bioRxiv Subject Collection: Genomics Bioinformatics https://biorxiv.org This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics" bioRxiv bioRxiv https://www.biorxiv.org/sites/default/files/bioRxiv_article.jpg https://www.biorxiv.org <![CDATA[ Spatiotemporal Heterogeneity of HPV Integration Architectures Drive Oncogenic Features of Oropharyngeal Cancer ]]> https://www.biorxiv.org/content/10.64898/2026.10.03.756294v1?rss=1 2026-10-10 doi:10.64898/2026.10.03.756294 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Ab initio CryoEM maps minimizing preferred orientation problems in heterogeneous mixtures: ReconSIREN ]]> https://www.biorxiv.org/content/10.64898/2026.10.03.756391v1?rss=1 2026-10-10 doi:10.64898/2026.10.03.756391 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Matrix-Mechanical Genetic Susceptibility and Reduced Inflammatory and Immediate-Early Programs in Keratoconus ]]> https://www.biorxiv.org/content/10.64898/2026.10.03.754609v1?rss=1 2026-10-10 doi:10.64898/2026.10.03.754609 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756312v1?rss=1 2026-10-10 doi:10.64898/2026.10.02.756312 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Point-Process Modelling of Cell-Type Interaction Structure in CosMx Glioma Data for Hypothesis-Driven Tumor Inference from scRNA-seq ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756019v1?rss=1 2026-10-10 doi:10.64898/2026.10.02.756019 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ From Sparse Visits to Continuous Molecular Trajectories with Flow Matching ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756304v1?rss=1 2026-10-10 doi:10.64898/2026.10.02.756304 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ RiboFlow v2: a configurable ribosome profiling pipeline reveals measurements sensitive to read-mapping methodology ]]> https://www.biorxiv.org/content/10.64898/2026.10.05.756038v1?rss=1 2026-10-10 doi:10.64898/2026.10.05.756038 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Pooled progeny sequencing effectively estimates polyandry in species with large families ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756305v1?rss=1 2026-10-10 doi:10.64898/2026.10.02.756305 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Systematic benchmark of demultiplexing workflows for direct RNA sequencing ]]> https://www.biorxiv.org/content/10.64898/2026.10.03.756430v1?rss=1 2026-10-10 doi:10.64898/2026.10.03.756430 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ A chromosome-level genome assembly of the chilli thrips Scirtothrips dorsalis Hood (Thysanoptera: Thripidae) ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757792v1?rss=1 2026-10-10 doi:10.64898/2026.10.08.757792 Cold Spring Harbor Laboratory 2026-10-10 <![CDATA[ Characterization of artificial riboswitches for Coxsackievirus B3 detection using machine learning ]]> https://www.biorxiv.org/content/10.64898/2026.10.04.756577v1?rss=1 2026-10-09 doi:10.64898/2026.10.04.756577 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ DEPICT enables sample-centric therapeutic prioritization across evolving and spatially heterogeneous tumor states ]]> https://www.biorxiv.org/content/10.64898/2026.10.07.756157v1?rss=1 2026-10-09 doi:10.64898/2026.10.07.756157 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Error correction of SARS-CoV-2 genomic sequences using a phylogenetic prior ]]> https://www.biorxiv.org/content/10.64898/2026.10.07.757202v1?rss=1 2026-10-09 doi:10.64898/2026.10.07.757202 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756336v1?rss=1 2026-10-09 doi:10.64898/2026.10.02.756336 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Genotypic Responses of Rice to Ammonium and Nitrate under Contrasting Water Regimes: Agronomic, Biochemical, and Gene-Expression Analyses ]]> https://www.biorxiv.org/content/10.64898/2026.10.04.756527v1?rss=1 2026-10-09 doi:10.64898/2026.10.04.756527 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ DECONVersation: Single Cell Foundation Model-Derived Embeddings for Robust Cell Type Deconvolution of Bulk RNA-seq ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756356v1?rss=1 2026-10-09 doi:10.64898/2026.10.02.756356 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ 'broadSeq', a benchmarking tool to contrast differential gene expression methods and identify when genomic neighbourhood matters ]]> https://www.biorxiv.org/content/10.64898/2026.10.03.756406v1?rss=1 2026-10-09 doi:10.64898/2026.10.03.756406 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ A human-in-the-loop approach for faster cell tracking ]]> https://www.biorxiv.org/content/10.64898/2026.10.06.756962v1?rss=1 2026-10-09 doi:10.64898/2026.10.06.756962 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Multi-omic long-read sequencing reveals nucleosome control of transcriptional fidelity at the isoform level ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757737v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.757737 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.756856v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.756856 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Random mtDNA mutagenesis maps genotype-phenotype associations across metabolic contexts and lineages ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757705v1?rss=1 100 mutations per molecule, impairs respiration, and causes lineage-specific developmental delay. Coupling single-cell transcriptomics with mtDNA genotyping revealed that selection on mutant genomes and their transcriptional consequences depend on metabolic state and developmental lineage. Obligate OXPHOS eliminates highly mutated cells by apoptosis, whereas glycolytic conditions promote their competitive displacement. Individual loci exert modest but non-redundant effects that predict cell state beyond aggregate mutation burden, and cancer-recurrent variants are enriched among mutations linked to reduced mitochondrial transcription. Thus, mtDIVE links mtDNA genotypes to cellular phenotypes, separating the consequences of mutation identity from mutational load. ]]> 2026-10-09 doi:10.64898/2026.10.08.757705 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Centromeric islands constrain CENP-A domain size and position ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757135v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.757135 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Scalable localization of clustering instability for spatial transcriptomics ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.738042v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.738042 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ qPyCR: A qPCR Data Analyzer for Template Quantification and the Detection of Performance Outliers ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757329v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.757329 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ High-throughput identification of chromatin-opening transcription factors ]]> https://www.biorxiv.org/content/10.64898/2026.10.07.757445v1?rss=1 2026-10-09 doi:10.64898/2026.10.07.757445 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ The adaptive architecture of tRNA dependencies across physiological tumor environments ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757597v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.757597 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Fine-tuning genomic models on rare splicing events identifies a novel biomarker of TDP-43 pathology ]]> https://www.biorxiv.org/content/10.64898/2026.10.07.757366v1?rss=1 2026-10-09 doi:10.64898/2026.10.07.757366 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Cerberus: bidirectional state space blocks improve accuracy and efficiency of regulatory sequence models ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756377v1?rss=1 2026-10-09 doi:10.64898/2026.10.02.756377 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ Probing Genomic Foundation Models with Splice-Variant Perturbations ]]> https://www.biorxiv.org/content/10.64898/2026.10.02.756289v1?rss=1 2026-10-09 doi:10.64898/2026.10.02.756289 Cold Spring Harbor Laboratory 2026-10-09 <![CDATA[ STEER-seq: a recombinase based platform for pooled multimodal single-cell perturbation screening ]]> https://www.biorxiv.org/content/10.64898/2026.10.08.757551v1?rss=1 2026-10-09 doi:10.64898/2026.10.08.757551 Cold Spring Harbor Laboratory 2026-10-09