bioRxiv Subject Collection: Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Bioinformatics"
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GenoSim: A Forward-Time Genotype Simulator for Clinical and Population Genetics with Population Stratification
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https://www.biorxiv.org/content/10.64898/2026.06.20.733503v1?rss=1
2026-06-25doi:10.64898/2026.06.20.733503Cold Spring Harbor Laboratory2026-06-25
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Evidence for post-allopolyploidy genetic exchanges between duplicated regions in three ancient polyploidies
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https://www.biorxiv.org/content/10.64898/2026.06.20.733495v1?rss=1
2026-06-25doi:10.64898/2026.06.20.733495Cold Spring Harbor Laboratory2026-06-25
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Ambiguity-Aware Multi-Stage Cell-Type Annotation for Spatial Transcriptomics
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https://www.biorxiv.org/content/10.64898/2026.06.21.733596v1?rss=1
2026-06-25doi:10.64898/2026.06.21.733596Cold Spring Harbor Laboratory2026-06-25
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A Visually Interpretable Histopathology-Based Immune Model Predicts T-effector Biology and Response to Immune checkpoint inhibition in Clear Cell Renal Cell Carcinoma Clinical Trial and Contemporary Real-World Datasets
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https://www.biorxiv.org/content/10.64898/2026.06.21.733614v1?rss=1
2026-06-25doi:10.64898/2026.06.21.733614Cold Spring Harbor Laboratory2026-06-25
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CREPAS: a reproducible nascent chromatin sequencing analysis pipeline for epigenome replication studies
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https://www.biorxiv.org/content/10.64898/2026.06.21.732899v1?rss=1
2026-06-25doi:10.64898/2026.06.21.732899Cold Spring Harbor Laboratory2026-06-25
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NanoCellAnnotator: Formalizing Expert Cell Type Annotation with Large Language Models
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https://www.biorxiv.org/content/10.64898/2026.06.21.728965v1?rss=1
2026-06-25doi:10.64898/2026.06.21.728965Cold Spring Harbor Laboratory2026-06-25
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Tissue-aware elastic net decomposition reveals shared and lineage-specific drug response biomarkers
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https://www.biorxiv.org/content/10.64898/2026.06.21.733619v1?rss=1
2026-06-25doi:10.64898/2026.06.21.733619Cold Spring Harbor Laboratory2026-06-25
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BGC-QDR: A Quantum-Assisted Pipeline for Biosynthetic Gene Cluster Discovery and Ranking from Environmental DNA
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https://www.biorxiv.org/content/10.64898/2026.06.21.733574v1?rss=1
2026-06-25doi:10.64898/2026.06.21.733574Cold Spring Harbor Laboratory2026-06-25
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Multi-Omics Study of Ancestry in Adults with Intracranial Cancers Glioma (MOSAIC)
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https://www.biorxiv.org/content/10.64898/2026.06.24.733669v1?rss=1
2026-06-25doi:10.64898/2026.06.24.733669Cold Spring Harbor Laboratory2026-06-25
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CNSigs: An R Package for the Identification of Copy Number Mutational Signatures
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https://www.biorxiv.org/content/10.64898/2026.06.21.733646v1?rss=1
3000), demonstrating high accuracy (average cosine similarity = 0.89). Pan-cancer application of CNSigs in the TCGA dataset resulted in derivation of 13 pan-cancer signatures which were significantly associated with disease-specific survival. Benchmarking CNSigs to two other CNA signature approaches within TCGA demonstrated non-overlapping signatures and favorable compute speed for CNSigs. We evaluated n=24 pairs of tumor and circulating tumor DNA (ctDNA) acquired at the same time and demonstrated that CNSigs are detectable and reproducible via ctDNA, with significant association of CNSig11 with metastatic triple-negative breast cancer progression-free survival for taxane but not platinum or capecitabine chemotherapy. CNSigs association with immunophenotype was evaluated in low-grade glioma (LGG) and CNSig 3 was found to be highly prognostic for LGG yet complementary to immune features. Conclusions: The CNSigs R package allows researchers to easily analyze their own samples to derive copy number signatures and evaluate clinical associations. We demonstrate potential application in ctDNA and association with treatment response. The development of this package allows further investigation of underlying processes that may be responsible for these CNA fingerprints.
