Somatic genomics as a discovery engine for biomedicine. #Genomics #CancerGenomics www.cell.com/cell/fulltex...

Somatic genomics as a discovery engine for biomedicine

Somatic genetics uses tissue mutations to understand aging, reveal disease mechanisms, and guide new therapies.

cell.com

Element reveals more information about their VITARI platform, a foray into the high-throughput sequencing market. sandiegomics.com/element-join...

Element Joins the High-Throughput Market with the VITARI Platform

Back at JPM Element teased that they would be coming out with the VITARI, a benchtop sequencer capable of generating whole genomes for $100. This would best Illumina’s list price of $200 with the N…

sandiegomics.com

GPTBioInsightor—Leveraging LLMs for transparent scRAN-Seq cell type annotations. #SingleCell #scRNAseq #LLMs #AI #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...

GPTBioInsightor—Leveraging LLMs for transparent scRAN-Seq cell type annotations

Abstract. Large language models (LLMs) are rapidly becoming indispensable across the life‑sciences spectrum, from literature mining through clinical decisi

academic.oup.com

Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM. #SpatialTranscriptomics #Isoforms @natbiotech.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies. #SingleCell #scRNAseq #Benchmarking #NARgenomicsAndBioinformatics 🧪🧬 🖥️ academic.oup.com/nargab/artic...

MobiCT: a UMI-based circulating tumor DNA analysis pipeline. #UMIs #cfDNA #Nextflow #Bioinformatics #Genomics #NARgenomicsAndBioinformatics 🧪🧬 🖥️ academic.oup.com/nargab/artic...

LinkML: An Open Data Modeling Framework. #DataModel #DataSharing #FAIRdata @gigascience.bsky.social academic.oup.com/gigascience/... linkml.io

An evaluation of computational methods for reconstruction of human viral DNA genomes. #ViralDNAgenomes #MethodBenchmarking @gigascience.bsky.social academic.oup.com/gigascience/...

Harnessing Artificial Intelligence for Genomic Variant Prediction: Advances, Challenges, and Future Directions. #GenomicVariants #VariantInterpretation #AI @gigascience.bsky.social academic.oup.com/gigascience/...

Translating short-form Python exercises to other programming languages using diverse prompting strategies. #LLMs #Programming #Bioinformatics #CodeTranslation @gigascience.bsky.social 🧪🧬 🖥️ academic.oup.com/gigascience/...

A comprehensive survey of genome language models in bioinformatics. #GenomeLanguageModels #gMLs #ModelsReview #Bioinformatics #Genomics #BriefingsInBioinformatics academic.oup.com/bib/article/...

REDAC: RNA-seq Expression Data Analysis Chatbot. #RNAseq #LLMss #DataAnalysis #DifferentialExpression #Sequencing #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...

VST-DAVis: An R shiny Application and web-browser for Spatial Transcriptomics Data Analysis and Visualization. #SpatialTranscriptomics #DataVisualization #RNAseq #Rshiny #Bioinformatics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...

ChromoMapper: a new tool to quickly compare large genome assemblies. #GenomeAssembly #GenomeComparison #Bioinformatics #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️ academic.oup.com/bioinformati...

Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing. #SingleCell #LongRead #Sequencing #scRNAseq #Isoforms #DifferentialExpression #Bioinformaticcs #Genomics 🧪🧬 🖥️ academic.oup.com/bioinformati...

ASTRO: Automated Spatial-Transcriptome whole RNA Output. #SpatialTranscriptomics #RNAseq #FFPE #Genome #Bioinformatics 🧪🧬 🖥️ academic.oup.com/bioinformati...

scSNViz: Visualization and analysis of Cell-Specific expressed SNVs. #SingleCell #scRNAseq #SNVs #DataVisualization #Genomics #Bioinformatics 🧪🧬 🖥️ academic.oup.com/bioinformati...

CiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

Search-and-remove genome editing allows selection of cells by DNA sequence. #GenomeEditing #CellSelection @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

Mapping single-cell diploid chromatin fiber architectures using DAF-seq. #SingleCell #ChromatinFiberArchitecture #Sequencing #Genomics @natbiotech.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.#SpatialTranscriptomics #StandardizedMetrics #DataRepository #BestPractices #OpenSourceSoftware #Genomics #Bioinformatics @natbiotech.nature.com www.nature.com/articles/s41...

Whole-genome landscapes of 1,364 breast cancers. #WGS #BreastCancer #Genomics @nature.com www.nature.com/articles/s41...

Insights into natural neocentromere evolution from a cattle T2T X chromosome. #CattleGenome #T2T #HaplotypeResolvedGenome #Centromeres #Genomics @natcomms.nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

Long-read metagenomics reveals phage dynamics in the human gut microbiome. #GutMicrobiome #Phages #LongReads #Sequencing #Genomics @nature.com 🧪🧬 🖥️ www.nature.com/articles/s41...

A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data. #RNAisoforms #GTEx #LongReads #Sequencing #Genomics #Bioinformatics #BMCgenomics link.springer.com/article/10.1...

Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics link.springer.com/article/10.1...

Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress. #SingleCell #scRNAseq #PlateBasedAssay #10X #Genomics #BMCgenomics link.springer.com/article/10.1...

SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets. #Metagenomics #AlignmentBasedSearches #Genomics #Bioinformatics #BMCbioinformatics link.springer.com/article/10.1...

MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation. #DataSimulation #CancerVariants #SequencingReads #ComputationalModelling #BMCBioinformatics 🧪🧬 🖥️ link.springer.com/article/10.1...

TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. #Microbiome #DataAugmentation #GenerativeModel #BMCbioinformatics 🧪🧬 🖥️ link.springer.com/article/10.1...