2026-Sep-04", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42697413/" }, { "pmid": "42697918", "doi": "10.1038/s41598-026-67949-1", "title": "Exploratory study on blood and urine transcriptomes for identifying miRNA biomarkers in pediatric febrile bacterial and viral infections.", "journal": "Scientific reports", "published": "2026-Sep-04", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42697918/" }, { "pmid": "42695374", "doi": "10.1177/15578666261484978", "title": "Dynamic Supervised Prelabel Diffusion for Single-Cell Clustering.", "journal": "Journal of computational biology : a journal of computational molecular cell biology", "published": "2026-Sep-04", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42695374/" }, { "pmid": "42695693", "doi": "10.1128/mra.00811-26", "title": "Meta-CD: a metagenomic sequencing coverage and depth calculator for target species.", "journal": "Microbiology resource announcements", "published": "2026-Sep-04", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42695693/" }, { "pmid": "42695909", "doi": "10.1021/acs.jproteome.6c00267", "title": "Identification of Glioblastoma Cell Surface Proteins and Assessment of Their Expression Across Patient-Derived Stem-Like Cell Cultures.", "journal": "Journal of proteome research", "published": "2026-Sep-04", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42695909/" }, { "pmid": "42624107", "doi": "10.1016/j.stem.2026.07.014", "title": "Morphogen-guided neocortical organoids with anteroposterior areal identity.", "journal": "Cell stem cell", "published": "2026-Sep-03", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42624107/" }, { "pmid": "42693238", "doi": "10.1038/s12276-026-01826-9", "title": "Proteomic analysis of pancreatic endocrine cells by mechanistic single-cell isolation identifies membrane pathways.", "journal": "Experimental & molecular medicine", "published": "2026-Sep-03", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42693238/" }, { "pmid": "42693270", "doi": "10.1038/s42003-026-10803-x", "title": "A who's who of cell types in skeletal muscle.", "journal": "Communications biology", "published": "2026-Sep-03", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42693270/" }, { "pmid": "42693326", "doi": "10.1007/s00335-026-10267-8", "title": "Machine learning identifies ac4C-related prognostic signature and TUBA1C as therapeutic target in COAD.", "journal": "Mammalian genome : official journal of the International Mammalian Genome Society", "published": "2026-Sep-03", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42693326/" }, { "pmid": "42349121", "doi": "10.1016/j.bbrc.2026.154180", "title": "Redirected T-cell cytotoxicity identifies BRD9-PTGES axis as an immune-sensitising vulnerability in ovarian cancer.", "journal": "Biochemical and biophysical research communications", "published": "2026-Sep-03", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42349121/" }, { "pmid": "42690060", "doi": "10.1128/spectrum.02472-26", "title": "Optimizing a culture-enriched hybrid metagenomics pipeline to assess the AMR footprint of livestock manure in anaerobic digestate.", "journal": "Microbiology spectrum", "published": "2026-Sep-03", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42690060/" }, { "pmid": "42710152", "doi": "10.1016/j.fsigen.2026.103616", "title": "Time heals all wounds: Identification of RNA biomarkers for forensic wound age estimation in human skin tissue samples.", "journal": "Forensic science international. Genetics", "published": "2026-Sep-02", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42710152/" }, { "pmid": "42704958", "doi": "10.1016/j.virol.2026.111069", "title": "Evaluating sampling strategies for the detection of avian influenza viruses in the environment.", "journal": "Virology", "published": "2026-Sep-02", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42704958/" }, { "pmid": "42684847", "doi": "10.1091/mbc.E25-11-0561", "title": "FusionX: Automated, Standardized quantification of cell-to-cell fusion across diverse systems.", "journal": "Molecular biology of the cell", "published": "2026-Sep-02", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42684847/" }, { "pmid": "42685250", "doi": "10.1093/pcp/pcag122", "title": "Grass Expression Atlas: an RNA-seq-based expression resource for grass species.", "journal": "Plant & cell physiology", "published": "2026-Sep-02", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42685250/" }, { "pmid": "42690902", "doi": "10.1021/acsbiomaterials.6c00235", "title": "Three-Dimensional Gelatin-Based Hydrogel Degradation and Cell Control by Two-Photon Excitation.", "journal": "ACS biomaterials science & engineering", "published": "2026-Sep-02", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42690902/" }, { "pmid": "42684056", "doi": "10.1093/bioinformatics/btag660", "title": "COBRA: Cell-type-specific Orthogonal Batch effect Removal Algorithm in single cell RNA-sequencing data.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Sep-02", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42684056/" }, { "pmid": "42709957", "doi": "10.1093/bib/bbag480", "title": "DPAS-Graph: adaptive spatial-feature relation learning for spatial RNA-to-protein prediction and virtual protein profiling.", "journal": "Briefings in bioinformatics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42709957/" }, { "pmid": "42704266", "doi": "10.1093/bib/bbag476", "title": "Interpretable deep neural network identifies robust biomarkers for diseases with mechanistic insights from omics data.", "journal": "Briefings in bioinformatics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42704266/" }, { "pmid": "42696754", "doi": "10.1093/bib/bbag469", "title": "Gene-Chronos: parameter-efficient developmental time inference using a pretrained single-cell foundation model.", "journal": "Briefings in bioinformatics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42696754/" }, { "pmid": "42467724", "doi": "10.1093/humupd/dmag018", "title": "Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.", "journal": "Human reproduction update", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42467724/" }, { "pmid": "42554056", "doi": "10.1242/dev.205701", "title": "EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation.", "journal": "Development (Cambridge, England)", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42554056/" }, { "pmid": "42685266", "doi": "10.1093/bib/bbag454", "title": "Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.", "journal": "Briefings in bioinformatics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42685266/" }, { "pmid": "42687870", "doi": "10.1088/1361-6439/ae9c4b", "title": "Microfluidic