Michael Love

Also linking to the previous thread by our co-author Sarah Zweifel @sarahbrotman.bsky.social on 'AdipoExpress', one of the meta-analysis eQTL studies compared here.

bsky.app/profile/sara...

Identification of de novo variants from parent-proband duos via long-read sequencing Determining de novo status is often what upgrades a variant from VUS to pathogenic, but it has not been possible without sequencing both biological parents. We developed, extensively evaluated, and ap...

🧬 New from @leandrosboukas.bsky.social & co
📄Identification of de novo variants from parent-proband duos via long-read sequencing
🖥️ github.com/sbergercnmc/...

Very happy to share our work with Seth Berger and UCI-GREGoR at @ajhgnews.bsky.social .

We developed and extensively evaluated a method - duoNovo - that uses long-read sequencing to detect de novo variants using *only one* biological parent. (1/n)

R package: github.com/sbergercnmc/...

Incorporating polygenic risk scores and social determinants of health across populations: Considerations and best practices in research Despite increasing focus on the intersection of genetic and social risk factors on health, heterogeneity in how these factors are measured, distributed, and analyzed across populations and datasets co...

🧬 New Review from Cromer et al!
📄 Incorporating polygenic risk scores and social determinants of health across populations: Considerations and best practices in research
#PRS #SDoH

Are you interested in understanding how social and structural determinants of health influence estimates of genetic risk? Looking for figures for teaching these concepts?

Check out our work on considerations for modeling them together, led by Sara Cromer and Dave Conti with @prsmethods.bsky.social

Mind the gap: Characterizing bias due to population mismatch in two-sample Mendelian randomization We demonstrate that differences between populations can lead to biased causal effect estimates in Mendelian randomization (MR), a causal inference method based on genetic data. We provide a broad empi...

📣New from Li & Morrison!
📄Mind the gap: Characterizing bias due to population mismatch in two-sample Mendelian randomization

Also this thread on pQTL / eQTL comparisons:

bsky.app/profile/tuul...

Thinking about where we are on the power curve is key. Noting also this thread from @ee-reh-neh.bsky.social:

bsky.app/profile/ee-r...

Here is the thread describing the preprint:

bsky.app/profile/mike...

Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social!

Connecting to some recent threads here:

Higher eQTL power reveals signals that boost GWAS colocalization Rosen et al. quantify how eQTL study sample size influences signal discovery and GWAS colocalization. Integrating evidence from recent eQTL studies, they show that limited statistical power influences...

🧬 New today!
📄 Higher eQTL power reveals signals that boost GWAS colocalization
🧑‍🤝‍🧑 @mikelove.bsky.social @klmohlke.bsky.social & colleagues

A pink and blue graphic reading "apply for our opportunity scholarship to posit::conf(2026)."

We are covering 40 people's travel, lodging, and registration for posit::conf() this fall! If you are from a group that is underrepresented in data science or open source, please consider applying for the Opportunity Scholarship—we'd love to have you join.

posit.co/blog/apply-t...

David Botstein, a titan within the scientific community, died last week. GSA mourns his passing and celebrates his legacy.

Read more about his significance to our community in this thread ⬇️🧵

My preprint on keju, a statistical tool for Massively Parallel Reporter Assay (MPRA) data, is out! keju improves sensitivity, calibration, and reliability over previous methods by closely modeling important uncertainty sources in MPRAs. Check it out: www.biorxiv.org/content/10.6... (1/n)

A key insight into current comparisons of genetic regulation of molecular traits:

Finally, today's offering! www.biorxiv.org/content/10.6...

This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social

Happy to share new manuscript I completed with @ee-reh-neh.bsky.social & @davisjmcc.bsky.social back in Melbourne. The work originally conceived by @ijbeasley.bsky.social focuses on how we can reconcile and meta-analyse eQTL studies across studies cohorts and ancestries. doi.org/10.64898/202...

The first fully Rust version of piscem! scRNA, scATAC, and bulk-RNA -> RAD files, accurately, in low memory, and FAST. And all in Rust :) anaconda.org/channels/bio...

Just found reviewer from @simonpcouch.com: Human-scale LLM code review, as if a member of the tidyverse team were there with you to workshop your code for reproducibility, readability, and resilience. Note it's still very experimental. #Rstats github.com/simonpcouch/...

Given the recent spicy #rstats threads, an important reminder:

There's no single right way to code

If it works for you, that's all that matters really

Be good to your fellow coders

exactly. they aren't the enemy. it's the person still using the wrong editor

Apply to be an Opportunity Scholar at posit::conf(2026) in Houston!
We’re offering 40 full-support scholarships for underrepresented groups in data science. Includes: 🎟️ Conference+Workshop pass 🏨 Hotel stay ✈️ Travel reimbursement
Apply by March 13: posit.co/blog/apply-t...
#positconf2026 #rstats

As I'm updating my NIH Biosketch for the N-th time this year, I made a Jekyll theme for students to familiarize themselves with this CV structure while building their online presence.

Demo: jefworks.github.io/online-biosk...
Fork to modify: github.com/JEFworks/onl...

#JustAcademicThings

We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: biorxiv.org/content/10.1...

🧵👇1/n

This is so fun :). Now you can build the sshash-rs index from within python as well (and even from a list of Python strings! Like always, it's required that there are no duplicate k-mers; the input must be an SPSS). Query individual k-mers, get their hit info, even create a streaming query engine!

If you are teaching any kind of statistics, probability or modeling classes, you'll love this website. Contains dozens of interactive simulations of random processes, with sliders, different visualizat options, and full numeric log ouput: www.randomservices.org/random/apps/...

`dplyr::if_else()` and `dplyr::case_when()` are up to 30x faster dplyr 1.2.0 comes with much faster and more memory efficient `if_else()` and `case_when()` functions!

Last week we released dplyr 1.2.0, but we left off something VERY important 🙂

`dplyr::if_else()` and `dplyr::case_when()` are now up to 30x faster and use 10x less memory!

We dive into how we achieved these numbers in this new #rstats post!

tidyverse.org/blog/2026/02...

crates.io: Rust Package Registry

@mikelove.bsky.social : There was PyDESeq2, and now there is rust_deseq2! crates.io/crates/rust_...

I started offering career advice to two junior colleagues today in separate meetings, and both times I caught myself thinking that, if I'm honest, I don't have very good advice on navigating the current funding and job climate. I think it's important to say that no one does.

We're donating PyDESeq2 to @scverse.bsky.social for long-term maintenance & development. Python reimplementation of DESeq2, ecosystem member since 2023, now in the hands of one of the best open source communities in omics. Good science requires good open source. github.com/scverse/PyDE...