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The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking
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https://www.biorxiv.org/content/10.64898/2026.06.22.733853v1?rss=1
2026-06-25doi:10.64898/2026.06.22.733853Cold Spring Harbor Laboratory2026-06-25
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Bamsnap-LRS: an automated batch visualization tool for long-read sequencing alignments
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https://www.biorxiv.org/content/10.64898/2026.06.21.733121v1?rss=1
2026-06-25doi:10.64898/2026.06.21.733121Cold Spring Harbor Laboratory2026-06-25
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Agnostic material classification using differential de Bruijn graphs of DNA imprints
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https://www.biorxiv.org/content/10.64898/2026.06.23.733838v1?rss=1
2026-06-25doi:10.64898/2026.06.23.733838Cold Spring Harbor Laboratory2026-06-25
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DextraDemixer enables accurate identification of antigen-specific T cells from pMHC multimer experiments
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https://www.biorxiv.org/content/10.64898/2026.06.23.733339v1?rss=1
2026-06-25doi:10.64898/2026.06.23.733339Cold Spring Harbor Laboratory2026-06-25
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ComplexDesign: sequence-hallucination design of protein binders bridging multiple proteins
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https://www.biorxiv.org/content/10.64898/2026.06.21.733655v1?rss=1
2026-06-24doi:10.64898/2026.06.21.733655Cold Spring Harbor Laboratory2026-06-24
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V3Cell: A Vision-Guided Virtual 3D Cell Framework for Phenotypic Modeling and Perturbation Prediction
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https://www.biorxiv.org/content/10.64898/2026.06.23.734130v1?rss=1
2026-06-24doi:10.64898/2026.06.23.734130Cold Spring Harbor Laboratory2026-06-24
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fastQpick: scalable bootstrap and subsampling of FASTQ reads
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https://www.biorxiv.org/content/10.64898/2026.06.23.734068v1?rss=1
2026-06-24doi:10.64898/2026.06.23.734068Cold Spring Harbor Laboratory2026-06-24
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RNabel-A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids
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https://www.biorxiv.org/content/10.64898/2026.06.22.733900v1?rss=1
2026-06-24doi:10.64898/2026.06.22.733900Cold Spring Harbor Laboratory2026-06-24
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Development of Deep-Learning Models that Predict Quantitative Protein-Ligand Interac-tions in Glycobiology as a part of a Capstone Course
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https://www.biorxiv.org/content/10.64898/2026.06.19.733466v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733466Cold Spring Harbor Laboratory2026-06-24
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A comprehensive analysis of calreticulin mutants reveals distinct biophysicochemical proprieties with a potential for refined targeted therapies
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https://www.biorxiv.org/content/10.64898/2026.06.19.733337v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733337Cold Spring Harbor Laboratory2026-06-24
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InVitroGap: an open-source tool for automated quantification of wound closure in the in vitro scratch assay
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https://www.biorxiv.org/content/10.64898/2026.06.19.733445v1?rss=1
0.05), strong pooled correlations (R square = 0.964 for RWD; R square = 0.983 for wound confluence), and small mean biases (absolute bias [≤] 1.64%). The tool successfully processed crisscross wounds from brightfield image series, and a complete four-timepoint series was analyzed in approximately 10 seconds, with robust performance across distinct cell morphologies and wound geometries. Conclusions: InVitroGap provides a transparent, computationally efficient, and platform-independent alternative for scratch assay analysis, delivering performance comparable to commercial systems while remaining freely accessible at https://invitrogap.vercel.app/.
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Generative Modeling of Mouse Embryogenesis for Fate and Disease Prediction
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https://www.biorxiv.org/content/10.64898/2026.06.18.733286v1?rss=1
2026-06-24doi:10.64898/2026.06.18.733286Cold Spring Harbor Laboratory2026-06-24
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Systematic benchmarking of multi-modal approaches for tumor-naive ctDNA detection and quantification
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https://www.biorxiv.org/content/10.64898/2026.06.19.733293v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733293Cold Spring Harbor Laboratory2026-06-24
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Statistical tests for bivariate spatial association across multi-omics data with disjoint coordinates
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https://www.biorxiv.org/content/10.64898/2026.06.19.732250v1?rss=1
2026-06-24doi:10.64898/2026.06.19.732250Cold Spring Harbor Laboratory2026-06-24
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trAIt: Species-by-Trait Data Retrieval using Large Language Models
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https://www.biorxiv.org/content/10.64898/2026.06.19.732660v1?rss=1
2026-06-24doi:10.64898/2026.06.19.732660Cold Spring Harbor Laboratory2026-06-24
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Beyond statistical significance: ranking transcription factor binding motifs by effect size
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https://www.biorxiv.org/content/10.64898/2026.06.19.732679v1?rss=1
2026-06-24doi:10.64898/2026.06.19.732679Cold Spring Harbor Laboratory2026-06-24
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SEMFA: A General Framework for Inferring Statistical Significance of Mahalanobis Similarity between Multi-Omics Profiled Samples Built on Multiple Factor Analysis
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https://www.biorxiv.org/content/10.64898/2026.06.18.733287v1?rss=1
2026-06-24doi:10.64898/2026.06.18.733287Cold Spring Harbor Laboratory2026-06-24
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Pharmacological Stratification of Public Bioactivity Databases: A Reusable, OECD-Anchored Curation and Benchmarking Framework Demonstrated for Opioid Receptors
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https://www.biorxiv.org/content/10.64898/2026.06.18.732083v1?rss=1
2026-06-24doi:10.64898/2026.06.18.732083Cold Spring Harbor Laboratory2026-06-24
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An atlas-scale generative model for unified representation learning of bulk RNA-seq data
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https://www.biorxiv.org/content/10.64898/2026.06.18.733198v1?rss=1
2026-06-24doi:10.64898/2026.06.18.733198Cold Spring Harbor Laboratory2026-06-24
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BATTLE-AMP: Benchmarking Antimicrobial Peptide Predictors
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https://www.biorxiv.org/content/10.64898/2026.06.19.733349v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733349Cold Spring Harbor Laboratory2026-06-24