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Billy

@williamrowell.dev
407 followers 1.4K following 4 posts

Geneticist, ersatz programmer, data nerd, comedy lover, and recovering academic. Trying to make it easier for people to analyze and interpret biological data. Bioinformatics Scientist @PacBio.bsky.social

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Reposted by Billy
Matt Holt @holtjma.bsky.social · 27/08/2026
Our article introducing Aardvark for variant benchmarking is now published in Genome Biology! “Aardvark: sifting through differences in a mound of variants” DOI: doi.org/10.1186/s130... GitHub: github.com/PacificBiosc... Follow along for some highlights… 1/N
doi.org
Client Challenge
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PacBio @pacbio.bsky.social · 09/07/2026
Missed PRISM in-person? PacBio PRISM 2026 presentations are now streaming on-demand! Get complete visibility into the methodologies and datasets shared at the bench on your own schedule. Stream here to fuel your next discovery: bit.ly/4f5FOs0 (Note: PRISM Fukuoka tracks coming soon!)
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Dare Obasanjo @carnage4life.bsky.social · 13/06/2026
AI is a force multiplier, but it’s uneven. One person becomes 5x more productive while another becomes 0.5x because their AI slop creates work for everyone else. The challenge will be how to test for this in interviews and reflecting it in performance reviews as people’s impact diverges.
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PacBio @pacbio.bsky.social · 26/06/2026
A new Nature Genetics piece from @radboudumc.bsky.social outlines Near-Perfect Genome Sequencing (NPGS): a framework combining long-reads, diploid assembly, pangenomes, and AI to shift from fragmented testing to a single comprehensive genomic assay. Read more here: go.nature.com/4ey5YF0 #PacBio
go.nature.com
Near-perfect genome sequencing in medical genetics - Nature Genetics
This Perspective introduces near-perfect genome sequencing, which encompasses diploid genome assembly, pangenome references and artificial intelligence-driven variant interpretation, and proposes a ro...
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PacBio @pacbio.bsky.social · 15/06/2026
Happening now at #ESHG2026: Nina Gonzaludo is at poster P20.155.E talking about an accelerated HiFi whole genome workflow for comprehensive, rapid long-read sequencing. She’s here until 13:45. Come stop by, ask questions, and chat with #PacBio!
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PacBio @pacbio.bsky.social · 14/06/2026
Next up, Adam Ameur shares that long-read WGS efforts are ongoing in Sweden for population genomics and clinical diagnostics. They bridge these projects by using a joint analysis framework and shared variant databases. #ESHG2026 #PacBio #ESHG
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PacBio @pacbio.bsky.social · 08/06/2026
Now published in AJHG: the HiFi Solves EMEA Consortium shows that a single PacBio HiFi whole genome, combined with Paraphase, can resolve clinically relevant variants in highly homologous genes and pseudogenes. Read the study: bit.ly/4v0TdZq #ClinicalGenomics #PacBio #HiFiSolves
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PacBio @pacbio.bsky.social · 04/06/2026
PacBio is proud to sponsor Big Slick 2026, joining an incredible community dedicated to advancing pediatric care and research at Children’s Mercy Kansas City. This partnership reflects our deep commitment to advancing genomics in rare disease and cancer research to serve patients and families.
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PacBio @pacbio.bsky.social · 26/05/2026
SPRQ-Nx chemistry is now shipping worldwide, bringing sub-$300 HiFi genomes to the Revio platform! This global rollout cuts sequencing costs by 30%, making it easier than ever to scale high-throughput workflows Full press release here: bit.ly/49HwmcL #SPRQNx #PacBio #HiFisequencing #Revio
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Alex Elizabeth Byrne McMillan @undeniablyalex.bsky.social · 23/05/2026
YOU’RE LISTENING TO SISYPHUS FM, THE HOME OF NON-STOP ROCK
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EpiCypher @epicypher.bsky.social · 21/04/2026
We are at PacBio PRISM 2026 and excited to connect with the community. Stop by Poster #13 on April 22, 6 to 9 PM PT to see how Fiber-seq LRS enables simultaneous chromatin architecture and DNA methylation profiling. What would you explore with a multiomic long-read assay? ow.ly/ImI850YJ1z3
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PacBio @pacbio.bsky.social · 21/04/2026
Happening now at #AACR26! Visit #PacBio Poster 5510 to see Zev Kronenberg present a new way to hunt for microsatellite instability in long-read data. See how the "Owl" tool is advancing bioinformatics workflows for MSI detection. 📍 Section 4, Board 15 ⏰ Until 5 PM
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Fulcrum Genomics @fulcrumgenomics.com · 21/04/2026
Deep QC should run on every sequencing dataset. In a new post, Fulcrum co-founder @tfenne.bsky.social explains why he built Riker, a modern successor to Picard designed to make rich sequencing QC fast enough to run every time. Blog: shorturl.at/oUTXk Repo: github.com/fulcrumgenom...