platform for nanoliter qPCR of several retinal pigment epithelial (RPE) cells.", "journal": "Journal of micromechanics and microengineering : structures, devices, and systems", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42687870/" }, { "pmid": "42689497", "doi": "10.1093/bib/bbag462", "title": "Correction to: scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets.", "journal": "Briefings in bioinformatics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42689497/" }, { "pmid": "42586759", "doi": "10.1101/gr.281717.125", "title": "Pattern-Filter structural validation of single-cell RNA-seq reads reduces artifactual barcodes and improves biological resolution.", "journal": "Genome research", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42586759/" }, { "pmid": "42680767", "doi": "10.1038/s41597-026-08216-w", "title": "A human epithelial cell cycle dataset.", "journal": "Scientific data", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42680767/" }, { "pmid": "42680839", "doi": "10.1038/s41588-026-02725-5", "title": "A single-cell atlas of multiple myeloma defines malignant archetypes and proliferative states.", "journal": "Nature genetics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42680839/" }, { "pmid": "42680886", "doi": "10.1038/s41564-026-02472-7", "title": "MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.", "journal": "Nature microbiology", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42680886/" }, { "pmid": "42681808", "doi": "10.1002/advs.77524", "title": "MethyAnno: An Interpretable Automated Annotation Method Leveraging Multi-Scale Information and Metric Learning Framework for scDNAm Data.", "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42681808/" }, { "pmid": "42683913", "doi": "10.3791/71114", "title": "A Cost-Effective Workflow for Mono- and Multiplex Immunofluorescence in Adherent Two-Dimensional Cell Cultures on Glass Coverslips.", "journal": "Journal of visualized experiments : JoVE", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42683913/" }, { "pmid": "42068934", "doi": "10.1016/j.talanta.2026.129896", "title": "A label-free impedance cytometry platform for multi-functional and high-precision bacterial characterization.", "journal": "Talanta", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42068934/" }, { "pmid": "42416368", "doi": "10.1088/2515-7647/ae7da3", "title": "FLIMExplorer: interactive GUI for object-based visualization and analysis of fluorescence lifetime images.", "journal": "JPhys photonics", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42416368/" }, { "pmid": "42501774", "doi": "10.1016/j.cbi.2026.112266", "title": "DINCH exposure contributes to osteoarthritis pathogenesis via TSPO-mediated chondrotoxicity: Evidence from in silico prediction to experimental validation.", "journal": "Chemico-biological interactions", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42501774/" }, { "pmid": "42531928", "doi": "10.1016/j.jhazmat.2026.143114", "title": "High-content imaging driven algal phenotypes enable precise multilevel discrimination of heavy metal stress.", "journal": "Journal of hazardous materials", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42531928/" }, { "pmid": "42678676", "doi": "10.1177/13872877261480719", "title": "Single-cell transcriptomic atlas of Alzheimer's disease middle temporal gyrus reveals region, cell type, and sex specificity of gene expression with novel genetic risk for MERTK in female.", "journal": "Journal of Alzheimer's disease : JAD", "published": "2026-Sep-01", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42678676/" }, { "pmid": "42712876", "doi": "10.1093/nargab/lqag109", "title": "VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance.", "journal": "NAR genomics and bioinformatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42712876/" }, { "pmid": "42707924", "doi": "10.1002/jgf2.70171", "title": "Prognosis of Patients Infected With Talaromyces marneffei Across Various Risk Factors.", "journal": "Journal of general and family medicine", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42707924/" }, { "pmid": "42709036", "doi": "10.1099/mgen.0.001799", "title": "Expanded detection of canine enteric viruses in UK dogs with diarrhoea.", "journal": "Microbial genomics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42709036/" }, { "pmid": "42242982", "doi": "10.1016/j.tig.2026.05.005", "title": "Identifying fate-determining transcription factors with single-cell omics.", "journal": "Trends in genetics : TIG", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42242982/" }, { "pmid": "42538409", "doi": "10.1038/s41388-026-03905-7", "title": "The establishment of prostate-specific, SKP2 humanized mice by CRISPR knock-in method reveals neoplastic initiation and microenvironmental reprogramming.", "journal": "Oncogene", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42538409/" }, { "pmid": "41866111", "doi": "10.1016/j.jgg.2026.03.014", "title": "Single-nucleotide transcription start sites profiling via Nascent Strand-Specific RNA sequencing uncovers IFN-γ-induced promoter dynamics.", "journal": "Journal of genetics and genomics = Yi chuan xue bao", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41866111/" }, { "pmid": "41735501", "doi": "10.1038/s41596-025-01329-3", "title": "Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions.", "journal": "Nature protocols", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41735501/" }, { "pmid": "42231007", "doi": "10.1038/s41559-026-03087-1", "title": "Alignment-free integration of single-nucleus ATAC-seq across species with sPYce.", "journal": "Nature ecology & evolution", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42231007/" }, { "pmid": "42498883", "doi": "10.1038/s41592-026-03174-y", "title": "Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain.", "journal": "Nature methods", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42498883/" }, { "pmid": "42694579", "doi": "10.1093/nargab/lqag104", "title": "Scalable joint non-negative matrix factorization for paired single cell gene expression and chromatin accessibility data.", "journal": "NAR genomics and bioinformatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42694579/" }, { "pmid": "42696306", "doi": "10.1002/cpz1.70460", "title": "A Step-by-Step Guide to Successful Multiparametric Microbiota Flow Cytometry.", "journal": "Current protocols", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42696306/" }, { "pmid": "41966920", "doi": "10.1016/j.tibtech.2026.03.017", "title": "Label-free, single-cell-precise, and