Ivan Ferreira

We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.

New preprint from the lab and wonderful work by Seppe de Winter:
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...

Come and join us in beautiful Krems - if you are a #regeneration aficionado you will not want to miss it! #EMBORegeneration @embo.org @isrbio.bsky.social

Nobel Laureate Professor Sir John Gurdon dies aged 92 It is with great sadness that the University shares the news of the death of Professor Sir John Gurdon, founder of the Gurdon Institute.

So sad to hear the news - John truly was an inspiration to so many, and one of a kind.

www.cam.ac.uk/research/new...

Early Career Opportunity
Mentorship & career development, access to world-class facilities, and a collaborative, supportive environment. We are particularly interested in researchers in Synthetic Dev. Biol. Mechanobiology and AI . #AcademicJobs #EarlyCareerResearcher #UCL #DevelopmentalBiology

Rapid epigenomic classification of acute leukemia - Nature Genetics The authors present a molecular classification of acute leukemia using 5-methylcytosine signatures, together with a neural network-based classifier for clinical use.

Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀

Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n

Ivory poaching and the rapid evolution of tusklessness in African elephants Intensive ivory poaching during a period of civil conflict caused the rapid evolution of tusklessness in an African elephant population.

Intense ivory poaching has led to the evolution of tusklessness in some African elephant populations, which might reduce poaching, but also happens to be an X-chromosome–linked dominant trait that is lethal to males #EleFunFactFriday #TheMoreYouKnow 💫 🧪 🐘

www.science.org/doi/10.1126/...

Have you heard of worm-like animals that create spirals on the seafloor, are more related to humans than actual worms, and produce super cute larvae? We’re obsessed with #AcornWorms!

Play #FathomVerse to find acorn worms and earn a special badge!

#AnimalsOfTheDeep @mbarinews.bsky.social

A busy tool wall in a shed. At the bottom there are instructions saying "Find the 10 hidden enhancers!" Across the wall between the tools are 10 enhancers, represented as DNA helices, but they are difficult to find in the style of a "hidden object" puzzle. Original photo by Lachlan Donald, https://www.flickr.com/photos/lox/9408028555

Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome?

Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more

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

An old image of a salivary gland chromosome from Drosophila melanogaster, with lines across different segments indicating contact points.

The original circos plot? From the 1947-1948 Carnegie Yearbook, the page prior to McClintock's Mutable Loci in Maize paper.

sea bottom of lavender colonial animals resembling big quill pens. central purple pink stalk with multiple white-purple arms

"Umiera" fields SEA PENS from Japan in full bloom! via @seacrop_ds at the other place Okinawa I think? #octocoralFriday

The genomic origin of the unique chaetognath body plan - Nature Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...

After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1

🫠🤦🏻

Congrats Mary!

Research Organisms in Flight: Revealing the Roots of Vertebrate Form… Organized by Tatjana Sauka-Spengler, Ph.D., and Ruth Williams, Ph.D.

One week left for early-'bird' (pun intended) registration...Join us @stowersinstitute.bsky.social @saukaspengler.bsky.social this fall for all the bird talk!! www.stowers.org/events/avian...

Congrats again, Jan and Marianne!

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.

This is the type of transgender mouse research that would get its money stripped away in the US... (jk jk) www.nature.com/articles/s41...

How a mysterious epidemic of kidney disease is killing thousands of young men Nature - Repeated damage from extreme heat over time seems to be a leading factor causing kidneys to fail.

Repeated damage from extreme heat over time seems to be a leading factor causing kidneys to fail

https://go.nature.com/3Ze2sri

Our brittle star patterning study is now out at EvoDevo! 🥳
doi.org/10.1186/s132...

@lowelab.bsky.social

Humpbacks crossing the ocean in front of Hopkins Marine Station

This is amazing. Really interesting science made accessible to non experts. I recommend tuning in if you can, even for a little while

A small cunner (Tautogolabrus adspersus) peers through strands of sugar kelp (Saccharina latissima) in a lush kelp forest ecosystem on Cashes Ledge in the Gulf of Maine.

Kelp forests on the coast of Maine are in decline owing to rapid ocean warming and are being replaced by turf algae, which alter the ecosystem’s chemistry, hindering the recovery of kelp forests.

Learn more in this week's issue of Science: scim.ag/4dwzl8j

David is a wise guy

so sorry, Maureen 😑😡

Hey Jeff! So nice to e-connect with u. I converted the seurat obj to anndata. Will use SEACells to summarize the whole dataset with ~9k metacells, happy to share once I finish! Think this ll make your beautiful data easier to query for any tasks that would be too intense using 500k cells. Thank you!

The promise and risks of deep-sea mining A vast treasure of critical minerals lies on the ocean floor. Should they be extracted to help fight climate change?

This is a story about deep sea mining, beautifully told.

Mining something that takes millions of years to form. What could go wrong? Ehm…🛢️👀

Letting an industry with a terrible record on land do the same in the ocean where there’s way less oversight. What could go wrong? 🤔

A purple jellyfish with a blue background, image from wikipedia

Image of pink jelly with blue background and cauliflower like mouth. Image by jonlape on iNaturalist, modified by @RebeccaRHelm with the text "this cauliflower is one giant bundle of a million microscopic mouths.

Image of pink jellyfish on blue background. By jonlape from iNaturalist

The cauliflower jelly is so named because it has a million microscopic mouths tucked inside giant frilly lips that, collectively, look like a cauliflower. It uses this madness of mouths to filter microscopic food from the water. It also has a knobby top, but it's function is a scientific mystery.

Thousands of by-the-wind sailors (Velella velella) washed up on the beach in Monterey!

The life of each of us began when a sperm and an egg came together. But what happens at a molecular level?

Our latest work in Cell led by @vdeneke.bsky.social & Andreas Blaha reveals a conserved fertilization complex that bridges sperm and egg in vertebrates! (1/11)

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