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Ivan Ferreira

@ptychodera.bsky.social
223 followers 197 following 76 posts

Biologist from 🇧🇷 jointly based at Stowers and the Hopkins Marine Station at Stanford | PhD from Oxford | genomics, embryos, worms, regeneration | USP and Butantan alumnus | my opinions

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Reposted by Ivan Ferreira
FlyBase @flybase.bsky.social · 20/08/2026
Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...
nature.com
Treat biological databases as infrastructure, not projects
Letter to the Editor
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Cedric Feschotte @cedricfeschotte.bsky.social · 24/09/2026
Thrilled to see this published today! Truly special because we made the initial discovery >15 yrs ago! We found two copies of a human gene called BC200 embedded in a human poxvirus. BC200 blurs the line between gene & transposon—both functional & mutagenic! www.science.org/doi/10.1126/... 🧵1/n
science.org
Escape of the BC200 gene to a human poxvirus reveals its persistent transposition in primates
Transposable elements mobilize within and occasionally between genomes, including from host to virus. We identified two insertions of the human BC200 noncoding RNA gene in the poxvirus molluscum conta...
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Current Biology @currentbiology.bsky.social · 17/09/2026
The new Current Biology Cat is #1 on @bsky.app. The wonders of the natural world still triumph over man-made madness!😻🙏 www.cell.com/current-biol...
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Coral City Camera @coralcitycamera.bsky.social · 05/08/2026
Serotonin maxxing w the CCC ☺️🔮🐠🐠🐠🐠🐠🐠🐠🐠 #sergeantmajor #fishparade #brainsaver #serotoninmaxxing #acosmosoffishes
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Dr. Lucky Tran @luckytran.com · 02/06/2026
Incredible! Scientists receive a rare standing ovation after announcing that a new treatment can double the survival time for pancreatic cancer, the deadliest cancer which was once considered “undruggable.” When we fund and support science, we can achieve anything! (Video: Dr. Wish Dhillon)
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Laurent Formery @laurentformery.bsky.social · 02/06/2026
Satisfying or disturbing to watch? 🤓
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Ivan Ferreira @ptychodera.bsky.social · 03/06/2026
things are getting weirdly cool in the echinox lab 🔥 looks like France is not only about croissants after all...
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Ivan Ferreira @ptychodera.bsky.social · 03/06/2026
For all undergrad/grad students and postdocs going to the #embo #regeneration meeting in Austria this year: highly recommend joining the trainee pre-meeting co-organized by Giulia, Carlos and Salome in beautiful Vienna! Honestly - just the chance to visit the Vienna BioCenter is worth it
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Reposted by Ivan Ferreira
Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
npr.org
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
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Reposted by Ivan Ferreira
c0nc0rdance @c0nc0rdance.bsky.social · 25/05/2026
This definitely forbidden gummy is in fact a moth larva of genus Olona (possibly Olona zolotuhini). It's *normal* to want to know what flavor it is, but the answer, unfortunately is "pain". Most species in this family are covered in tiny stinging spines connected to poison glands. (📷: Janice Ang)
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Reposted by Ivan Ferreira
Sternberg Lab @sternberglab.bsky.social · 21/05/2026
1/8 🚨 New preprint from the @sternberglab.bsky.social & @martinjinek.bsky.social labs! CRISPR-associated transposases (CASTs) insert large DNA cargoes at precise genomic locations — no double-strand breaks needed.
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Pawel Burkhardt @pawelburkhardt.bsky.social · 23/05/2026
A fossil nervous system meets modern neurobiology. We found that a living comb jelly preserves neural architecture remarkably similar to those inferred from Cambrian fossils over 500 million years old 🤩. www.biorxiv.org/content/10.6...
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PLOS Biology @plosbiology.org · 22/05/2026
Bilaterian BMP signaling gradients suggest an ancestral anti-neural role. Study of #cnidarians shows that #BMP signalling promotes neurogenesis; its "anti-neural" function is a side effect of its role in the DV axis @paulknabl.bsky.social @genikhovich.bsky.social @plosbiology.org 🧪 plos.io/4dJHoiR
In the box jellyfish Tripedalia cystophora, BMP signaling is active in ganglionic neurons of the umbrella, the ring nerve and in the rhopalium. Top left: Oral view of the umbrella, black arrowheads highlight the location of the rhopalia (rh). Top right: lateral and frontal detail of the rhopalium anatomy. Bottom, from left to right: pSMAD1/5 activity in the rhopalia, lateral view of the rhopalium, view from the top highlights pSMAD1/5 activity around the stalk, detailed view of the pit eye and the area around it (pSMAD1/5 is observed in a sector of the pit eye retina, the upper lens eye and some cells between the pit eye and the stalk).