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PacBio @pacbio.bsky.social · 26/03/2026
Successful AI models are built on data that is high-quality, complete, and rich in biological context. Basecamp Research is using PacBio HiFi sequencing to move beyond fragmented snapshots and build a richer map of biology. Read the blog here: bit.ly/4svvj6N #PacBio #HiFisequencing #Genomics
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How HiFi metagenomic sequencing is powering AI-driven discovery with Basecamp Research - PacBio
Basecamp Research’s recent selection of PacBio HiFi sequencing to support its Trillion Gene Atlas initiative highlights an important shift in biological AI.
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PacBio @pacbio.bsky.social · 30/03/2026
Long-read sequencing is reshaping our understanding of human genetic variation. Register to see how population-scale #PacBio HiFi WGS uncovers previously hidden structural variants driving disease associations at scale. Sign up for the webinar: bit.ly/4uUclIz #HiFisequencing
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PacBio @pacbio.bsky.social · 12/03/2026
New preprint: Hunting for MSI in long-read data with Owl 🦉 Owl is an MSI caller purpose-built for #PacBio HiFi and integrated into our somatic workflow. Data: • Low baseline (~1–5%) • 15–18% MSI-H instability • Links GGAA repeats to EWS::FLI1 fusion Preprint here: bit.ly/4beWECU
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Billy @williamrowell.dev · 12/03/2026
See you at P165 in 16 minutes. #ACMGmtg26
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PacBio @pacbio.bsky.social · 12/03/2026
Happening today at 12:15 PM! Join Matt Holt at #ACMGMtg26 for his talk on how #PacBio HiFi sequencing enables the discovery of pharmacogenomic haplotypes. 📍 Platform C ⏰ 12:15 PM Not attending? Learn more about StarPhase for HiFi PGx in this explainer video: bit.ly/4b4ACUA
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PacBio @pacbio.bsky.social · 02/03/2026
Rare Disease Month reminded us why we show up for families and the science driving answers. We’re not stopping there. Pre-registration is open for Seq It Forward: Run for Rare 5K in June, supporting iHope and rare disease families. Register: bit.ly/4u33kwB #SeqItForward5K #PacBio #RareDisease #5K
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PacBio @pacbio.bsky.social · 02/03/2026
Want epigenetic information automatically included in your sequencing runs? HiFi sequencing detects 5mC and 6mA directly from native DNA and combines multiple passes of the same molecule to generate long reads with greater than 99.9% accuracy. See how: bit.ly/3YSPBdo #PacBio #HiFisequencing
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PacBio @pacbio.bsky.social · 24/02/2026
HiFi sequencing can reveal rare and complex variants, but interpretation requires diverse background datasets. PacBio and DNAstack are supporting the first global federated dataset of HiFi whole genomes through the HiFi Solves Global Consortium. Details: bit.ly/4kQ0bMk #WeCareForRare
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Chris Saunders @ctsa.bsky.social · 20/02/2026
By both improving accuracy and unifying assembly-based and mapping-based inferences, the portello approach has the potential to substantially improve analysis for rare-disease and other WGS applications. See our new preprint here: doi.org/10.64898/202...
doi.org
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Chris Saunders @ctsa.bsky.social · 20/02/2026
What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)
Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.
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PacBio @pacbio.bsky.social · 09/02/2026
You’ve heard the buzz around a more affordable long-read genome with SPRQ-Nx. Now we’re letting the data do the talking. Newly published WGS datasets across human, plant, and animal genomes show you don’t need to compromise data quality for affordability. Explore the data: bit.ly/3O7BAGv #PacBio
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How SPRQ-Nx enables affordable long-read whole genome sequencing without added complexity - PacBio
With the introduction of SPRQ-Nx, HiFi sequencing has now become the most affordable long-read sequencing technology to date.
