There's a new paper from the labs of Qing Nie, Fabian Theis, and Xiangmin Xu UC Irvine highlighting that "collaborative updating and accessibility are required ... [for] practical [single-cell] atlas updating": biorxiv.org/content/10.110… biorxiv.org/content/10.110…

I suspect this is a huge problem, that is being greatly underestimated / ignored.

Detecting rare subpopulations of M. tuberculosis using PacBio Onso (SBB) short read platform. Detected mutations from 0.01 – 0.001% frequency at 100K depth or >0.1% frequency at 20K depth, comparable to SBS with SMOR error correction. bmcgenomics.biomedcentral.com/articles/10.11…

#bioinformatics peeps! Version 0.6.1 of oarfish—our tool for transcript quantification from long-read #RNAseq reads—is out! It brings some cool new features & quality-of-life improvements. Check it out in the link, but here’s my favorite new feature! 1/ github.com/COMBINE-lab/oa…

What's your vision for the future of #genomics? 🧬 Tell us in 5 words or less, and your response could be featured in a special #ASHG24 video. Plus, it might earn you a prize! Share your thoughts and help shape the future. T&Cs apply: bit.ly/3O3AfhD #PacBio

BREAKING: U.S. Faces Unprecedented COVID-19 Surge with 1.2 Million New Cases Daily As of August 26, 2024, the U.S. is grappling with an alarming surge in COVID-19 infections, with a record-breaking 1.2 million new cases reported each day. 1 in 41 people is currently infected.

We've updated the PacBio Kinnex single-cell RNA SMRT Link v13.1 troubleshooting guide to cover what are the metrics you should expect and how to analyze not officially tested kits such as GEM-X. #bioinformatics pacb.com/wp-content/upl…

We released a new version of StarPhase that includes a new debug output for inspecting CYP2D6 alignments against the identified consensus haplotypes. I have found this useful for identifying reads that span multiple consensus components (e.g. a duplication). Example *4x2/*5:

Join the #Kinnex community and be part of the #RNA revolution! Unlock cleaner, higher-quality data with full-length RNA info, enabling isoform discovery, cell type-specific detection, and metagenomic identification. Discover more: bit.ly/3Z3DafU #PacBio

All compbiologists and wet-lab biologists working with compbio folks should print this & paste it on their doors and monitors. Too many folks think comp analysis is just a way to create pretty figs for a decorative ad for the data. Rigor is paramount. There should no compromise.

I used to call myself an extroverted introvert but maybe I’m an ambivert?! 🤔

Identifying structural variations in gut phagenome using PacBio long-reads (+improved assembled ref genome) found abundant horizontal gene transfer between phage-bacteria and other microorganisms. SVs were called using four callers: pbsv, cuteSV, Sniffles, SVIM.

My coworkers are funny XDDD PacBio

BREAKING: Up to 50% of Americans Expected to Be Infected in Current COVID-19 Wave. The current COVID-19 wave in the U.S. has resulted in approximately 24.3% of Americans being infected since May 2, and around 19.3% since the surge began on June 23.

The PacBio SMRT Conserve grant is open! Win free sequencing for your efforts to sequence an endangered vertebrate species! Submission ends Sept 30th. programs.pacb.com/l/1652/2024-08…

Use of 26 PacBio Iso-Seq cell line data to build a RNA foundation model LoRNA to predict transcriptome architecture, including isoform abundance, exonic structures, and variant pathogenicity. #bioinformatics biorxiv.org/content/10.110…

Kicking off the PacBio NYC event ❤️❤️❤️❤️

Sebra: PacBio Iso-Seq in pre-implantation embryo find novel isoforms rich in antisense and intergenic. Conserved in primates, suggesting driving recent evolution. pubmed.ncbi.nlm.nih.gov/37903791/

Knowles: use of PacBio Kinnex bulk RNA-Seq data to validate isoform knockdown in Cas13d system biorxiv.org/content/10.110…

We’re proud to announce the HiFi Solves Sub-fertility Consortium, an innovative collaboration spanning leading centers across the Asia-Pacific region to advance fertility research with the goal of revolutionizing care for millions affected by subfertility and recurrent pregnancy