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Philip Ball @philipcball.bsky.social · 22/05/2026
A phase 1 clinical trial of base editing to treat beta-thalassaemia looks promising. Wow, this genome-editing technique is moving fast! www.nature.com/articles/s41...
nature.com
Clinical application of base editing for treating β-thalassaemia - Nature
A clinical phase 1 trial of a single infusion of CS-101, CD34+ cells modified using a transformer base editor to reactivate fetal haemoglobin production, led to early and enduring transfusion independ...
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Melanie Mitchell @melaniemitchell.bsky.social · 21/05/2026
"Science is not simply a sequence of tasks that can be optimized....The scientific system thrives on inefficiency: redundant efforts, failed attempts, and divergent paths. These are not costs to be eliminated but sources of discovery." Excellent essay! ⬇️ www.science.org/doi/10.1126/...
science.org
Progression without progress
Progress in the use of artificial intelligence (AI) to advance scientific discovery has made it increasingly realistic to envision automated “end-to-end science” (ETES) systems: integrated pipelines t...
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Massimo (mirror) @rainmaker1973-m.bsky.social · 19/05/2026
The Skeleton Panda Sea Squirt (Clavelina Ossipandae) is a translucent reef-dwelling creature whose rib-like structures and panda-like markings give it a spooky look. Found in Southeast Asia, it filters seawater and helps keep coral ecosystems healthy. Original post
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Dezene Huber 🍁 🌻 @dezene.me · 17/05/2026
“…a past strong El Niño event wiped out 77 percent of the islands' penguins. In addition, the climate pattern destroyed 97 percent of shallow water coral.” If this El Niño turns out as predicted, it will have devastating effects on biodiversity across the globe. www.newsweek.com/super-el-nin...
newsweek.com
Most Galapagos penguins could be killed this year, here's why
More than three-quarters of the penguins' population died during a separate strong El Niño event, fueling concerns for this year.
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Roberto Mayor Lab @mayorlab.bsky.social · 16/05/2026
PL retweet. Developmental Biology Course (Quintay). More information: biodesarrollo.unab.cl
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Nature @nature.com · 15/05/2026
Half of laboratory mice are not what scientists think they are go.nature.com/437pTDZ
go.nature.com
Genetic survey exposes flaws in widely used mouse models
A survey of more than 300 mouse strains has found widespread discrepancies between how mutant mice are reported and their actual genetic make-up.
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💖 Birdhism Jen @birdhism.com · 15/05/2026
Striped cuckoo (Tapera naevia) chicks utilize specialized, cryptic plumage that mimics the texture and color of pinecones for camouflage. #birds
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Natalie Bennett @nataliegreenpeer.bsky.social · 14/05/2026
How little we know of the amazing #biodiversity on this planet that we are fast trashing phys.org/news/2026-05...
phys.org
Hairy new fish species discovered in the Great Barrier Reef
Swimming among the corals of the Great Barrier Reef is a fish that could be a doppelganger for the famous Sesame Street character Mr. Snuffleupagus. This bright orange-red, hairy, long-snouted ghost p...
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Tschopp Lab @tschopplab.bsky.social · 14/05/2026
One of my dream projects, ever since joining here in Basel, out now in @nature.com : single-cells 🤝 eco-morphological proxies rdcu.be/fiyso How cells and tissues adapt to dietary niches... Thanks and congrats to Antoine, Walter, and all the other co-authors for this great collaboration!! 🙏🥳
rdcu.be
Adaptive cellular evolution in the intestine of hyperdiverse cichlid fishes
Nature - Single-cell transcriptomics combined with morphological and ecological data show that the rapid evolutionary radiation of cichlid fishes in Lake Tanganyika was accompanied by dietary...
