Michael Love

GitHub - numbats/autoAlt Contribute to numbats/autoAlt development by creating an account on GitHub.

Are you interested in adding alt text to your publications? It helps share your data visualisations with vision impaired readers. Try out github.com/numbats/auto... to get a reasonable first draft or maybe complete text. @r-forwards.hachyderm.io.ap.brid.gy @rladies.org @rconsortium.bsky.social

“Brilliance wrapped in modesty, decency, and good humor.” So true. 😭 May his memory be a blessing.

We learned today that Paul Rathouz of UT-Austin (previously Chicago and UW-Madison) died on Dec. 10.

Few people I've known have enwrapped their brilliance with such modesty, decency, and good humor.

A mensch's mensch. RIP.

I’m teaching a course on data wrangling with R & the tidyverse for @stathorizons.bsky.social in January. Filled to the brim with ways to do the stuff you have to do before you can run any of your spiffy models and that often breezily gets glossed over even though it’ll take up 90% of your time.

Enabling Discovery Through Genomics (EDGE)

The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at BIOEDGE@nsf.gov if you have questions. www.nsf.gov/funding/oppo...

Ten years ago I had sent off my applications for faculty positions and found out that I was getting an interview with Chapel Hill Biostatistics.

Let us know, e.g. @stemang.bsky.social or I if you have any ideas for something to post re: use cases for tidyomics to share or to develop.

tidyomics project 🔛 R-bloggers!

www.r-bloggers.com/2025/10/the-...

Thanks to @stemang.bsky.social, Maria Doyle @bioconductor.bsky.social, @jhsanchez.bsky.social, Mengyuan Shen, Jonathan Carroll and others in tidyomics for testing and getting this up and running

Impressive!

A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines Feng et al. present the first genome-scale CRISPR interference perturbation map with scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering population-scale CRISPR pe...

Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...

YouTube video by 3Blue1Brown Terence Tao on the cosmic distance ladder

www.youtube.com/watch?v=YdOX...

en.wikipedia.org/wiki/Hertzsp...

"Hertzsprung–Russell diagram. A plot of luminosity (absolute magnitude) against the colour of the stars ranging from the high-temperature blue-white stars on the left side of the diagram to the low temperature red stars on the right side."

Is this the coolest scatterplot?

The most-cited neuroscience papers from the past 30 years Highly cited papers reflect the surge in artificial-intelligence research in the field and other technical advances.

Pretty neat to see our paper - led by @kr-maynard.bsky.social @lcolladotor.bsky.social on the 2021 list of most cited neuroscience papers 🧠🔬🧪

www.thetransmitter.org/publishing/w...

As promised, a longer thread on what I consider to be some of the most interesting and important contributions of this paper (1/10)

Consider submitting an abstract for an invited talk or poster at STATGEN 2026 by December 15th!

Amazing keynote speakers and statistical leaders in #genetics and #genomics! 👏

Hope to see you there! statgen26.emory.edu

🧪 🧬 🖥️ 🧠 #statssky #imaging #SingleCell #spatial #omics #DigitalPathology

A nice paper on distilling AI-based splicing models into much simpler additive models:

"[...] the distilled models achieve this without modeling RNA structure or feature interactions, indicating that [AI]-based splicing models recognize exons primarily through simple additive sequence features."

High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape Helmy et al. provide a collection of high-quality mouse reference genomes. They were able to resolve some of the most complex regions among mouse genomes that are involved in immune defense. These fin...

High-quality mouse reference genomes [PacBio Long Read genomes of 17 strains] reveal the structural complexity of the murine protein-coding landscape, Cell Genomics. www.cell.com/cell-genomic... Genomes and annotations here: projects.ensembl.org/mouse_genomes/

📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!

🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K

Apply here: t.co/B7SLZzQFKu

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

1/n

⏰ Only a few hours left to register!

Don’t miss today’s Bioconductor Seminar Series session:
“Deep-learning-based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines.”

🗓️ December 2, 2025
🕒 9PM CET / 3PM EST / 12PM PST

👉 Register here: dfci.zoom.us/webinar/regi...

Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix Observational studies are commonly used in psychology and epidemiology to identify risk factors correlated with health outcomes. However, these studies are vulnerable to confounding when shared geneti...

Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)

Join EMBL's Interdisciplinary Postdoc Programme!
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.

In particular: AI&Theory, use mathem. models, physics principles and AI

www.embl.org/about/info/p...

Excited to share that our article on accurate sample deconvolution of pooled snRNA-seq data using sex-dependent gene expression patterns is live on NAR Genomics and Bioinformatics! 🎉

Check it out here: doi.org/10.1093/narg...

#NARGenomicsandBioinformatics #snRNAseq #Genomics #Bioinformatics

Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics - Nature Metabolism Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with genes, pathway analysis in metabolomics often yields misleading or nonsensical results.

#Throwback 🧪

COMMENT | Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics

KS Lee, X Su & T Huan

Figure 1. Proteome compleasm scores for predicted transcripts by annotation method for vertebrates. The score is calculated as 1 − (number missing BUSCOs/total number of BUSCOs searched).

Joint distributions of number of predicted CDSs (normalized by number of NCBI predictions) over median predicted CDS length (nor- malized by median NCBI CDS length) for the reference species for each taxonomic group we examined, as well as M. musculus. Dotted lines indi- cate equivalence to NCBI annotation, such that methods that are closest to the intersection of those lines best approximate CDS length and number of NCBI annotations. A “P” indicates that the method only makes protein- coding predictions.

Building better genome annotations across the tree of life
genome.cshlp.org/content/35/5...
TOGA, BRAKER3, and the RNA-seq assembler StringTie are top performers when benchmarking 12 different methods for 21 different species spanning vertebrates, plants, and insects.

PanSN-spec: Pangenome Sequence Naming
github.com/pangenome/Pa...

SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction https://www.biorxiv.org/content/10.1101/2025.11.25.690514v1

Portrait photo Katy Börner

📣 Listen to the BIH Lecture " Multiscale Human Reference Atlas - An Ontological Bridge Between Anatomy and Disease" by Stiftung Charité visiting fellow Prof. Dr. @katyborner.bsky.social.

📅 December 5, 2025, 12:00 - 1:00 pm, online via Zoom

➡️ tinyurl.com/4p9cjhph

Foto © Andreas Bueckle

GitHub - BiocPy/GenomicRanges: Container class to represent genomic locations and support genomic analysis Container class to represent genomic locations and support genomic analysis - BiocPy/GenomicRanges

The GenomicRanges (github.com/BiocPy/GenomicRanges) package for Python got a major speed boost (v0.7.0+) thanks to Aaron’s blazing-fast C++ nclist interval indexing!

#Bioinformatics #Genomics #Bioconductor