Nikki Gentle

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

David Baltimore, Nobel-Winning Molecular Biologist, Dies at 87

A giant in molecular biology and virology has passed. RIP David Baltimore.

www.nytimes.com/2025/09/07/s...

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis - Nature N-glycans on glycoRNAs prevent innate immune sensing of endogenous small RNAs, and the natural mechanism they use demonstrates how glycoRNAs exist on the cell surface and in the endosomal network with...

Hi everybody! I am super excited to share the work done during my PhD published in @nature today! We describe a new mechanism of self- vs. non-self RNA discrimination by showing how N-glycans shield glycoRNAs from stimulating endosomal RNA sensors www.nature.com/articles/s41...

Systematic benchmarking of basecalling models for RNA modification detection with highly multiplexed nanopore sequencing Nanopore direct RNA sequencing (DRS) holds promise for advancing our understanding of the epitranscriptome by detecting RNA modifications in native RNA molecules. Recently, Oxford Nanopore Technologie...

🚨 New preprint alert 🚨
We systematically benchmarked @nanoporetech.com 's modification-aware basecalling models released for RNA on sets of in vitro and in vivo sequences and made some curious observations 🧬🔍.
bit.ly/4lXqNul
Follow along for a little recap (1/12)

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

IL-10 targets IRF transcription factors to suppress IFN and inflammatory response genes by epigenetic mechanisms - Nature Immunology Ivashkiv and colleagues show that IL-10 inhibits the expression and DNA binding of IRF1 and IRF5, two transcription factors that have an amplifying role in the induction of inflammatory NF-κB target g...

#EpigeneticPower! Ivashkiv, Mishra &co show @natimmunol.bsky.social that anti-inflammatory IL-10 epigenetically silence IRF1 & IRF5 gene transcription by decreasing H3K27ac & chromatin accessibility, thus preventing sustained #interferons & IL6/TNF signaling! www.nature.com/articles/s41...

Systemic inflammation impairs myelopoiesis and interferon type I responses in humans
www.nature.com/articles/s41...
@natimmunol.bsky.social

This statement from the NSF is insane.

Science is, in essence, designed to separate the true from the false.

Understanding how falsehoods spread is key to the scientific endeavor. It is not a violation of free speech to be proven wrong.

"A GO term analysis? how is this helpful?"

Meme of a drunk guy yelling at an unimpressed girl in a nightclub; the caption reads "I have been so fortunate as to be distinguished by the patronage of the right honourable Lady Catherine de Bourgh"

Apropos of nothing... a series of Pride and Prejudice memes.

“Orchestrated assault”: New tsunami of NIH grant cuts hits South Africa hard Agency moves to terminate nearly 1000 awards, including programs involving “DEI”

Exclusive from me and Jon Cohen @science.org: NIH is terminating nearly 1000 grants in a series of batches. One, which conducts HIV and TB clinical trials in South Africa, was labelled as a "DEI" study that "harms the health of Americans." www.science.org/content/arti...

[BREAKING] Trump ends SA’s HIV and TB research grants - Bhekisisa Cancellation letters, which end millions of rands of South African universities’ US-government funded HIV and TB research grants with immediate effect, started to roll in over the weekend. Fears are r...

BREAKING Frightening cuts: In South Africa, #HIV and #TB cancellation letters for research grants funded by the US government started to roll in over the weekend.. bhekisisa.org/health-news-...

South Africa and Trump — how we respond will come to define our country While the current dispute between South Africa and the Trump administration raises big questions about our foreign policy, we should not forget who we are as a nation. How our government responds to U...

South Africa and Trump — how we respond will come to define our country.
"It is worth reiterating: the only reason the issue is so consequential is because of the economic and military power of the US." www.dailymaverick.co.za/article/2025...

Toward single-molecule protein sequencing using nanopores - @unigroningen.bsky.social go.nature.com/3FL0g3k

Fear spreads that NIH will terminate grants involving South Africa Trump has promised to cut off funding, claiming nation discriminates against white citizens

www.science.org/content/arti...

Instead of using ChatGPT, why not just get a family member to lie to you while they set fire to a tree?

Lesotho HIV programmes collapse after USAID decision The US funding cuts have sparked fear of a surge in new infections as antiretroviral medicines become harder to get.

Here is what killing #USAID funding does--it kills #Basotho who are HIV positive. Pulling funding with no warning to a program that serves 350,000 HIV+ in #Lesotho and leaving them without access to life-saving meds.

Callous.
Uncaring.
Immoral.

www.dailymaverick.co.za/article/2025...

Our HIV response will collapse without US funding - unless we act urgently Reassurances that state clinics will pick up the lost services are empty

groundup.org.za/article/sout...

Our HIV response will collapse without US funding - unless we act urgently Reassurances that state clinics will pick up the lost services are empty

South Africa faces its worst health crisis in 20 years. Worse than COVID, and one that will overshadow diabetes as a major killer, while pouring petrol on a dwindling TB fire. But it is preventable if our government steps up urgently.

Read groundup.org.za/article/sout... by Francois Venter

James Harrison, whose rare blood helped save millions of babies, dies at 88 By donating blood over 1,100 times, James Harrison helped develop Anti-D, a life-saving treatment for newborns at risk of Rhesus disease

The most extraordinary thing about James Harrison, who donated his rare plasma every 2 weeks for over 60 years and saved the lives of an estimated 2.4 million babies, is that he had to overcome a FEAR OF NEEDLES.

www.independent.co.uk/news/world/a...

Trump orders immediate end to USAID funding for HIV organisations in SA | News24 Pepfar-funded HIV organisations in South Africa, who receive their funds through the United States Agency for International Development, woke up to letters that were sent overnight telling them their ...

www.news24.com/news24/south... A lot of people will die.

RNA xkcd.com/3056

📣Excited to share my last postdoc paper with
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵

Applicants of Black or mixed Black heritage can apply to my lab through the new Future Leaders in Biomedical Sciences programme. www.crick.ac.uk/careers-and-...

PREPRINT! Park et al. makes the case that we may be misunderstanding heterochromatin for past 30 years due to ChIP-Seq biases... 1/n

The distribution of highly deleterious variants across human ancestry groups A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry...

“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?

I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Description of image: Workflow for identifying high-quality ASBs through baal-nf. ChIP-sequencing data from genotyped cell lines is used to infer ASBs at heterozygous SNPs using BaalChIP. Identified ASBs are further characterized by mapping them to JASPAR and NoPeak motifs for a given TF. High-quality ASBs show concordance in the corrected allelic ratio and motif score difference.

What DNA variants alter transcription factor (TF) binding affinity? Here, we describe a new workflow baal-nf. We used it to trawl through 6017 ChIP-Seq data sets for 558 TFs and 46 genotyped cell lines, finding 298,783 allele-specific binding sites (ASBs).
www.biorxiv.org/content/10.1...
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How has native RNA sequencing contributed to epitranscriptomic research? This is one of the main questions we addressed in our recent review by @evamarianovoa.bsky.social and I now live in Molecular Cell #RNAsky #RNA #nanopore
authors.elsevier.com/a/1kS2f3vVUP...

I knew one day I’d have to watch powerful men burn the world down – I just didn’t expect them to be such losers | Rebecca Shaw Elon Musk and Mark Zuckerberg’s desperation to be cool as they suck up to Donald Trump is so cringe it makes my skin crawl

😄 "I knew one day I’d have to watch powerful men burn the world down – I just didn’t expect them to be such losers." www.theguardian.com/commentisfre...