Biophysics & Systems Biology · Life Sciences
Bioinformatics
The newest papers in Bioinformatics that ReadSearch has read, newest first. Each links to its own page, with its authors, date, where it was published and the original.
27 papers, from 3 November 2026 to 5 November 2026: 27 bioRxiv preprints.
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Newest papers
TIGRdisco: a tool for the discovery of TIGR arrays and TIGR-associated Tas proteins from nucleotide sequences
Tandem Interspaced Guide RNA (TIGR)-TIGR-associated protein (Tas) systems mediate DNA targeting through a hypercompact Tas effector, guided by dual spacers within a tigRNA that is processed from…Earl Grey ParTEA: scalable, consistent transposable element annotation from pangenomes to deep phylogenetic scopes
Transposable elements (TEs) are major drivers of genomic diversity, yet understanding their mobility and functional impact requires their accurate description in genomes.Cellular composition and the interpretation of candidate RNA readouts of trogocytosis in colorectal cancer
RNA measurements of genes associated with trogocytosis may reflect cellular composition rather than contact-dependent membrane acquisition.NeuroWeave-3D: Uncertainty-Aware Evidence Completion for Brain Tumor Segmentation with Missing MRI Modalities
Multi-parametric MRI segmentation models are accurate when all prescribed sequences are available but can be brittle under missing or corrupted modalities.Computational Analysis of Antioxidant Effects on Stress Response Mechanisms in Candida albicans
Candida albicans was used as a eukaryotic model to study aging and oxidative stress response pathways focused on NAD dependent deacetylases, Sir2 and SIRT3.Decision benchmarking of cryo-EM re-refinement
Map fit is widely used in cryo-EM re-refinement.Reference-Guided De Novo Retrieval of 3D Chromatin Organizational Features with Representation Learning
Chromosome conformation maps reveal spatial genome organization through recurring contact patterns, some associated with established architectural features and others with less understood biological…Top2All: Benchmarking sparse-to-transcriptome reconstruction from high-expression profiles across sex- and sex-steroid-defined conditions
Transcriptome-wide profiling at single-cell resolution is limited by sparse detection of gene expression, raising the question of how much transcriptomic information can be recovered from a small…SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq
Long-read RNA sequencing captures full-length transcripts, yet current annotation pipelines fail to properly curate the data for gene prediction.The Segmentome: a novel representation of the DNA methylome identified by a Bayesian HMM framework
DNA methylation is organized along the genome into regions of relatively stable methylation (i.e. fully methylated or fully unmethylated regions), separated by transition zones.An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings
Clinical genome sequencing pipelines change often, and each change requires proportionate revalidation.Layer-Specific Source-Anchored Transfer Learning for Multi-Omics Survival Prediction in Younger Breast Cancer Patients
Younger breast cancer patients (<50 years) often present with more aggressive disease and distinct molecular characteristics, yet predictive models for this group are underpowered due to small…TensorPLS: an R package for exploring molecular and temporal patterns in longitudinal omics data using PLS-DA
Longitudinal omics datasets combine high-dimensional repeated measurements with missing observations, complicating supervised modelling and temporal interpretation.SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets
Global syntheses of 16S rRNA metabarcoding data rely on combining datasets, yet amplicon sequence variants generated with different primer pairs can rarely be compared directly.Marker-specific pixel attribution for single-cell protein quantification with PixAQ
Imaging mass cytometry (IMC) typically quantifies all markers within the same cell mask, although their signals have distinct spatial distributions.Redesigning the Eterna100 RNA design benchmark for the Vienna 2 folding engine
The rational design of RNA is becoming important for rapidly developing technologies in medicine and biochemistry, spurring development of numerous RNA secondary structure design algorithms and…JUMP Cell Painting chemical dataset: Morphological map of 115,796 compounds in human cells
Image-based profiling decodes complex cellular states for high-impact biological and therapeutic applications, yet a large, public reference dataset of chemical perturbations has been lacking.scRM: A single-cell foundation model trained on scRNA-seq reads
To our knowledge, scRM is the first single-cell foundation model trained on sequencing reads, demonstrating that raw data pretraining is not only feasible but competitive at a fraction of the…FastaGuard: FASTA preflight QC for modern bioinformatics pipelines
FastaGuard is a streaming, explainable FASTA preflight QC tool that validates assembly FASTA files, detects structural and composition red flags, and emits a versioned multi-format report with an…A comparison of two culture and three sequencing methods for detection of the urobiome
Standard urine culture (SUC), the clinical reference method, is optimized for fast-growing aerobes and misses much of the urinary microbiota.