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PacBio @pacbio.bsky.social · 24/04/2025
A first in human genomics: a 4-generation pedigree reference, now in Nature. Built with #PacBio HiFi, it maps de novo mutation rates, reveals paternal bias, and captures high mutation rates in tandem repeats—even in Y and repeat-rich regions. Paper here: go.nature.com/4lGMPlP #TheresHiFiForThat
go.nature.com
Human de novo mutation rates from a four-generation pedigree reference - Nature
Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set t...
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inversion.bsky.social @inversion.bsky.social · 23/04/2025
Long-read sequencing of large pedigrees is an ideal way to map all classes of denovo mutations! A collaboration between University of Utah, University of Washington, and PacBio. Glad to be a part of this project 👏 www.nature.com/articles/s41...
nature.com
Human de novo mutation rates from a four-generation pedigree reference - Nature
Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set t...
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Jon Belyeu @jonbelyeu.bsky.social · 22/04/2025
I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: www.biorxiv.org/content/10.1.... Here’s a summary of the results:
biorxiv.org
Complex structural variant visualization with SVTopo
Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...
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Austin @tenantfromhell.bsky.social · 12/04/2025
7500 research staff at the University of California filed a petition to form a union with UAW today at the Public Employment Relations Board in Oakland. While the work is really just beginning, we have had thousands of conversations to get here. We're going to win ✊
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Chris Saunders @ctsa.bsky.social · 10/04/2025
Also worth noting that a substantial new sawfish CNV integration feature will be coming as a preview release on GitHub later this month, which I’ll also be detailing as a poster presentation at ESHG. Looking forward to sharing more about this soon.
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ESHG Conference 2025
ESHG 2022 COVID-19 Information Discover the ESHG 2025 - Hybrid Conference programme. We are proud to announce the confirmed 2025 speakers. Stay updated on matters related to the ESHG soc...
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Chris Saunders @ctsa.bsky.social · 10/04/2025
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n) doi.org/10.1093/bioi...
doi.org
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling
AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu
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Colette Delawalla, PhD @cdelawalla.bsky.social · 09/02/2025
Get in Dorks, we are going protesting. STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS. More information to come.
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medRxivpreprint @medrxivpreprint.bsky.social · 11/02/2025
Long-read sequencing resolves the clinically relevant CYP21A2 locus, supporting a new clinical test for Congenital Adrenal Hyperplasia www.medrxiv.org/content/10.1101/202…
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Christian Gilissen @christiangilissen.bsky.social · 13/01/2025
Have a look at our latest work on PacBio LRS showing its potential as a single technology to accurately identify all types of clinically relevant variants. www.sciencedirect.com/science/arti...
sciencedirect.com
HiFi long-read genomes for difficult-to-detect, clinically relevant variants
Clinical short-read exome and genome sequencing approaches have positively impacted diagnostic testing for rare diseases. Yet, technical limitations a…
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Matt Holt @holtjma.bsky.social · 11/12/2024
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N Pre-print: doi.org/10.1101/2024... Repo: github.com/PacificBiosc...
github.com
GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
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Sarah Doom @sarahdoom.bsky.social · 23/11/2024
ICYMI my poster at #AMPath24, I'm sharing it here. Folks interested in long reads to resolve complex loci like repeat expansions relevant to neuro disease and carrier screening, check it out! @pacbio.bsky.social collab with @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social and many others
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Sarah Doom @sarahdoom.bsky.social · 23/11/2024
@sedlazeck.bsky.social AMPath24 talk about long reads highlighting TRGT tool by @egor-dolzhenko.bsky.social and @guilhermesena1.bsky.social and others for HiFi sequencing by @pacbio.bsky.social
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Armin Töpfer @armintoepfer.com · 15/11/2024
If you are a #C++ developer, either have a #bioinformatics or #CUDA background, and take pride in your engineering and/or algorithmic skills, I'm looking for a Senior Staff Engineer at @pacbio.bsky.social. You can work remotely. Feel free to ping me or go to pacb.com/careers Please spread the word
pacb.com
Careers - PacBio
PacBio is always looking to add the best and brightest minds to our world-class company. Our highly interdisciplinary team is best suited for individuals who are creative, forward thinking, and who ap...