monomeric-unit-resolved monitoring of biopolymer fermentation by ramanomics.", "journal": "Trends in biotechnology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41966920/" }, { "pmid": "42011599", "doi": "10.1080/01478885.2026.2648709", "title": "TissuStamp: a novel high-throughput tissue transfer workflow for FFPE spatial biology assays.", "journal": "Journal of histotechnology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42011599/" }, { "pmid": "42315933", "doi": "10.1038/s44320-026-00223-8", "title": "Interpretable multi-omics integration across mixed-order tensors with MANTRA.", "journal": "Molecular systems biology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42315933/" }, { "pmid": "42499344", "doi": "10.1002/nep3.70047", "title": "An open-source pipeline for longitudinal single-cell tracking and cell-cycle/migration coupling analysis for neurotherapeutic screening.", "journal": "Neuroprotection (Chichester, England)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42499344/" }, { "pmid": "42474199", "doi": "10.1128/spectrum.00374-26", "title": "Clinical impact of metagenomic next-generation sequencing for pathogen identification and guided therapy in pediatric intensive care unit patients with severe pulmonary infections.", "journal": "Microbiology spectrum", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42474199/" }, { "pmid": "42505127", "doi": "10.1128/spectrum.00013-26", "title": "Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.", "journal": "Microbiology spectrum", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42505127/" }, { "pmid": "42517626", "doi": "10.1128/spectrum.00938-26", "title": "Metaviromic profiling of mosquito excreta using superhydrophobic collection devices expands the known RNA virome of North America.", "journal": "Microbiology spectrum", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42517626/" }, { "pmid": "42523101", "doi": "10.1128/spectrum.00970-26", "title": "Metagenomic next-generation sequencing for tuberculosis diagnosis: enhanced performance and cost-effectiveness.", "journal": "Microbiology spectrum", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42523101/" }, { "pmid": "42547805", "doi": "10.1038/s41593-026-02387-w", "title": "Developing mouse inhibitory neuron single-cell transcriptomes reveal distinct modes of cell-type diversification.", "journal": "Nature neuroscience", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42547805/" }, { "pmid": "42549916", "doi": "10.1128/spectrum.04057-25", "title": "Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.", "journal": "Microbiology spectrum", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42549916/" }, { "pmid": "40789829", "doi": "10.1007/s12539-025-00752-0", "title": "SANNO: A Graph-Transformer Enhanced Optimal Transport Tool for Spatial Transcriptomic Annotation.", "journal": "Interdisciplinary sciences, computational life sciences", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/40789829/" }, { "pmid": "41118050", "doi": "10.1007/s12539-025-00778-4", "title": "DEAPLOG: Differential Expression Analysis and Pseudo-Temporal Locating and Ordering of Genes in Single-Cell Transcriptomic Data.", "journal": "Interdisciplinary sciences, computational life sciences", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41118050/" }, { "pmid": "41120648", "doi": "10.1007/s12539-025-00773-9", "title": "DiTSim: A Diffusion-Transformers Based Single-Cell ATAC-seq Data Simulator.", "journal": "Interdisciplinary sciences, computational life sciences", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41120648/" }, { "pmid": "41385424", "doi": "10.1109/TBME.2025.3643493", "title": "A Sparse Constrained Optimization Method for Resolving Coincident Single-Cell Events in Microfluidic-Based Impedance Sensing.", "journal": "IEEE transactions on bio-medical engineering", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41385424/" }, { "pmid": "41443473", "doi": "10.1016/j.jare.2025.12.027", "title": "Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens.", "journal": "Journal of advanced research", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41443473/" }, { "pmid": "41742663", "doi": "10.1177/10849785261422983", "title": "Mechanobiological Ultrasound Simulation Reveals Suppression of Epithelial-to-Mesenchymal Transition and Stemness Programs in Colorectal Cancer.", "journal": "Cancer biotherapy & radiopharmaceuticals", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41742663/" }, { "pmid": "41793277", "doi": "10.1002/evj.70154", "title": "Transcriptomic signatures reveal systemic adaptations and immune modulation in response to training and competitive racing in horses.", "journal": "Equine veterinary journal", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41793277/" }, { "pmid": "41864285", "doi": "10.1016/j.healun.2026.03.011", "title": "Genome-wide association study reveals two novel genetic loci associated with chronic lung allograft dysfunction.", "journal": "The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41864285/" }, { "pmid": "41932047", "doi": "10.1016/j.ultras.2026.108083", "title": "Precise capture of heterogeneous microscale targets using an integrated spherical vortex acoustic tweezer.", "journal": "Ultrasonics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41932047/" }, { "pmid": "41963033", "doi": "10.1016/j.fm.2026.105049", "title": "A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.", "journal": "Food microbiology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/41963033/" }, { "pmid": "42030968", "doi": "10.1016/S1473-3099(26)00106-4", "title": "The impact of clinical metagenomic testing on patient management: facts versus fantasy.", "journal": "The Lancet. Infectious diseases", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42030968/" }, { "pmid": "42066541", "doi": "10.1016/j.diagmicrobio.2026.117442", "title": "Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.", "journal": "Diagnostic microbiology and infectious disease", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42066541/" }, { "pmid": "42085838", "doi": "10.1016/j.diagmicrobio.2026.117449", "title": "From culture to metagenomics: A paradigm shift in diagnosing infective endocarditis.", "journal": "Diagnostic microbiology and infectious disease", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42085838/" }, { "pmid": "42097460", "doi": "10.1016/j.jneumeth.2026.110789", "title": "A novel method to sort and enrich sensory neurons.", "journal": "Journal of neuroscience methods", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42097460/" }, { "pmid": "42102983", "doi": "10.1016/j.ymeth.2026.04.015", "title": "TEAMSTER: End-to-end pipeline for generation, processing, and automated quantitative image analysis of 3D tumour spheroids for nanobiology.", "journal": "Methods (San Diego, Calif.)