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jsantoyo.bsky.social
Molecular & Computational Biologist at the University of Edinburgh #Genomics #Bioinformatics #Sequencing Head of Edinburgh Genomics 🧬 🖥️ Opinions my own. He/Him Lab: https://genomics.ed.ac.uk/ LinkedIn: https://www.linkedin.com/in/javiersantoyolopez/
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With the new #PacBio Ampli-Fi protocol, you can now sequence genomes with as little as 1 ng of DNA! Paired with our #HiFisequencing technology, it provides a powerful solution for assembling high-quality genomes with exceptional accuracy. bit.ly/3Cidm6R    #AGBT #AGBT2025 #AGBTGM

submitted 3 days ago • 0 comments

Current AIRR-seq methods have limitations. At #AGBT25, Melissa Smith showcases how #PacBio highly accurate long reads provide the resolution needed to fully understand immune responses—paving the way for better immunotherapy and precision genomic medicine. #AGBTGM

submitted 3 days ago • 0 comments

Applying the FAIR Principles to computational workflows. #FAIR #Workflows #Bioinformatics #Genomics #ScientificData 🧬 🖥️ www.nature.com/articles/s41...

submitted 3 days ago • 0 comments

Sequencing by Expansion (SBX) — a novel, high-throughput single-molecule sequencing technology. #SBX #SequencingByExpansion #Nanopores #Sequencing #Genomics #Roche 🧬 🖥️ www.biorxiv.org/content/10.1...

submitted 3 days ago • 0 comments

It seems @BioMath will get a 2x300 on the NovaseqX @illumina #AGBT25

submitted 4 days ago • 1 comment

Comparing the predictors of mutability among healthy human tissues inferred from mutations in single-cell genome data. #MutabilityPredictors #SingleCellGenome #Genetics 🧬 academic.oup.com/genetics/adv...

submitted 5 days ago • 0 comments

Automated plasmid design for marker-free genome editing in budding yeast. #PlasmidDesign #YeastGenomeEditing #G3 🧬 academic.oup.com/g3journal/ad...

submitted 5 days ago • 0 comments

A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition. #UrochloaDecumbensGenome #ChromosomeLevelAssembly #HaplotypeResolved #G3 #Genomics 🧬 academic.oup.com/g3journal/ad...

submitted 5 days ago • 0 comments

A chromosome-level genome assembly of the European green toad (Bufotes viridis). #GreenToaddGenome #ChromosomeLevelAssembly #G3 🧬 academic.oup.com/g3journal/ad...

submitted 5 days ago • 0 comments

scHiGex: predicting single-cell gene expression based on single-cell Hi-C data. #SingleCell #GeneExpression #HiC #NARGenomicsAndBioinformatics #Genomics 🧬 🖥️ academic.oup.com/nargab/artic...

submitted 6 days ago • 0 comments

Small but mitey: a gapless telomere-to-telomere assembly of an unidentified mite with a streamlined genome. #EriophyoidMiteGenome #ChromosomeLevelAssembly #Genomics @genomebiolevol.bsky.social academic.oup.com/gbe/advance-...

submitted 6 days ago • 0 comments

Biodepot Launcher: an app to install, manage and launch bioinformatics workflows. #Bioinformatics #Workflows @gigabytejournal.bsky.social 🧬 🖥️ gigabytejournal.com/articles/146

submitted 6 days ago • 0 comments

SqueezeCall: nanopore basecalling using a Squeezeformer network. #Nanopore #Basecalling #LongRead #Sequencing #Bioinformatics @nanoporetech.com @gigabytejournal.bsky.social gigabytejournal.com/articles/148

submitted 6 days ago • 0 comments

xRead: a coverage-guided approach for scalable construction of read overlapping graph. #LongRead #Sequencing #GenomeAssembly #OverlappingGraphs #Bioinformatics @gigascience.bsky.social academic.oup.com/gigascience/...

submitted 6 days ago • 0 comments

The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus. #FloweringCherry #ChromosomeLevelAssembly #Genomics @gigascience.bsky.social academic.oup.com/gigascience/...

submitted 6 days ago • 0 comments

ELLIPSIS: Robust quantification of splicing in scRNA-seq. #Splicing #RNAseq #Bioinformatics academic.oup.com/bioinformati...

submitted 7 days ago • 0 comments

HTSinfer: Inferring metadata from bulk illumina RNA-Seq libraries. #RNAseq #Transcriptomics #Sequencing #Bioinformatics academic.oup.com/bioinformati...

submitted 7 days ago • 0 comments

Roche’s Fantasy Sequencer Slowly Turning Into a Fantastic Reality #sequencing #nanopore #genomics sandiegomics.com/roches-fanta...

submitted 8 days ago • 1 comment

PRISM 2025 is almost here! Join the brightest minds in genomics to explore cutting-edge tools, keynotes, and innovative technologies. Don’t miss your chance to connect, learn, and help shape the future of genomics. Secure your place today: bit.ly/3CF86KZ #PacBioPRISM #PacBio

submitted 7 days ago • 0 comments

🧬Nanopore sequencing enables direct and accurate detection of 5-methylcytosine and 5- hydroxymethylcytosine, providing a simultaneous readout of modification states on both strands of DNA from a single molecule. www.nature.com/articles/s42...

submitted 7 days ago • 0 comments

3 wks left for our funding goal! TY again to Plant Biology Exploratory Research Microgrant for supporting our project to get HS students to use Nanopore Sequencing in the classroom to study plant microbiomes! If you would like to donate: shorturl.at/8i4tG

submitted 7 days ago • 1 comment

Illumina unveils first-of-its-kind spatial transcriptomics technology. #Illumina #SpatialTranscriptomics www.illumina.com/company/news...

