A mechanism for adaptive genome regulation in cancer - Nature In this Perspective article, a theoretical framework for how the AP-1 family of transcription factors mediates cellular adaptation in cancer drug resistance is proposed.

a wonderful Perspective article www.nature.com/articles/s41...

If you use dim. reduction, you may be interested in two recent preprints we've posted on contrastive PCA:
The Rayleigh Quotient and Contrastive Principal Component Analysis I & II
w/ Maria Carilli & Kayla Jackson. They cover a lot of ground from theory to practice. 1/🧵

🚨 New lab preprint alert! 🚨
A study 6 years in the making, made possible by @simonsfoundation.org support : "A multi-omic atlas in the African turquoise killifish reveals increased glucocorticoid signaling as a hallmark of brain aging" now on #biorXiv: www.biorxiv.org/content/10.6... A 🧵 1/11 🧪🖥️🧬

Immune evasive DNA donors and recombinases license kilobase-scale writing - Nature INSTALL overcomes fundamental challenges for DNA delivery and integration methods by synergizing immune-stealth nucleic acids with recombinases to enable kilobase-scale integration strategies without ...

Today in @nature.com we introduce INSTALL, which bypasses mammalian DNA immune sensing to enable non-viral DNA integration with recombinases—a step toward safe, and mutation-agnostic genome editing. 🧬 🧵 (1/13)

www.nature.com/articles/s41...

@harvardmed.bsky.social @mgbresearch.bsky.social

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

Inclusion bias affects common variant discovery and replication in a health-system linked biobank We quantify inclusion bias in a health-system-linked biobank using classification models to distinguish enrolled individuals from the background population. To evaluate its impact on genetic findings ...

Inclusion bias in #GWAS of #EHR traits

"By weighting the sample using inverse probability weights derived from probabilities of enrollment, we replicate 54% more known GWAS variants" 😱

#statgen

www.cell.com/ajhg/fulltex...

Ever receive a BAM aligned to “GRCh38” and realize that could mean several different references?

We just released ref-solver, a tool that identifies the reference genome behind BAM/CRAM/FASTA files by comparing sequence dictionaries to known builds.

🔗 whatsmygenome.fulcrumgenomics.com

Read more 👇

This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice.

Wild rice is a perennial, creeping plant. The secret to its perennial growth habit lies in a developmental reversal directed by small RNAs. This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice.

Learn more: https://scim.ag/40GOjDb

Join us May 15 - July 31 for a 10-week Introduction to R Workshop! 🔢 Learn data import, wrangling, visualization, functions, pipelines, and basic stats with R and the tidyverse. No prior experience needed.

🕐 Fridays, 1–2 PM EST
📍 UConn Storrs (room TBD)
💰 $600 ($500 UConn affiliates)

Hypothesis: A modern human range expansion ~300,000 years ago explains Neandertal origins www.biorxiv.org/content/10.64898/2026.03...

BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing www.biorxiv.org/content/10.64898/2026.03...

Ambient RNA & barcode swapping is a serious issue in single-cell genomics. Tools such as CellBender, scAR, DecontX & SoupX. We have developed CellSweep which is faster (in some cases by a lot) and much more accurate. Extensively tested and benchmarked. www.biorxiv.org/content/10.6... 1/

After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data!

But first, I would like to talk a bit about RNA velocity and normalization. 1/

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza.

Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.

What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)

I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e...
This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

Our paper is now out in Nature:

“Ancient co-option of LTR retrotransposons as yeast centromeres”

www.nature.com/articles/s41...

A short thread on how retrotransposons helped give rise to yeast point centromeres.

1/14

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

How The Shingles Vaccine Protects Against Dementia The mechanisms behind varicella zoster virus-induced dementia pathology

This is the first time that I’ve seen an actual, mechanistic explanation for how the shingles vaccine may protect against dementia. Very interesting! If you’re in your 50s, definitely get your vaccine.

profbubak.substack.com/p/how-the-sh...

A friend from Kerala recommends Birds of Southern India by Richard Grimmett or Birds of South India by Bikram Grewel. He's a phenomenal naturalist who could probably connect you with a guide as well 😉

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!

www.nature.com/articles/s41...

New preprint!! 🚨 Did you know that many vertebrate species determine sex based on environmental conditions rather than chromosomes? Some turtles, like Trachemys scripta, rely on temperature. We learned more about how this happen molecularly.👇
www.biorxiv.org/content/10.6...

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Preprint: Genome-Scale Perturb-Seq in Primary Human CD4+ T Cells Maps Context-Specific Regulators of T Cell Programs and Human Immune Traits
papers.ssrn.com/sol3/papers.... @marsonlab.bsky.social @jkpritch.bsky.social

Join us February 24-26 for a Virtual RNA-seq Analysis Workshop! 🧬Learn QC, alignment, differential expression, and enrichment using a reference genome.

🕙 10 AM – 2 PM ET
💻 MS Teams + recordings
💰 $500 ($400 UConn)

Register: bioinformatics.uconn.edu/cbc-workshops/

#RNAseq #Bioinformatics #Workshop

We still have space in our variant calling workshop happening next week!