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42102983/" }, { "pmid": "42119744", "doi": "10.1016/j.biortech.2026.134854", "title": "Late-window oxygen pulsing unlocks lignin-carbohydrate shielding and enhances fiber deconstruction during maize stover fermentation.", "journal": "Bioresource technology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42119744/" }, { "pmid": "42128199", "doi": "10.1016/j.joca.2026.05.005", "title": "The zone of calcified cartilage: A human explant culture model and a proof-of-concept transcriptomic study of 3D laser-cut interface tissue.", "journal": "Osteoarthritis and cartilage", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42128199/" }, { "pmid": "42128337", "doi": "10.1016/j.tox.2026.154496", "title": "Bisphenol A induces osteoporosis by targeting LAMA4 and OLR1: Novel insights into environmental bone toxicity.", "journal": "Toxicology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42128337/" }, { "pmid": "42142794", "doi": "10.1016/j.bone.2026.117937", "title": "Macrophage reprogramming nodes for bone repair identified by single-cell and spatial omics.", "journal": "Bone", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42142794/" }, { "pmid": "42165803", "doi": "10.1177/10766294261449450", "title": "Antimicrobial Activity of Eugenol Against NDM-Producing Escherichia coli: An In Vitro and In Vivo Study.", "journal": "Microbial drug resistance (Larchmont, N.Y.)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42165803/" }, { "pmid": "42179332", "doi": "10.1002/med.70061", "title": "Insights From Spatiality: Accelerating Pharmaceutical Research Using Mass Spectrometry Imaging.", "journal": "Medicinal research reviews", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42179332/" }, { "pmid": "42202548", "doi": "10.1016/j.cancergen.2026.05.005", "title": "TFRC-mediated immune exclusion as a therapeutic vulnerability in cervical cancer: A comprehensive analysis based on the cancer immunoediting process.", "journal": "Cancer genetics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42202548/" }, { "pmid": "42267961", "doi": "10.1177/15578666261457147", "title": "Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.", "journal": "Journal of computational biology : a journal of computational molecular cell biology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42267961/" }, { "pmid": "42276945", "doi": "10.1016/j.jbiosc.2026.05.004", "title": "Cas9-PALB2 fusion protein enhances CRISPR/Cas9 mediated gene knock-in efficiency.", "journal": "Journal of bioscience and bioengineering", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42276945/" }, { "pmid": "42288243", "doi": "10.1016/j.ijid.2026.108885", "title": "Diagnostic performance and clinical impact of metagenomic next-generation sequencing in 841 patients with suspected lower respiratory tract infections: A 4-year retrospective study from a tertiary hospital in Shenzhen, China.", "journal": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42288243/" }, { "pmid": "42292695", "doi": "10.1016/j.bbrep.2026.102662", "title": "Automated method for determining the zeta potential of red blood cells via motion tracking in microelectrophoresis.", "journal": "Biochemistry and biophysics reports", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42292695/" }, { "pmid": "42296430", "doi": "10.1002/bit.70267", "title": "GeneSEA Explorer: An R Shiny Tool for Differential Gene Expression Analysis With Shannon's Entropy Aggregation.", "journal": "Biotechnology and bioengineering", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42296430/" }, { "pmid": "42308801", "doi": "10.1016/j.micron.2026.104065", "title": "Touching the cell without contact: a comprehensive review of scanning ion conductance microscopy methodologies for advanced subcellular mechanical imaging.", "journal": "Micron (Oxford, England : 1993)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42308801/" }, { "pmid": "42310259", "doi": "10.1007/s12282-026-01883-y", "title": "Identifying breast cancer subtypes and exploring spatial expression patterns of the key subtype-specific gene based on pathological images, single-cell sequencing, and spatial transcriptomic data.", "journal": "Breast cancer (Tokyo, Japan)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42310259/" }, { "pmid": "42331233", "doi": "10.1016/j.nbd.2026.107500", "title": "A blood transcriptomic signature anchored to central nervous system pathology enables noninvasive detection of multiple sclerosis.", "journal": "Neurobiology of disease", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42331233/" }, { "pmid": "42360629", "doi": "10.1007/s40121-026-01372-x", "title": "Diagnostic Performance and Cost-Effectiveness of BALF mNGS in Older Adults with Pulmonary Infections.", "journal": "Infectious diseases and therapy", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42360629/" }, { "pmid": "42367641", "doi": "10.1097/BS9.0000000000000304", "title": "Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.", "journal": "Blood science (Baltimore, Md.)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42367641/" }, { "pmid": "42373542", "doi": "10.26508/lsa.202603759", "title": "Democratized single-cell proteomics resolves cell state heterogeneity in skin tumors.", "journal": "Life science alliance", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42373542/" }, { "pmid": "42380019", "doi": "10.1002/npr2.70150", "title": "Sleep Deprivation and Neuronal Hyperexcitation Share Transcriptomic Signatures.", "journal": "Neuropsychopharmacology reports", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42380019/" }, { "pmid": "42391672", "doi": "10.1016/j.tranon.2026.102879", "title": "Single-cell and machine learning-based neural regulation signature for prognosis prediction and immunotherapy response in lung adenocarcinoma.", "journal": "Translational oncology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42391672/" }, { "pmid": "42419494", "doi": "10.1016/j.jbi.2026.105078", "title": "scCLIP: A contrastive masked-reconstruction framework for paired single-cell multi-omics integration.", "journal": "Journal of biomedical informatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42419494/" }, { "pmid": "42424801", "doi": "10.1016/j.tranon.2026.102899", "title": "Molecular characterization of cell dynamics during osteosarcoma