submitted 7 days ago • 0 comments

Roche Plans 2026 Launch for SBX Nanopore Sequencing Platform. #Roche #SBX #Sequencing #Nanopore @genomeweb.bsky.social www.genomeweb.com/sequencing/r...

submitted 7 days ago • 0 comments

A sneak peek at Roche’s nanopore sequencer. Really makes me wish I was going to #AGBT this year! #genomics #nanopore #sequencing sandiegomics.com/roche-has-en...

submitted 12 days ago • 3 comments

Kudos to the #EdinburghGenomics team for delivering such a fantastic #NGS library prep training course! 👏 🧬 And a huge thanks to New England Biolabs 🦋, especially Max Fritsch and Michael Skelly, for their support in making this training possible! 🎉

submitted 15 days ago • 0 comments

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

submitted 17 days ago • 0 comments

An ecosystem for producing and sharing metadata within the web of FAIR Data. #SharingMetadata #FAIRdata @gigascience.bsky.social 🧬 🖥️ academic.oup.com/gigascience/...

submitted 17 days ago • 0 comments

Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colors. #PontederiaCordataGenome #ChromosomeLevelAssembly #PlantGenomics #DNAresearch academic.oup.com/dnaresearch/...

submitted 17 days ago • 0 comments

Last week, we hosted a fantastic seminar with #Illumina on single-cell analysis! Great discussions, insightful questions, and plenty of inspiration for future research. Thanks to everyone who joined, and especially to Laura and Pauline from #illumina ! #Genomics #SingleCell

submitted 17 days ago • 0 comments

And @pacbio.bsky.social updated the ultralow protocol based on our results. Checkout www.pacb.com/blog/new-amp...

submitted 17 days ago • 0 comments

In our latest @biorxiv-genomic.bsky.social preprint, we describe our approach to use PacBio HiFi reads to detect somatic TE transposition -- good enough to detect rare events that are present in only single cells. Led by Andrea Movilli. #plantscience www.biorxiv.org/content/10.1...

submitted 18 days ago • 4 comments

cfDNA UniFlow: a unified preprocessing pipeline for cell-free DNA data from liquid biopsies. #cfDNA #DataProcessing #SnakeMake @gigascience.bsky.social 🧬 academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis. #AsianIcefishGenome #ChromosomeLevelAssembly @gigascience.bsky.social academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq. #GalaxyTraining #SingleCell #BioinformaticsTraining #Bioinformatics @gigascience.bsky.social 🧬 🖥️ academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks. #LianchengDucksGenome #ChromosomeLevelAssembly #PlumagePhenotype @gigascience.bsky.social academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

Data reuse in agricultural genomics research: challenges and recommendations. #AgriculturalGenomics #GenomicsDataReuse @gigascience.bsky.social academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity. #EurasianMinnowGenome #ChromosomeLevelAssembly @gigascience.bsky.social 🧬 academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

Micromix: web infrastructure for visualizing and remixing microbial ‘omics data. #MicrobialOmicsData #DataVisualization @gigascience.bsky.social academic.oup.com/gigascience/...

submitted 18 days ago • 0 comments

Single-cell and spatial transcriptomics illuminate bat immunity and barrier tissue evolution. #BatImmunity #SingleCell #Transcriptomics #Genomics #MolecularBiologyEvolution 🧬 academic.oup.com/mbe/advance-...

submitted 18 days ago • 0 comments

Genome assembly of a living fossil, the Atlantic horseshoe crab Limulus polyphemus, reveals lineage-specific whole genome duplications, transposable element-based centromeres and a ZW sex chromosome system. #AtlanticHorseshoeCrabGenome #ChromosomeLevelAssembly 🧬 academic.oup.com/mbe/advance-...

submitted 18 days ago • 0 comments

Homologous recombination shapes the architecture and evolution of bacterial genomes. #HomologousRecombination #BacterialGenomes @narjournal.bsky.social 🧬 academic.oup.com/nar/advance-...

submitted 18 days ago • 0 comments

OrthoBrowser: Gene Family Analysis and Visualization. #GeneFamilies #OrthologousGenesVisualization #Bioinformatics @bioinfoadv.bsky.social 🧬 🖥️ academic.oup.com/bioinformati...

submitted 18 days ago • 0 comments

Boosting GPT Models for Genomics Analysis: Generating Trusted Genetic Variant Annotations and Interpretations through RAG and fine-tuning. #GPT #LLMs #Genomics #GeneticVariants @bioinfoadv.bsky.social 🧬 🖥️ academic.oup.com/bioinformati...

submitted 18 days ago • 0 comments

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications. #GeneDuplications #R #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

submitted 18 days ago • 0 comments

tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. #TelomericRepeats #AssembledGenomces #LongReads #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

submitted 18 days ago • 1 comment

GenomeDecoder: Inferring Segmental Duplica-tions in Highly-Repetitive Genomic Regions. #GenomicDuplications #RepetitiveRegions #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

submitted 18 days ago • 0 comments

Embed-Search-Align: DNA Sequence Alignment using Transformer models. #DNAalignment #TransformerModels #LLMs #LargeLanguageModels #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

submitted 18 days ago • 0 comments

Check out our new preprint describing CiFi - a method that couples 3C and PacBio HiFi sequencing with low input requirements. We apply it to human GM12878 to better characterize chromatin across repetitive regions, as well as single insect samples (a mosquito and a Mediterranean fruit fly).

submitted 23 days ago • 0 comments

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline. #StructuralVariants #GenomeAssembly #Bioinformatics #Genomics @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

submitted 20 days ago • 0 comments

It’s a privilege to announce Solve-RD’s latest manuscript based on years of work: “Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses” www.nature.com/articles/s41... A thread (1/n)

submitted 42 days ago • 1 comment