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 13/05/2026
While BioNtech & Moderna become household names because of their Covid vaccines, those emerged from different projects: finding ways to treat the most challenging cancers. They hypothesized that we could vaccinate patients against their own tumors, & evidence is mounting that they were right! 1/n 🧪
https://www.nature.com/articles/s41586-025-10004-2
Individualized mRNA vaccines evoke durable T cell immunity in adjuvant TNBC

    U. Sahin, M. Schmidt, E. Derhovanessian, A. Cortini, I. Vogler, T. Omokoko, E. Godehardt, S. Attig, S. Newrzela, J. Grützner, N. Bidmon, S. Bolte, S. Brachtendorf, T. Stuhlmann, D. Langer, D. Brüne, J. Blake, A. Feldner, H. Lindman, A. Schneeweiss, M. Eichbaum & Ö. Türeci 
Triple-negative breast cancer (TNBC) is frequently associated with metastatic relapse, even at an early stage1. Here we assessed an individualized neoantigen mRNA vaccine in 14 patients with TNBC following surgery and after neoadjuvant or adjuvant therapy. In peripheral blood of nearly all patients, high-magnitude, vaccine-induced, mostly de novo T cell responses to multiple neoantigens were detected that remained functional for several years. Characterization of individual patients revealed that a large proportion of these T cells developed into two subsets: a late-differentiated phenotype with markers indicative of ‘ready-to-act’ cytotoxic effector T cells, and T cells with a stem cell-like memory phenotype. Eleven patients remained relapse-free for up to six years post-vaccination. Recurrence occurred in three patients: the individual with the weakest vaccine-induced T cell response relapsed, but achieved complete remission on subsequent anti-PD-1 therapy; another patient had a tumour with low major histocompatibility complex (MHC) class I expression with MHC class I-deficient cells growing out under vaccination; and the third patient was BRCA-positive and had a recurrence from a genetically distinct primary tumour. These findings demonstrate the feasibility of individualized RNA vaccines in TNBC, document persistence of vaccine-induced, functional neoantigen-specific T cells and provide insights into possible immune escape mechanisms that will guide future approaches.
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Stowers Institute @stowersinstitute.bsky.social · 11/05/2026
(2/2) Learn more about the new @cellpress.bsky.social study on Stowers.org: bit.ly/42t1Uik
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Stowers Institute @stowersinstitute.bsky.social · 11/05/2026
(1/2) 🧵 What tells a cell what to become? New #research from @saukaspengler.bsky.social & @fabiantheis.bsky.social @helmholtzmunich.bsky.social @ox.ac.uk published in Cell explores how gene regulatory networks guide cell fate — using a new #AI framework the team developed called RegVelo.
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 08/05/2026
Did you know that Pierre Chambon's laboratory was the first to use the term "nucleosome" in 1975 ? www.cell.com/cell/fulltex...
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Palma Polyak @palmapolyak.bsky.social · 09/05/2026
Truly historic & moving scenes from the inaugural session of the Hungarian Parliament. A children’s tambura band from a tiny village playing a folk song often described as the unofficial Roma anthem. MPs were tearing up & so were many more of us watching. After all those years of hate. 🎥 telex.hu
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Ivan Ferreira @ptychodera.bsky.social · 09/05/2026
We @lowelab.bsky.social had a blast hosting @ostratodd.bsky.social at the Hopkins Marine Station! A fantastic day talking all things bioluminescence, ostracods, chitons, repeatability, contigency, phylogeny, courtship, mentoring, surfing, baseball, brewing and all The first of many visits I hope!
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Jenna Norton @jenna-m-norton.bsky.social · 08/05/2026
If you are a member of the scientific community wondering how to meet this moment, check out this excellent discussion between @holdenthorp.bsky.social and @timothysnyder.bsky.social. youtu.be/IWNDMwimUP0?...
youtu.be
Lessons in resistance for the scientific community
YouTube video by Science Magazine Podcasts
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Nature @nature.com · 08/05/2026
Iconic British naturalist David Attenborough, whose work has shaped science for decades, turns 100 today go.nature.com/4dbRFUB
go.nature.com
A life in pictures: Celebrating Attenborough at 100
As the British naturalist celebrates a milestone birthday, we take a look at how his work has shaped science.