progression.", "journal": "Translational oncology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42424801/" }, { "pmid": "42429909", "doi": "10.1007/s10067-026-08295-5", "title": "Integrated machine learning framework identifies EPSTI1 as a key diagnostic biomarker for Sjögren's disease: multi-cohort transcriptomic validation and single-cell characterization.", "journal": "Clinical rheumatology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42429909/" }, { "pmid": "42434339", "doi": "10.1016/j.bbrep.2026.102683", "title": "A hybrid machine learning framework with two-step feature selection for identifying key biomarkers and drug targets in monkeypox.", "journal": "Biochemistry and biophysics reports", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42434339/" }, { "pmid": "42438676", "doi": "10.1016/j.aninu.2026.01.015", "title": "Chromatin accessibility of the jejunum in two high-yielding laying hen strains under divergent mineral phosphorus supply during the transition to egg laying.", "journal": "Animal nutrition (Zhongguo xu mu shou yi xue hui)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42438676/" }, { "pmid": "42441075", "doi": "10.1093/nargab/lqag070", "title": "A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.", "journal": "NAR genomics and bioinformatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42441075/" }, { "pmid": "42442222", "doi": "10.1016/j.tranon.2026.102911", "title": "Multi-omics analysis of arginine metabolism in ovarian cancer: A prognostic signature and GTF2F2-driven stromal remodeling.", "journal": "Translational oncology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42442222/" }, { "pmid": "42452972", "doi": "10.1002/glia.70202", "title": "Navigating Human Astrocyte Differentiation: Direct and Rapid One-Step Differentiation of Induced Pluripotent Stem Cells to Functional Astrocytes Supporting Neuronal Network Development.", "journal": "Glia", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42452972/" }, { "pmid": "42454225", "doi": "10.1093/nargab/lqag066", "title": "Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.", "journal": "NAR genomics and bioinformatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42454225/" }, { "pmid": "42456224", "doi": "10.1016/j.jiph.2026.103301", "title": "Chronic prosthetic joint infection caused by Coxiella burnetii diagnosed by metagenomic next-generation sequencing: A case report and literature review.", "journal": "Journal of infection and public health", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42456224/" }, { "pmid": "42462808", "doi": "10.1016/j.jinsphys.2026.105037", "title": "Establishment of a new germ-free Spodoptera frugiperda model to explore the gut microbiota on larval, pupal development and adult reproduction.", "journal": "Journal of insect physiology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42462808/" }, { "pmid": "42463025", "doi": "10.1016/j.critrevonc.2026.105490", "title": "Single-cell transcriptomics decodes the immunological landscape of thyroid cancer: Implications for immunotherapeutic targeting and precision oncology.", "journal": "Critical reviews in oncology/hematology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42463025/" }, { "pmid": "42478602", "doi": "10.1177/15578666261465432", "title": "scDFVA: Single-Cell Deep Clustering by Fusing Variational Graph Attention Autoencoder and ZINB-Based Autoencoder.", "journal": "Journal of computational biology : a journal of computational molecular cell biology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42478602/" }, { "pmid": "42484744", "doi": "10.1007/s10147-026-03133-9", "title": "Identification and functional validation of lipid droplet-associated prognostic biomarkers in breast cancer via integrative multi-omics and machine learning approaches.", "journal": "International journal of clinical oncology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42484744/" }, { "pmid": "42488460", "doi": "10.1093/nargab/lqag080", "title": "metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.", "journal": "NAR genomics and bioinformatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42488460/" }, { "pmid": "42490033", "doi": "10.1007/s10120-026-01777-0", "title": "Multimodal features and prognostic risk assessment in locally advanced gastric cancer patients following neoadjuvant therapy based on machine learning algorithms: a multicenter study.", "journal": "Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42490033/" }, { "pmid": "42492364", "doi": "10.1016/j.tranon.2026.102927", "title": "Integrative single-cell and machine learning analysis identifies a tumor doubling time-related prognostic signature and therapeutic targets in head and neck squamous cell carcinoma.", "journal": "Translational oncology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42492364/" }, { "pmid": "42496614", "doi": "10.1002/1545-5017.70548", "title": "RNA-seq Molecular Risk Classification Refines Prognostic Stratification in Childhood B-Cell Acute Lymphoblastic Leukemia Treated With the CCCG-ALL-2020 Protocol: A Real-World Cohort Study.", "journal": "Pediatric blood & cancer", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42496614/" }, { "pmid": "42522643", "doi": "10.1111/liv.70823", "title": "Gene-Based Clustering Identifies QSOX1 and IL1RAP as Biomarkers of Metabolic Dysfunction-Associated Steatotic Liver Disease.", "journal": "Liver international : official journal of the International Association for the Study of the Liver", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42522643/" }, { "pmid": "42597889", "doi": "10.1016/j.engmic.2026.100292", "title": "SuSha: A multi-model ensemble learning framework for predicting microbial salinity adaptation.", "journal": "Engineering microbiology", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42597889/" }, { "pmid": "42629583", "doi": "10.1111/acel.70677", "title": "LivAge: An Online Aging Clock for Murine Transcriptomic Age Estimation.", "journal": "Aging cell", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42629583/" }, { "pmid": "42631664", "doi": "10.1111/acel.70683", "title": "Network Model to Predict Age-Related Transcriptional Reprogramming.", "journal": "Aging cell", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42631664/" }, { "pmid": "42638396", "doi": "10.1002/jimd.70236", "title": "From Single Cells to Diagnosis: Proteomics Technologies in the Multi-Omics Landscape of Rare and Mitochondrial Diseases.", "journal": "Journal of inherited metabolic disease", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42638396/" }, { "pmid": "42656980", "doi": "10.1016/j.ocarto.2026.100862", "title": "Unraveling