@posit.co Positron Server is now free for academic JupyterHub with a teaching license. Students get a full data science IDE (Python/R, debugger, data viewer) in-browser, no install needed. blog.jupyter.org/positron-ser...

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

A new release of mcptools, an #rstats package implementing the Model Context Protocol, is now on CRAN! It's a patch release with several security-oriented fixes. github.com/posit-dev/mc...

Release mcptools 1.0.1 · posit-dev/mcptools

This release includes several security-oriented fixes, in addition to a couple quality of life improvements for multi-user and multi-session workspaces: The server now chooses its R session at too...

github.com

Exciting news for the RNA research community! The Human RNome Project has been launched: a global effort to map all human RNAs and their chemical modifications. Proud to support it and contribute to the article in Genome Biology doi.org/10.1186/s130... #RNA #bioinformatics #RNAstructure #modomics

Unlocking the regulatory code of RNA: launching the Human RNome Project - Genome Biology

The human RNome, the complete set of RNA molecules in human cells, arises through complex processing and includes diverse molecular species. While research traditionally focuses on four canonical nucl...

genomebiology.biomedcentral.com

1/ I'm excited to share that we're launching NECB 2026, the inaugural New England Computational Biology Symposium. Oct 1-2 at Microsoft Research New England, Cambridge. Two days of keynotes,talks, and posters to bring our community together across institutions.Space is limited. newenglandcompbio.org

Admirable clarity @science.org

David Roberts@volts.wtf · 2w ago

Whew, the editors of @science.org are getting real.

Region-Level Design and Analysis of CRISPR Perturbation Screens with FRACTEL https://www.biorxiv.org/content/10.64898/2026.07.06.736794v1

Silhouette score is unsuitable as a metric for single-cell data integration go.nature.com/4fcQzZr rdcu.be/fpOKP

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology

Silhouette score is unsuitable as a metric for single-cell data integration.

go.nature.com

Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg

Efficient evidence-based genome annotation with EviAnn

Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.

rdcu.be

Last thing I did before vacation was submit a public comment on the destructive OMB proposal through @standupforscience.net and e-mail my reps again! Comments close July 13th

New preprint with @kanishkadey.bsky.social's group. We asked: can you connect what happens to beta cells under nutrient stress in a dish to T2D genetics and dietary patterns in ~46K people? We built a "dish-to-biobank" framework to find out. #StemCells #UKBiobank www.biorxiv.org/content/10.6...

A dish-to-biobank framework links β-cell nutrient-stress programs to genetic and dietary risk for Type 2 Diabetes

Type 2 diabetes (T2D) arises from genetic susceptibility and chronic metabolic stress, but whether these converge on shared molecular programs in human populations remains unclear. Here, we develop a ...

biorxiv.org

Air 0.10.0 is out now! - Enforce `<-` or `=` throughout your #rstats code (only one of these is correct though 😉) - Tighter Positron and RStudio integration - pre-commit / prek support - stdin support - Install with uv, mise, or pixi Read all about it! opensource.posit.co/blog/2026-06...

Air 0.10.0

Air 0.10.0 is here! This release rounds up everything new since 0.8.2: a new `assignment-style` option, tighter Positron and RStudio integrations, installation via uv and friends, pre-commit support, ...

opensource.posit.co

📣 Postdoc opportunity in the StatDivLab (aka the Willis Lab) at the University of Washington. Amy Willis is doing the some of the most exciting/impactful work in microbiome biostats right now. Highly recommend. Job ad below👇 apply.interfolio.com/188571

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

First week back to regular scheduled work has been crazy, but I want to once again thank the organisers for selecting my talk and everyone who came to the session!

"Program managers would normally rush to inform potential and current grantees about such dramatic changes. But the memo tells program managers to keep their mouths shut. 'This information is highly confidential...Please do not communicate anything to PIs.'” www.science.org/content/arti...

