Epinoma (EpiAmp) open.substack.com/pub/albertvi...
Bioinformatics Scientist / Next Generation Sequencing, Single Cell and Spatial Biology, Next Generation Proteomics, Liquid Biopsy, SynBio, Compute Acceleration in biotech // http://albertvilella.substack.com
41,350 followers 128,092 following 2,322 posts
view profile on Bluesky
Epinoma (EpiAmp) open.substack.com/pub/albertvi...
This makes the GeneMind FastaSeq S the fastest short read NGS sequencer by some margin able to do PE150 runs.
Next week, Boris Johnson with advice on monogamy. ~AA
I am unsure.
At least we know GP is not shorting the stock based on their comments on #oxfordnano this morning....
Oxford @nanoporetech.com briefly recovering the 200 GBPP mark this morning, now down to 177p.
And each UK biobank participant provides extensive phenotypic data (eg health questionnaires, demographics, proteomics, metabolomics…). So this is a major step in linking genetic variation to diseases and improving diagnostics.
A big challenge in genetics is linking genetic variations to an outcome (disease). Variations can be single DNA base changes, additions or deletions of DNA, which are found in a percentage of the population In this latest paper, they identified ~1.5 billion variations.
To put this into context, the Human Genome Project built a single human genome reference by sequencing DNA from a handful of people. It cost ~$3B and took 13 years. The latest work is nearly half a million people, done at a rate of ~115,000 genomes/year, and a few hundred dollars per genome.
Post by @steveharvey, not on Bluesky, on the UK Biobank latest release of 500k whole genomes: A mind-blowing paper from the UK Biobank last week: whole genome sequencing of 490,640 participants.
Scientists no Longer Find Twitter Professionally Useful, and have Switched to Bluesky url: academic.oup.com/icb/article-...
BBC News - White House defends Robert F Kennedy Jr amid CDC turmoil www.bbc.com/news/article...
Work done at @harvard.edu
CO2 capture from ambient air www.nature.com/articles/s41...
Dave Baker, not on bluesky, on the issues of the 600 cycle kit on Illumina NextSeq 2000 instrument.
No notes
2 hours for SE50, 3 hours for SE100, and 6.8 hours for PE150 runs. The platform offers multiple reagent configuration up to 600bp that support an output range of 20M-80M reads and 2Gb-24Gb.
@genemind, not on Bluesky, have put out an announcement video for their new FastaSeq S small-scale NGS sequencer: 6.8hr for PE150 reads! www.youtube.com/watch?v=QmQj...
Stephane Budel from @Decibio, not on Bluesky, on the Nvidia $NVDA customers/ecosystem
Andy Watson, not on Bluesky, on the #AI revolution vs the #NGS revolution
That ol’ New York-London spread isn’t just for market geeks anymore. 🤡 @joncooper-us.bsky.social
10x Genomics @10xgenomics.bsky.social nearing 6 months high in today's trading session
The new CDC Director has been booted. Chaos is the new norm.
Waymo (Google) is way ahead of Tesla in robotaxi tech. www.thestreet.com/technology/t...
Illumina CEO sees path to stable growth, even as its academic customers face funding uncertainty www.statnews.com/2025/08/26/i... via @statnews.com
Different results than those found in preserved samples www.nature.com/articles/s41...
“Intel warned government intervention could harm the company’s international sales, which make up 76 percent .. It said the company could face .. backlash from investors, employees, customers, suppliers, foreign governments .. as well as possible litigation.” www.washingtonpost.com/technology/2...
GIROUX: “.. Tesla could fall 90% tomorrow, and I wouldn’t buy a share, because it’s just crazy overvalued. Palantir, I wouldn’t buy a share — crazy overvalued. Costco Wholesale —[at a price of] 49 times earnings, Walmart, 37 times — doesn’t make any sense.” @electrek.co electrek.co/2025/08/25/t...
One way of solving the issue...
Sums it up.
The Hunger Games are here.
A new in browser visualization and analysis tool for spatial biology! rakaia.io
From @christophburch, not on #Bluesky, highlights a paper on the mechanisms and roles in anti-agind and disease prevention www.sciencedirect.com/science/arti...
#Xenium Protein is shipping now! Jump right in & discover how same-section spatial RNA & protein unlocks a new world of #immunology & #oncology insights with better characterization of immune & tumor microenvironments, improved data confidence, & more. See for yourself: https://bit.ly/3HmusmS
From @AriWagen and @ishaanganti, not on #Bluesky, on the use of Boltz-2 for protein-ligand binding-affinity prediction. There's a big gap between docking (fast) and FEP (slow); Ishaan worked in this gap on Pareto improvements to MM/GBSA & PBSA.