the pathogenic mechanisms of osteoarthritis and obesity: An integration of GWAS, cellular specificity, and spatial transcriptomics.", "journal": "Osteoarthritis and cartilage open", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42656980/" }, { "pmid": "42671929", "doi": "10.1002/cpz1.70458", "title": "Massively Parallel Profiling of Single-Cell RNA Dynamics Using Well-TEMP-seq.", "journal": "Current protocols", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42671929/" }, { "pmid": "42672076", "doi": "10.1111/aji.70317", "title": "Feto-Maternal Microchimerism and the Brain: Mechanisms, Neurological Implications, and Translational Perspectives.", "journal": "American journal of reproductive immunology (New York, N.Y. : 1989)", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42672076/" }, { "pmid": "42676509", "doi": "10.1093/nargab/lqag099", "title": "From rules to foundation models: a comprehensive review of machine learning approaches for siRNA design.", "journal": "NAR genomics and bioinformatics", "published": "2026-Sep", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42676509/" }, { "pmid": "42745950", "doi": "10.1007/s13205-026-05058-6", "title": "Stratifying lung adenocarcinoma: a novel prognostic model based on mitochondrial outer membrane permeabilization activity.", "journal": "3 Biotech", "published": "2026-Oct", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42745950/" }, { "pmid": "42806854", "doi": "10.1080/07853890.2026.2740261", "title": "Diagnostic value of metagenomic next-generation sequencing for bacterial and fungal detection and its role in antimicrobial therapy adjustment in critically ill patients with non-resolving pneumonia.", "journal": "Annals of medicine", "published": "2026-Dec", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42806854/" }, { "pmid": "42802576", "doi": "10.1080/07853890.2026.2735720", "title": "MERTK-related engulfment of norepinephrinergic neuronal presynaptic membrane by astrocytes following acute TBI and potentiation effect of peripheral nerve modulation.", "journal": "Annals of medicine", "published": "2026-Dec", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42802576/" }, { "pmid": "42703061", "doi": "10.1080/0886022X.2026.2718935", "title": "Circadian reprogramming of inflammation and metabolism in chronic kidney disease.", "journal": "Renal failure", "published": "2026-Dec", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42703061/" }, { "pmid": "42703320", "doi": "10.21037/jgo-2026-0363", "title": "Construction of molecular signatures based on the co-expression network of NECSO-related gene TRPM4 and its prognostic value in hepatocellular carcinoma.", "journal": "Journal of gastrointestinal oncology", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42703320/" }, { "pmid": "42633560", "doi": "10.1093/bioinformatics/btag639", "title": "GAMclust: identification of regulated metabolic modules in bulk, single cell and spatial gene expression data.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42633560/" }, { "pmid": "42616853", "doi": "10.1093/bioinformatics/btag623", "title": "Pesci: fast and user-friendly software to compare single-cell gene expression across species.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42616853/" }, { "pmid": "42625378", "doi": "10.1093/bioinformatics/btag627", "title": "Modtector: ultra-fast modification signal mining on mapped sequencing reads.", "journal": "Bioinformatics (Oxford, England)", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42625378/" }, { "pmid": "42669717", "doi": "10.1007/s10142-026-02024-6", "title": "Integration of artificial intelligence and multi-omics for precision medicine.", "journal": "Functional & integrative genomics", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42669717/" }, { "pmid": "42671485", "doi": "10.1007/s10495-026-02424-w", "title": "Integrated pan-cancer analysis reveals a cancer-associated fibroblast oxidative stress response signature predicting immunotherapy response and prognosis.", "journal": "Apoptosis : an international journal on programmed cell death", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42671485/" }, { "pmid": "42671697", "doi": "10.1007/s10534-026-00880-0", "title": "Identification of iron and zinc responsive TonB-dependent transporters in Pseudomonas aeruginosa.", "journal": "Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42671697/" }, { "pmid": "42673766", "doi": "10.1016/j.ebiom.2026.106465", "title": "An integrated reference atlas of human skeletal muscle.", "journal": "EBioMedicine", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42673766/" }, { "pmid": "42674874", "doi": "10.1016/j.tim.2026.08.005", "title": "The multifaceted role of atomic force microscopy in bacteriology.", "journal": "Trends in microbiology", "published": "2026-Aug-31", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42674874/" }, { "pmid": "42679777", "doi": "10.1016/j.bios.2026.119174", "title": "Sulfonated cobalt phthalocyanine coupled with poly(dopamine-co-sulfobetaine methacrylate) for single-cell electrochemical monitoring of glutathione.", "journal": "Biosensors & bioelectronics", "published": "2026-Aug-29", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42679777/" }, { "pmid": "42683911", "doi": "10.1021/jasms.6c00183", "title": "A Protocol for Multivariate Data Visualization and Pseudotime Modeling for Analysis of Disease Trajectories Detected by Mass Spectrometry Imaging.", "journal": "Journal of the American Society for Mass Spectrometry", "published": "2026-Aug-29", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42683911/" }, { "pmid": "42673706", "doi": "10.1016/j.placenta.2026.08.339", "title": "Placental transcriptomics identifies a candidate HLA-DQA2-FGL2 immune signature in gestational diabetes mellitus.", "journal": "Placenta", "published": "2026-Aug-29", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42673706/" }, { "pmid": "42687963", "doi": "10.21203/rs.3.rs-10731867/v1", "title": "Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states.", "journal": "Research square", "published": "2026-Aug-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42687963/" }, { "pmid": "42675750", "doi": "10.1097/MD.0000000000050486", "title": "An Aspergillus luchuensis isolated from a patient with hemoptysis insights from a comprehensive genome-based analysis: Case report.", "journal": "Medicine", "published": "2026-Aug-28", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42675750/" }, { "pmid": "42676027", "doi": "10.1021/acssensors.6c01742", "title": "High-Dimensional SERS