Exclusive: NSF slashes research programs to support new tech initiative, insiders say

Unexpected shift in funds has meant sharp drop in grants this fiscal year

science.org

🧩 Talk Spotlight: @hadley.nz shares 20 years of tidyverse lessons; data grammar that shaped how we think about wrangling. Plus, his take on AI's impact on future data science workflows 🚀 #SciPy2026 🔗 scipy2026.scipy.org

Computational analysis of DNA methylation from long-read sequencing go.nature.com/3RqrPlc #Review by @yileifu.bsky.social, @timp0.bsky.social & @sedlazeck.bsky.social @bcmhouston.bsky.social @jhu.edu

Computational analysis of DNA methylation from long-read sequencing - Nature Reviews Genetics

Long-read sequencing technologies can directly profile methylation modifications across the genome. In this Review, Fu et al. overview the long-read computational tools to identify and compare methyla...

go.nature.com

Happy to share that this work led by @mihkeljesse.bsky.social has now been published at PLOS Genetics! journals.plos.org/plosgenetics... A couple of thoughts below.

Ultra-fast genetic colocalisation across millions of association signals

Author summary Over 90% of human genetic variants associated with human traits and diseases lie in non-coding regions of the genome, making it difficult to interpret the mechanisms by which these vari...

journals.plos.org

@mihkeljesse.bsky.social · 11mo ago

After 1.5 years of work in @kauralasoo.bsky.social’s lab, we finally published my preprint! We introduce gpu-coloc, a GPU-accelerated implementation of coloc, show comparability to CLPP and aim to provide practical guidelines. Now accessible on BioRxiv: www.biorxiv.org/content/10.1...

After 1.5 years of work in @kauralasoo.bsky.social’s lab, we finally published my preprint! We introduce gpu-coloc, a GPU-accelerated implementation of coloc, show comparability to CLPP and aim to provide practical guidelines. Now accessible on BioRxiv: www.biorxiv.org/content/10.1...

Ultra-fast genetic colocalisation across millions of traits

Colocalisation is a powerful approach to assess if two genetic association signals are likely to share a causal variant. However, association analyses in large biobanks and molecular quantitative trai...

biorxiv.org

Aggregating many experiments into one zero-shot protein language model score obscures that current models cannot meaningfully rank a set of fit mutations or prioritize new-to-nature functions @clauswilke.com www.biorxiv.org/content/10.6...

Ensembl 116 + Ensembl Genomes 63 are out! Explore new pig, cattle, and oat genomes, updated alignments and new VEP plugins It’s a milestone! Our last on the current platform. New data from here on is via beta.ensembl.org More info on our blog: zurl.co/MrJ2A

If you don't know David Hockney, check out his work. I especially love the winter -> spring transitions with a focus on light

Jim Parrett 🍁@jymn.bsky.social · 2mo ago

David Hockney (July 9 1937 - June 11, 2026)

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

Having a visual component when you are teaching a new concept is always something I value. I went back and redid some old diagrams as animations This website has all mp4, gif and code for you to use yourself in slides of websites! emilhvitfeldt.github.io/tidy-animati... #rstats #quarto #dataBS

Very excited to share our new review on the complexity of SMA genetics, now online @cp-trendsgenetics.bsky.social! General interest in complex genetics? Want to know more about long-read sequencing? Segmental duplications? ✅✅✅ Have a look! www.cell.com/trends/genet...

The SMN locus in the T2T era: Structure, gene conversion, and clinical implications

Long-read sequencing, paralog-aware variant calling, and telomere-to-telomere (T2T) human genome assemblies now enable the resolution of copy-, haplotype-, and nucleotide-level complexities in segment...

cell.com

#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...

Release v4.0.0 · rust-bio/rust-bio

4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...

github.com

The recently-released rammap from Jeremy Wang and @lh3lh3.bsky.social is, indeed, looking like a strong contender to replace minimap2-rs in oarfish!

One way we made it fast was by mapping with simpleaf (github.com/COMBINE-lab/...) 🥳 This gives a ~50x speed-up over CellRanger, and natively produces spliced vs unspliced reads. Percent spliced reads is IMO *the* most important QC metric for single nuclei data (link.springer.com/article/10.1...).

GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler

A rust framework to make using alevin-fry even simpler - COMBINE-lab/simpleaf

github.com