CausalGRN: deciphering causal gene regulatory networks from single-cell CRISPR screens https://www.biorxiv.org/content/10.64898/2025.12.30.692369v1

Do transcriptional activators work on any promoter? Our data says no. 🙅‍♂️ Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬

…and we don’t have this matrix at good completeness & precision, despite many efforts (including our own 👇). Hopefully we will in not too distant future, but given the difficulty of this task, I’m not holding my breath regarding virtual cells. pubmed.ncbi.nlm.nih.gov/41173850/

Looking into industry bioinformatics / comp bio / data science careers. If you have any leads, message me! CV is in bio. Currently a postdoc data scientist at @mdanderson.bsky.social, have published work in both wet + dry lab multi-omics of non-model organisms & humans. 🧪🧬🖥️

Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...

Little over a month left to submit an abstract to #EuroBioC2026 (eurobioc2026.bioconductor.org/pages/submis...), which will be held in Turku, Finland. Here are a couple of Finnish Christmas traditions that you might not know:

Our new preprint is out: www.biorxiv.org/content/10.6... We show that GRN benchmarks commonly used can overestimate performance due to negative-sampling choices, sometimes allowing simple degree-based baselines to rival more complex GNNs. A reminder of why bias-aware evaluation matters!

Biologists who teach: in what order do you teach the four forces of evolution? Genetic drift first or selection first? And I'm still struggling to smoothly fit in HWE so that its utility is emphasized (students focus so much on how likely it is that assumptions are violated). #iteachbio 🧪 #Evolution

Thanks to the AWS Open Data program, this dataset along some derived data is also openly accessible via @AWSCloud at openhgl.s3.us-east-1.amazonaws.com/index.html

I have seen many people say that no academic needs to use LLMs for writing, because of course we are all already excellent at writing. I fear that risks exacerbating imposter syndrome in early career researchers. I therefore want to raise my hand and say while I enjoy writing, I find it hard.

Announcing the Ascona Workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems" on 28 June - 3 July 2026 in Ascona, CH www.huber.embl.de/group/events... Reserve the dates!

HAPPY HOLIDAYS TO ALL OF YOU!🎄✨

A nice summary of the year from the R Consortium. Expanded FDA file format support is huge r-consortium.org/posts/expand...

I asked participants for tips attending scientific conferences #BES2025 youtu.be/ow_ickvkvbA?...

So question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?

CSAMA 2026 - Biological Data Science Summer School Bressanone-Brixen, South Tyrol / Italy 24-29 May 2026 csama2026.bioconductor.eu Statistical & computational methods for single cell and spatial omics, with lectures and hands-on exercises in R/Bioconductor.

"The only kind of thinking that matters in science is structured thinking. The only way to give structure and substance to your thoughts is to write them down. Writing. Is. Thinking." Thinking about this in the context of AI tools....

📣 Opportunity for Pre-conference Workshops - EuroBioC2026 EuroBioC2026 will host on-site pre-conference workshops on 1–2 June 2026 in Turku, Finland, ahead of the main conference. If you’re interested in hosting a workshop, submit your interest here by 30 Jan 2026: docs.google.com/forms/d/16MR...

My lab is recruiting postdocs in AI/ML for genetics & genomics through the Malone Postdoctoral Fellows program. Apply by Jan 30! Lots of other great labs across the Malone Center as well.

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

How excited am I allowed to be about Josh Starmer of #StatQuest joining us on the #DSHangout this week?! BECAUSE I AM EXCITED! Josh makes me feel seen bc we both love explaining stats stuff in friendly ways, helping folks, & not taking ourselves too seriously #databs #rstats #python #datascience

Deadline today for submitting abstracts to STATGEN 2026 in Atlanta, May 18-20 bsky.app/profile/step...

The last #tidyomics meeting of the year is in 2 days. Everyone welcome! - 16 Dec, 3:30 pm (EST; New York) - 16 Dec, 9:30 pm (CET; Berlin) - 17 Dec, 7:30 am (AEDT; Melbourne) We will chat about plans for next year. Zoom link: shorturl.at/Epbbc @mikelove.bsky.social @bioconductor.bsky.social

🇸🇰 Slovakia has become the newest member to join #ELIXIR, following the signature of the ELIXIR Consortium Agreement by the Ministry of Education, Research and Youth. 🙌 This brings the number of ELIXIR members to 23. Read the news 👉 https://loom.ly/h4CyhJo

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.

The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at [email protected] 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.

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

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...

Is this the coolest scatterplot?

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 [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...

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

#Throwback 🧪 COMMENT | Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics KS Lee, X Su & T Huan

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