Mapping of Single Circulating Tumor Cells Deciphers the Phenotypic Landscape and Stratifies Metastatic Risk in Pancreatic Cancer.", "journal": "ACS sensors", "published": "2026-Aug-26", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42676027/" }, { "pmid": "", "doi": "10.64898/2026.09.22.26363644", "title": "Maternal immune gene expression trajectories and dynamic genetic regulation throughout pregnancy", "journal": "medrxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.22.26363644" }, { "pmid": "", "doi": "10.64898/2026.09.23.26363823", "title": "Direct Pan-Cancer Multi-Omic Analysis of Radiotherapy Response Reveals Coding and Regulatory Genomic Variation, and Extracellular Adaptive Programs Underlying Radioresistance", "journal": "medrxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.23.26363823" }, { "pmid": "", "doi": "10.64898/2026.08.14.26360452", "title": "Methylation-driven Cancer Genes and Methylation Profiling in Glioma: A Comparative Study between East Asian and non-Hispanic White Populations", "journal": "medrxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.14.26360452" }, { "pmid": "", "doi": "10.64898/2026.09.21.749940", "title": "A Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease", "journal": "biorxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.21.749940" }, { "pmid": "", "doi": "10.64898/2025.12.08.693051", "title": "Spatially resolved contrastive analysis of perturbation-driven microenvironmental heterogeneity across tissues and conditions", "journal": "biorxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2025.12.08.693051" }, { "pmid": "", "doi": "10.64898/2026.08.26.747234", "title": "Pruning the Search, Not the Signal: Adaptive-Banding Needleman-Wunsch Sequence Alignment via Protein Language Model Confidence", "journal": "biorxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.26.747234" }, { "pmid": "", "doi": "10.64898/2026.09.16.752180", "title": "Disruption of a Structural Niche for Otoconia Maintenance May Underlie Common Vestibular Disorders", "journal": "biorxiv preprint", "published": "2026-09-25", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.16.752180" }, { "pmid": "", "doi": "10.64898/2026.09.22.26363641", "title": "Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria", "journal": "medrxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.22.26363641" }, { "pmid": "", "doi": "10.64898/2026.09.21.753337", "title": "A Computational Pipeline for Retinal Capillary Blood Flow Measurement using Adaptive Optics Line Confocal Ophthalmoscopy", "journal": "biorxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.21.753337" }, { "pmid": "", "doi": "10.1101/2024.12.25.630221", "title": "ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants", "journal": "biorxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.1101/2024.12.25.630221" }, { "pmid": "", "doi": "10.64898/2026.09.22.753406", "title": "An NR2F1-dependent retinoic acid network controls retinal specialization in mice and reveals foveal hypoplasia in patients with BBSOAS", "journal": "biorxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.22.753406" }, { "pmid": "", "doi": "10.64898/2026.09.22.752128", "title": "Speciesformer learns conserved cellular states for cross-species generative virtual cell modeling", "journal": "biorxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.22.752128" }, { "pmid": "", "doi": "10.64898/2026.09.21.751588", "title": "Stromal innervation is prognostic in non-muscle-invasive bladder cancer and predicted by a distinct microenvironmental transcriptomic signature", "journal": "biorxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.21.751588" }, { "pmid": "", "doi": "10.64898/2026.09.21.753290", "title": "Lineage-informed factor analysis reveals heritable programs of single-cell gene expression", "journal": "biorxiv preprint", "published": "2026-09-23", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.21.753290" }, { "pmid": "", "doi": "10.64898/2026.09.09.26362619", "title": "A gut microbiome-derived risk score is associated with future cancer development", "journal": "medrxiv preprint", "published": "2026-09-15", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.09.09.26362619" }, { "pmid": "", "doi": "10.64898/2026.05.26.727917", "title": "platpy: A spatial-first framework for multi-layer spatial transcriptomic analysis", "journal": "biorxiv preprint", "published": "2026-09-05", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.05.26.727917" }, { "pmid": "", "doi": "10.64898/2026.08.18.745395", "title": "A chromosome-scale genome assembly of the Swiss Lolium multiflorum ecotype Tremona reveals a scalable method to purge spurious duplications", "journal": "biorxiv preprint", "published": "2026-09-05", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.18.745395" }, { "pmid": "", "doi": "10.64898/2026.08.04.741960", "title": "Minimizing time in culture: A prototypic autologous manufacturing workflow for monoclonal iPSC lines within seven weeks", "journal": "biorxiv preprint", "published": "2026-09-05", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.04.741960" }, { "pmid": "", "doi": "10.64898/2026.08.26.746766", "title": "Timing of metabolomics-driven supplementation strategies affects protein expression in E. coli-based cell-free expression systems", "journal": "biorxiv preprint", "published": "2026-08-27", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.26.746766" }, { "pmid": "", "doi": "10.64898/2026.08.26.747243", "title": "Fusion-derived phospho-neoepitopes define a prioritized candidate neoantigen repertoire in MASLD-HCC", "journal": "biorxiv preprint", "published": "2026-08-27", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.26.747243" }, { "pmid": "", "doi": "10.64898/2026.08.26.747200", "title": "GABAergic Circuit Activation Induces a Therapeutically Responsive State for anti-PD-L1 Immunotherapy in Glioblastoma", "journal": "biorxiv preprint", "published": "2026-08-27", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.26.747200" }, { "pmid": "", "doi": "10.64898/2026.08.26.747240", "title": "Glutamatergic Neuron-Meningioma Synapse Interaction Promotes Brain-Invasive Tumor Growth", "journal": "biorxiv preprint", "published": "2026-08-27", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.26.747240" }, { "pmid": "", "doi": "10.64898/2026.08.26.746777", "title": "The Neural Impact Score benchmarks drugs in Multi-Region Brain Organoids", "journal": "biorxiv preprint", "published": "2026-08-27", "topic": "bioinformatics", "url": "https://doi.org/10.64898/2026.08.26.746777" }, { "pmid": "42801158", "doi": "10.2147/IDR.S632502", "title": "Diagnostic