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PacBio @pacbio.bsky.social · 13/11/2024
We can see there's already excitement for Vega on Bluesky. ✨ What do you think about the first #PacBio HiFi benchtop system?
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Armin Töpfer @armintoepfer.com · 12/11/2024
I think I'll try hiring @pacbio.bsky.social a #bioinformatics engineer with modern C++ skills. Interested? You can be remote in the US, UK, Germany, or Switzerland. Goals: implement crazy algorithms for on-instrument sequence data processing and improve existing solutions. Contact me.Spread the word
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Better Things Are Possible @internethippo.bsky.social · 09/02/2024
Waking up in my own normal body and freaking out like the guy who woke up as a bug
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Matt Holt @holtjma.bsky.social · 08/11/2024
My poster on long read pharmacogenomics with #PacBio HiFi is up for today at #ASHG24. Ping me on here if you want to meet before the poster session!
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Dan Portik @dportik.bsky.social · 30/10/2024
A new #metagenomic binning algorithm has appeared: TaxVAMB Looks like it may outperform SemiBin2 for @PacBio HiFi datasets (human gut). I use the long-read mode of SemiBin2 in the HiFi-MAG-Pipeline and it works great. Time to run some benchmarks! www.biorxiv.org/content/10.1...
biorxiv.org
Binning meets taxonomy: TaxVAMB improves metagenome binning using bi-modal variational autoencoder
A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. Currently, unsupervised and self-supervised deep learning based methods using co-abun...
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Dan Portik @dportik.bsky.social · 29/10/2024
The new #PacBio SPRQ chemistry for the Revio system has some big advantages for micro and #metagenomics: - Input requirements drop from 2 micrograms to 500 nanograms (per SMRT cell) - 30% increase yield per cell (~90Gb -> 120Gb) www.pacb.com/press_releas...
pacb.com
PacBio Announces SPRQ Chemistry for Revio Sequencing Systems, a Major Advance Reducing the Cost of a HiFi Human Genome to less than $500 - PacBio
New long-read sequencing chemistry reduces DNA input requirements four-fold, enables a 33% increase in data output per SMRT Cell, improves methylation calling, and expands support for multiomics Trans...
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Matt Holt @holtjma.bsky.social · 28/10/2024
Interested in long-read pharmacogenomics? Then I have some exciting things to show you at #ASHG24... Looking forward to next week in Denver! #PacBio #PGx
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Matt Holt @holtjma.bsky.social · 15/03/2024
Giulia Del Gobbo #ACMGMtg24 on lessons learned with Care4Rare using #PacBio #HiFi: need platform matched controls, discovering overlooked variants, phasing aid in interpretation, need specialized STR tools, and higher resolution of structural variants.
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Matt Holt @holtjma.bsky.social · 15/03/2024
Emily Farrow #ACMGMtg24 on "Unveiling the power of #HiFi genome sequencing: one test to rule them all?" Clinical validation of #PacBio Revio; overall high validation accuracy; 26/50 cases with solves; average 25 day TAT; combination evaluation of SNV, CNV, SV, and methylation.
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Matt Holt @holtjma.bsky.social · 09/02/2024
We just added a methylation segmentation algorithm for PacBio HiFi data to our MethBat tooling (beta). If you are interested in trying it out, we would greatly appreciate any feedback on the performance and possible extensions! Release here: github.com/PacificBiosc...
github.com
Release MethBat v0.9.0 · PacificBiosciences/MethBat
Changes Adds a new segmentation mode based on Circular Binary Segmentation. This mode generates a BED file of methylated, unmethylated, and ASM regions. The mode is executed with methbat segment ....
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Matt Holt @holtjma.bsky.social · 26/01/2024
Excited to announce that our accompanying paper on HiPhase has been published today, I'll highlight some of the additions in this thread! #PacBio #HiFi “HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing”: doi.org/10.1093/bioi...
doi.org
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Billy @williamrowell.dev · 13/01/2024
Listening to _Four Thousand Weeks_ at 2x speed to save time.
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John Greally @greally.bsky.social · 09/11/2023
With our outstanding partners at @GeneDx , @PacBio and @GoogleHealth, we will take on the biggest genomic diagnostic challenge of all, diagnosing rare diseases in individuals who are not only extensively tested already, but are from genetic ancestries ignored by medical genomics
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