From @adityatomar.bsky.social, not active on #Bluesky, 🚨 Introducing XQuant, which leverages underutilized compute units to eliminate the memory bottleneck for LLM inference! Paper: arxiv.org/pdf/2508.10395
From @vraserx, not on #Bluesky, Projected AI task length at 80% success.
Publication alert! 🚨 Dr Zhiyu Dai & team use 10x Genomics Xenium to perform high-resolution spatial transcriptomics on fixed frozen mouse lung tissue. This method allows for precise map gene expression, revealing cellular changes in diseases like PH. www.sciepublish.com/article/pii/...
Benagen-ONT (not on #Bluesky) highlights a recent paper on The association between gut microbiota composition and cardiometabolic parameters in healthy adults. bmcmicrobiol.biomedcentral.com/articles/10....
The models from DeepVariant (and friends) have shown how not everything needs to be Illumina reads out there to squeeze all the signal in the data. Another example here for Roche SBX Duplex data, the technology that will become commercially available in 2026.
Zhangyu You, Jiahao Ma, Hongzong Li, Ye-Fan Hu, Jian-Dong Huang: BConformeR: A Conformer Based on Mutual Sampling for Unified Prediction of Continuous and Discontinuous Antibody Binding Sites https://arxiv.org/abs/2508.12029 https://arxiv.org/pdf/2508.12029 https://arxiv.org/html/2508.12029
Unlocking the full potential of Oxford Nanopore reads with NOVOLoci. #Nanopore #Sequencing #GenomeAssembly #HaplotypeAwareAssembler @nanoporetech.com @biorxiv-bioinfo.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...
Subscribe to Rhymes with Haystack for more analyses on Natera and other Cancer Dx companies albertvilella.substack.com
The exact label/CDx language regulators accept—and whether payers restrict coverage to the Signatera assay specifically.
Whether benefit holds across PD-L1 status, nodal stage, neoadjuvant chemo history, and urothelial vs variant histology.
Caveats / what to watch next: Full data (hazard ratios, subgroup effects, toxicity, absolute benefit) and peer-reviewed publication/podium presentation.
Science & trial design: IMvigor011 strengthens the case for ctDNA as a decision and potential surrogate endpoint in peri-operative trials. Anticipate replication attempts in other cancers and more MRD-enriched Phase III designs.
(treat MRD-positive; surveil MRD-negative, with therapy on conversion). Timing and frequency of testing from the protocol (serial testing up to 12 months) will likely inform practice.
Guideline implications: If the full dataset confirms OS/DFS and safety, expect NCCN/ESMO discussions about routine post-op ctDNA testing in MIBC to stratify adjuvant therapy
Roche/Genentech gains a biomarker-driven win in bladder cancer to counter past setbacks, potentially challenging adjuvant nivolumab’s “treat-most” footing with a “treat-the-MRD-positive” alternative. (Nivolumab remains the current adjuvant standard of care broadly.)
Market impact: Natera $NTRA gets a major validation of Signatera’s clinical utility in urology, likely accelerating payer coverage and oncologist adoption across tumor types.
with Signatera positioned as the CDx. Watch for sBLA/Cdx filings and wording tied to Signatera specifically.
Regulatory pathway opens for a biomarker-restricted label and a companion diagnostic. Since IMvigor010 (all-comers) was negative, a positive, MRD-selected Phase III result gives Roche/Genentech a plausible route to seek an adjuvant Tecentriq label limited to Signatera-positive MIBC,
Expect growing use of surveillance with therapy on ctDNA conversion. (Full long-term data still needed.)
MRD-negative patients may safely avoid adjuvant therapy (at least initially). Prior IMvigor011 surveillance analyses showed excellent short-term outcomes for serial Signatera-negative patients, supporting de-escalation for those who remain MRD-negative.
Topline results show statistically significant gains in both DFS and OS for the treated, ctDNA-positive group—evidence that the assay isn’t just prognostic; it’s predictive of immunotherapy benefit.
Clinical practice will tilt toward “test, then treat.” IMvigor011 prospectively tested patients after cystectomy with Signatera and randomized only ctDNA-positive (MRD-positive) patients to atezolizumab vs placebo.
From @genomeweb.bsky.social , Natera announced this week that Signatera-positive patients treated with Genentech's Tecentriq (atezolizumab) in the Phase III IMvigor011 trial experienced statistically significant improvements in both disease-free and overall survival. What are the implications?
For more on RNAseq and scRNA-seq, follow Rhymes with Haystack albertvilella.substack.com
Practical notes & limitations It’s not single-cell; think low-input bulk. Still requires careful nuclei prep and run-on handling; results are complementary to, not a replacement for, steady-state RNA-seq (you’ll often want both).
In stem-cell models, Integrator/INTS11 acts very early in development (as early as embryonic day 2) and likely at transcription initiation, revising prior views.
