Genomics & Bioinformatics #Omics #NGS #LongReads 🧪🧬 🖥️ Opinions my own. He/Him LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/https://bsky.app/profile/jsantoyo.bsky.socialhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mghevgx2as2qSomatic genomics as a discovery engine for biomedicine. #Genomics #CancerGenomics https://www.cell.com/cell/fulltext/S0092-8674(26)00119-407 Mar 2026 08:11 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mghevgx2as2qhttps://bsky.app/profile/jsantoyo.bsky.social/post/3md3fch3j4s2cGPTBioInsightor—Leveraging LLMs for transparent scRAN-Seq cell type annotations. #SingleCell #scRNAseq #LLMs #AI #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbag025/843607623 Jan 2026 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3md3fch3j4s2chttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcwl2dzwt52jMapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM. #SpatialTranscriptomics #Isoforms @natbiotech.nature.com 🧪🧬 🖥️ https://www.nature.com/articles/s41587-025-02965-621 Jan 2026 11:30 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcwl2dzwt52jhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcwgtn37qg2iEvaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies. #SingleCell #scRNAseq #Benchmarking #NARgenomicsAndBioinformatics 🧪🧬 🖥️ https://academic.oup.com/nargab/article/8/1/lqaf215/841521821 Jan 2026 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcwgtn37qg2ihttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcweelqkup2mMobiCT: a UMI-based circulating tumor DNA analysis pipeline. #UMIs #cfDNA #Nextflow #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️ https://academic.oup.com/nargab/article/8/1/lqaf212/841521221 Jan 2026 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcweelqkup2mhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcufocou3i2iLinkML: An Open Data Modeling Framework. #DataModel #DataSharing #FAIRdata @gigascience.bsky.social https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giaf152/8378082 linkml.io20 Jan 2026 14:49 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcufocou3i2ihttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcozofm65v2hAn evaluation of computational methods for reconstruction of human viral DNA genomes. #ViralDNAgenomes #MethodBenchmarking @gigascience.bsky.social https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giaf159/840529418 Jan 2026 11:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcozofm65v2hhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcovgkjyoi2xHarnessing Artificial Intelligence for Genomic Variant Prediction: Advances, Challenges, and Future Directions. #GenomicVariants #VariantInterpretation #AI @gigascience.bsky.social https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giag004/841968118 Jan 2026 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcovgkjyoi2xhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcosxtl6ou2vTranslating short-form Python exercises to other programming languages using diverse prompting strategies. #LLMs #Programming #Bioinformatics #CodeTranslation @gigascience.bsky.social 🧪🧬 🖥️ https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf149/837380818 Jan 2026 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcosxtl6ou2vhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcopodc2rs2iA comprehensive survey of genome language models in bioinformatics. #GenomeLanguageModels #gMLs #ModelsReview #Bioinformatics #Genomics #BriefingsInBioinformatics https://academic.oup.com/bib/article/27/1/bbaf724/842612418 Jan 2026 08:32 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcopodc2rs2ihttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcn5djg4if2xREDAC: RNA-seq Expression Data Analysis Chatbot. #RNAseq #LLMss #DataAnalysis #DifferentialExpression #Sequencing #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️ https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf321/840564617 Jan 2026 17:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcn5djg4if2xhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcmybavgw32rVST-DAVis: An R shiny Application and web-browser for Spatial Transcriptomics Data Analysis and Visualization. #SpatialTranscriptomics #DataVisualization #RNAseq #Rshiny #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbag007/841849617 Jan 2026 16:00 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcmybavgw32rhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcmk7o55pq25ChromoMapper: a new tool to quickly compare large genome assemblies. #GenomeAssembly #GenomeComparison #Bioinformatics #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️ https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbag005/841849717 Jan 2026 11:49 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcmk7o55pq25https://bsky.app/profile/jsantoyo.bsky.social/post/3mcmexqk2cf2hAnalyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing. #SingleCell #LongRead #Sequencing #scRNAseq #Isoforms #DifferentialExpression #Bioinformaticcs #Genomics 🧪🧬 🖥️ https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf664/838151517 Jan 2026 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcmexqk2cf2hhttps://bsky.app/profile/jsantoyo.bsky.social/post/3mcmcixkdyw25ASTRO: Automated Spatial-Transcriptome whole RNA Output. #SpatialTranscriptomics #RNAseq #FFPE #Genome #Bioinformatics 🧪🧬 🖥️ https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf688/841591117 Jan 2026 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcmcixkdyw25https://bsky.app/profile/jsantoyo.bsky.social/post/3mcm77fyhvm25scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️ https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btag023/842559517 Jan 2026 08:32 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3mcm77fyhvm25https://bsky.app/profile/jsantoyo.bsky.social/post/3ma42akdszm2yCiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️ https://www.nature.com/articles/s41467-025-66918-y16 Dec 2025 11:30 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3ma42akdszm2yhttps://bsky.app/profile/jsantoyo.bsky.social/post/3ma3w2chdqx2rSearch-and-remove genome editing allows selection of cells by DNA sequence. #GenomeEditing #CellSelection @natcomms.nature.com 🧪🧬 🖥️ https://www.nature.com/articles/s41467-025-66896-116 Dec 2025 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3ma3w2chdqx2rhttps://bsky.app/profile/jsantoyo.bsky.social/post/3ma3tlhjtu72oMapping single-cell diploid chromatin fiber architectures using DAF-seq. #SingleCell #ChromatinFiberArchitecture #Sequencing #Genomics @natbiotech.nature.com 🧪🧬 🖥️ https://www.nature.com/articles/s41587-025-02914-316 Dec 2025 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3ma3tlhjtu72ohttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7zjrs5dpg2cStandardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.#SpatialTranscriptomics #StandardizedMetrics #DataRepository #BestPractices #OpenSourceSoftware #Genomics #Bioinformatics @natbiotech.nature.com https://www.nature.com/articles/s41587-025-02811-915 Dec 2025 11:30 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7zjrs5dpg2chttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7zfliurdw2cWhole-genome landscapes of 1,364 breast cancers. #WGS #BreastCancer #Genomics @nature.com https://www.nature.com/articles/s41586-025-09812-315 Dec 2025 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7zfliurdw2chttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7zd4jx4d22eInsights into natural neocentromere evolution from a cattle T2T X chromosome. #CattleGenome #T2T #HaplotypeResolvedGenome #Centromeres #Genomics @natcomms.nature.com 🧪🧬 🖥️ https://www.nature.com/articles/s41467-025-65778-w15 Dec 2025 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7zd4jx4d22ehttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7mqrwtfix2xLong-read metagenomics reveals phage dynamics in the human gut microbiome. #GutMicrobiome #Phages #LongReads #Sequencing #Genomics @nature.com 🧪🧬 🖥️ https://www.nature.com/articles/s41586-025-09786-210 Dec 2025 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7mqrwtfix2xhttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7kjighcr22wA bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data. #RNAisoforms #GTEx #LongReads #Sequencing #Genomics #Bioinformatics #BMCgenomics https://link.springer.com/article/10.1186/s12864-025-11919-w09 Dec 2025 12:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7kjighcr22whttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7kgyfktja2kGenome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics https://link.springer.com/article/10.1186/s12864-025-12167-809 Dec 2025 11:30 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7kgyfktja2khttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7kcrumxmh2xPlate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress. #SingleCell #scRNAseq #PlateBasedAssay #10X #Genomics #BMCgenomics https://link.springer.com/article/10.1186/s12864-025-12286-209 Dec 2025 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7kcrumxmh2xhttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7kacycvkm2bSeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets. #Metagenomics #AlignmentBasedSearches #Genomics #Bioinformatics #BMCbioinformatics https://link.springer.com/article/10.1186/s12859-025-06297-909 Dec 2025 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7kacycvkm2bhttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7hscxcrgc2kMOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation. #DataSimulation #CancerVariants #SequencingReads #ComputationalModelling #BMCBioinformatics 🧪🧬 🖥️ https://link.springer.com/article/10.1186/s12859-025-06292-008 Dec 2025 10:15 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7hscxcrgc2khttps://bsky.app/profile/jsantoyo.bsky.social/post/3m7hpu3s45o2uTaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. #Microbiome #DataAugmentation #GenerativeModel #BMCbioinformatics 🧪🧬 🖥️ https://link.springer.com/article/10.1186/s12859-025-06312-z08 Dec 2025 09:31 +0000at://did:plc:oij6dmtiwwevddoiyroctsds/app.bsky.feed.post/3m7hpu3s45o2u