Javier Santoyo

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…

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

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

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

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...

Universal noninvasive prenatal diagnosis for monogenic disorders using cell-free plasma DNA. #cfDNA #MonogenicDisorders #PrenatalDiagnosis #GenomeMedicine
link.springer.com/article/10.1...