What they used it for (initial studies) Two Molecular Cell papers from the Sylvester team applied rPRO-seq to the Integrator complex: In neurons, INTS11 emerged as a regulator of genes implicated in neurodevelopmental disorders.
What you measure/learn Active transcription dynamics (initiation, pausing, and elongation) rather than steady-state RNA levels—useful for mechanism and rapid responses
Cleaner libraries: uses P-3′App-DNA adapters and a DBO during ligation to reduce side products/adapter dimers and loss of RNA. Validated on limited samples: the study highlights successful mapping from 5k cells (mouse hematopoietic progenitors and neurons).
What’s new vs. classic PRO-seq Much faster & lower input: libraries in ~12 hours from as few as ~5,000 cells (vs. days and millions of cells for many nascent RNA methods).
rPRO-seq is a streamlined variant of PRO-seq that profiles nascent RNA—what RNA polymerase II is transcribing right now—at (near) nucleotide resolution across promoters, gene bodies, and enhancers. Same core nuclear run-on idea of PRO-seq but compresses the workflow and lowers input requirements.
Exit through a gift shop... LOL
More on Rhymes with Haystack albertvilella.substack.com
While Foundation Medicine remains flat in the number of assays performed, other companies like Tempus AI $TEM and Guardant Health $GH are growing their numbers.
@lesterpoon.bsky.social (not active here since the past 4 months) writes about the change in fate between Foundation Medicine (now part of Roche) and other prominent players in the field of Cancer Diagnostics via NGS:
Short-read technology Ultima Genomics (not on Bluesky) published the technical details of their ppmSeq double-strand sequencing method for highly accurate short-read sequencing.
Post by @leipzig.bsky.social (not active here), on the public github repos of DNA sequencing and multiomics companies, with Oxford @nanoporetech.com on top, followed by Illumina, PacBio, @10xgenomics.bsky.social , Roche and Nanostring (now @brukerspatial.bsky.social )
"Europe doesn't innovate"? Isn't what they say in the good ol' US of A.?
Instead of sanctions he got an invitation from Donald Trump to a summit. www.bbc.co.uk/news/live/c2...
This is an astounding amount of disruption for the chips sector. On Friday, Trump suggested the charge on imported semiconductors could be even higher. “I’m going to have a rate that is going to be 200%, 300%?” Trump said. finance.yahoo.com/news/trump-s...
Ermmm...
Rose Petals
Makes me want to watch 'Coming to America' and the scenes with the cavalcade.
Good.
Maybe we shouldn't be cutting interest rates yet? #econobits
More info at bit.ly/ngsspecs
In #NextGenSequencing news, Illumina has started selling the non-Plus version of their low-throughput MiSeq i100 instrument, which comes at a list price of $49k. This is similar to the MiSeq i100 Plus version but cannot perform 100M runs.
The details of the Tahoe-100M model are on Nima's Bluesky recent posts.
@therealnima.bsky.social Nima Alidoust on the new Virtual Cell Models project for @tahoetherapeutics.bsky.social
Worth noting that the #Galaxy project and the #Bioinformatics community lost one of their main contributors in 2020: James Peter Taylor galaxyproject.org/jxtx/
Nextflow, one of the most prominent workflow managers in #Bioinformatics, continues to grow acceptance in the field. Snakemake also growing, with Galaxy having retreated in the last few years.
Oxford Nanopore chief to step down after two decades on.ft.com/3JrbcF7
Oxford Nanopore co-founder to step down as chief executive www.uktech.news/medtech/oxfo... #UKtech
Seen on another social media platform
Another sign of the deflated biotech environment: Greater Boston's lab availability in the past decade, it's gone up in 2025 Q1 to 30-40% levels. www.boston.com/real-estate/...
Chinese scientists have developed the best shortest-path algorithm in 41 years! A team from Tsinghua University has broken Dijkstra’s “sorting barrier” — the first improvement since 1984. arxiv.org/pdf/2504.17033
Update from @kirk3gaard.bsky.social on Oxford Nanopore dorado basecalling in a variety of NVIDIA cards and Apple Silicon devices. Full table in the link here github.com/Kirk3gaard/2...
Found via @carlquintanilla.bsky.social account, there will now be "Export Tariffs" because... why not?
Oxford Nanopore @nanoporetech.com CEO will leave the company in 2026 after 20 years in the role.
Another 10 year Illumina employee departing the company
Big news in Multi-Omics with @10xgenomics.bsky.social acquiring Scale Biosciences! Read the deets at albertvilella.substack.com
Twist Bio 2025 Q2 results open.substack.com/pub/albertvi...
Is CycloneSeq infringing on ONTs patents? open.substack.com/pub/albertvi...
Illumina 2025 Q2 results open.substack.com/pub/albertvi...