Performance of Bronchoalveolar Lavage Fluid Metagenomic Next‑generation Sequencing versus Conventional Microbiological Tests in Immunocompromised and Immunocompetent Patients with Pulmonary Infection.", "journal": "Infection and drug resistance", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42801158/" }, { "pmid": "42784630", "doi": "10.1371/journal.pone.0359153", "title": "scLTF: A self-training clustering framework for large-scale single-cell RNA-Seq data.", "journal": "PloS one", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42784630/" }, { "pmid": "42789536", "doi": "10.1371/journal.pone.0349692", "title": "Integrative transcriptomic analysis of peripheral blood identifies NETosis-associated programs and a stratified adaptive immune suppression pattern in severe acute pancreatitis.", "journal": "PloS one", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42789536/" }, { "pmid": "42789583", "doi": "10.1371/journal.pone.0358259", "title": "Integrative computational analysis of public fecal lipidomics and transcriptomics datasets suggests a candidate association between the COX-2 pathway and CE(20:4) in colorectal adenoma-carcinoma progression.", "journal": "PloS one", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42789583/" }, { "pmid": "42781492", "doi": "10.1136/bmjonc-2026-001159", "title": "Cytotoxic T-cell exhaustion analyses by in situ single-cell immunofluorescence in relation to colorectal cancer patient age, tissue bacteria and mortality.", "journal": "BMJ oncology", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42781492/" }, { "pmid": "42774927", "doi": "10.18332/tid/230997", "title": "Identification of key molecular targets in nicotine-induced spontaneous abortion through network toxicology and multi-omics integration.", "journal": "Tobacco induced diseases", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42774927/" }, { "pmid": "42769759", "doi": "10.2147/JIR.S622559", "title": "Deciphering the Immune Landscape of Abdominal Aortic Aneurysm: A Machine Learning and Cross-Species Validated Multi-Omics Approach.", "journal": "Journal of inflammation research", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42769759/" }, { "pmid": "42746583", "doi": "10.2147/ORR.S634292", "title": "Current Concepts in Periprosthetic Joint Infection: Modern Biomarkers, Microbiome Insights, Molecular Diagnostics, and Emerging Prevention Strategies.", "journal": "Orthopedic research and reviews", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42746583/" }, { "pmid": "42748134", "doi": "10.1371/journal.pone.0339543", "title": "From in silico prediction to experimental validation: Identification of drugs and novel synergistic combinations that inhibit growth of inflammatory breast cancer cells.", "journal": "PloS one", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42748134/" }, { "pmid": "42741419", "doi": "10.2147/COPD.S618802", "title": "Identification and Validation of a Two-Gene NK Cell-Related Risk Model for COPD: Integration of Single-Cell and Bulk RNA-Seq Analysis.", "journal": "International journal of chronic obstructive pulmonary disease", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42741419/" }, { "pmid": "42718951", "doi": "10.1177/20417314261488568", "title": "The dental pulp as a high-resolution model for neurovascular niche biology.", "journal": "Journal of tissue engineering", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42718951/" }, { "pmid": "42725323", "doi": "10.1093/bioadv/vbag255", "title": "Fedflow: cloud orchestration for federated learning with the FeatureCloud platform.", "journal": "Bioinformatics advances", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42725323/" }, { "pmid": "42707798", "doi": "10.3389/fcell.2026.1923026", "title": "Multi-omics mapping of PSC genetic risk to a high TWAS-active JAML+ lipid-associated macrophage program: bridging single-cell heterogeneity, spatial fibrotic niches, and machine learning selection.", "journal": "Frontiers in cell and developmental biology", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42707798/" }, { "pmid": "42699249", "doi": "10.2147/IDR.S620236", "title": "Diagnostic and Therapeutic Impact of Metagenomic Next-Generation Sequencing in Tuberculous Osteoarticular Infections with Negative or Confounding Conventional Cultures.", "journal": "Infection and drug resistance", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42699249/" }, { "pmid": "42702944", "doi": "10.1002/biof.70149", "title": "Immune-Like Malignant Epithelial Programs Shape Tumor-Immune Interactions and Inform Prognostic Stratification in Lung Adenocarcinoma.", "journal": "BioFactors (Oxford, England)", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42702944/" }, { "pmid": "42694451", "doi": "10.1155/humu/3241521", "title": "Potentially Deleterious Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) in the Human MCPH1 Gene: Systematic In Silico Predictions and Implications for Structure and Function.", "journal": "Human mutation", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42694451/" }, { "pmid": "42689238", "doi": "10.2147/IJN.S622301", "title": "Selenium-Doped Calcium Hydroxide Nanoparticles Inhibit Osteoclasts and Promote Osteogenesis for Osteoporosis Treatment.", "journal": "International journal of nanomedicine", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42689238/" }, { "pmid": "42691061", "doi": "10.1371/journal.pone.0357585", "title": "High AUROC can mask decision failure in sepsis transcriptomic classifiers: Preprocessing stability outweighs post hoc calibration across cohorts.", "journal": "PloS one", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42691061/" }, { "pmid": "42683062", "doi": "10.2147/JIR.S608906", "title": "PRKCB Mediates Ferroptosis-Immune Crosstalk in Acute Lung Injury: Insights from Integrated Single-Cell Transcriptomics.", "journal": "Journal of inflammation research", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42683062/" }, { "pmid": "42665402", "doi": "10.21873/invivo.14442", "title": "Constitutional Ring Chromosomes in Greek Pediatric Patients: A 50-year Single-center Cytogenetic Study.", "journal": "In vivo (Athens, Greece)", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42665402/" }, { "pmid": "42666044", "doi": "10.1002/biof.70141", "title": "Multicohort Construction, Immune Landscape Analysis, and PCOLCE2 Functional Validation of an Inflammation-Related Prognostic Model in Colorectal Cancer.", "journal": "BioFactors (Oxford, England)", "published": "2026", "topic": "bioinformatics", "url": "https://pubmed.ncbi.nlm.nih.gov/42666044/" } ]