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 07/05/2026
#RIP Pierre Chambon (1931-2026) 1963 PARP 1970 RNA Pol II 1975 Nucleosome 1977 Split genes 1980 Promoter 1983 enhancer 1986 Nuclear receptor
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Bob Kopp @bobkopp.net · 07/05/2026
In retrospect, forcing the entire campus to move from our locally hosted, open source LMS to a commercial, single point of failure LMS that also happens to be owned by a company that wants to turn all our labor into AI training data may not have been a good idea.
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Nat Prunet @nat-prunet.bsky.social · 05/05/2026
Louse imaged on @zeiss-microscopy.bsky.social #lightsheet 7 #microscope by @carsten-wolff.bsky.social @mblscience.bsky.social @aqlm.bsky.social #microscopy
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MC Gambetta @mcgambetta.bsky.social · 04/05/2026
Hello all, our lab is recruiting a PhD candidate to study how 3D genome folding impacts gene regulation in development. We're located at the Center for Integrative Genomics department of the University of Lausanne, Switzerland. Please email me if interested. #PhDPosition, #PhDOpportunity
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Aydan Bulut-Karslioglu @bulutkarslioglu.bsky.social · 03/05/2026
Very excited to share our newest findings! A very long team effort pursued by multiple team members -to frantically reproduce everything over and over-, we show mTOR-Polycomb synergy at promoters of developmental master regulator TFs in ESCs prior to their expression. www.biorxiv.org/content/10.6...
biorxiv.org
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Nancy Knowlton @nancyknowlton.bsky.social · 02/05/2026
www.fws.gov/rivers/carp/...
fws.gov
Endangered mussel is found in Michigan for the first time since 1987 | U.S. Fish & Wildlife Service
Freshwater mussels aren’t usually the first animals on people’s minds when they think of what inhabits our rivers and streams. However, these filter feeders are crucial and fundamental players in all ...
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Alfonso Martinez Arias @amartinezarias.bsky.social · 02/05/2026
A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵
cell.com
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organis...
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Daniel Babcock @babcockflylab.bsky.social · 02/05/2026
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Ivan Ferreira @ptychodera.bsky.social · 02/05/2026
🔥
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Yehu Moran @yehumoran.bsky.social · 01/05/2026
A very nice piece about our latest paper published in Open Biology by @royalsocietypublishing.org It's about how venom-producing stinging cells use chromatic modifications to determine their biochemical identity: royalsociety.org/blog/2026/04...
royalsociety.org
The secret life of stinging cells: chromatin regulation in sea anemones | Royal Society
This Open Biology study uncovers how specialised stinging cells used for prey capture and defence, are regulated at a deeper level than ever before.
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Simone Conradi @sconradi.bsky.social · 29/04/2026
A stunning visualization born from a collaboration with @manlius.bsky.social : 55,486 galaxies and 29,555 streamlines tracing how matter flows across our local universe, built on data from the CosmicFlows-4 project. Article in the first reply 👇
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Joachim Frank @joachim123.bsky.social · 29/04/2026
I came here in 1975. I'm a Nobel Prize-winning scientist born in Germany during WWII, came here in 1975 thinking there was no way fascism could take hold in this country. I was wrong. I don't not want to be book-ended by two fascist regimes. We will stand up and set things right.
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Development @dev-journal.bsky.social · 28/04/2026
John Gurdon (1933-2025) Sir John Gurdon was a towering figure in developmental biology, respected and admired throughout the world. In this Obituary, Jim Smith writes about his legacy. journals.biologists.com/dev/article/...
Sir John Gurdon
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David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 26/04/2026
Small Rays in Shallow Waters Flaunt Fake Eyes to Ward Off Predators | Discover Magazine
discovermagazine.com
Small Rays in Shallow Waters Flaunt Fake Eyes to Ward Off Predators
Discover how iconic eyespots evolved in certain ray and skate species, a defense trait surprisingly common across the animal kingdom.
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Chemistry World @chemistryworld.com · 24/04/2026
New research shows the pitfalls of ‘reducing an organic system to machine-like parts and assuming that specificity is intrinsic to those parts.’ @philipcball.bsky.social www.chemistryworld.com/opinion/coll...
chemistryworld.com
Collective interactions dominate gene regulation in eukaryotes
A new technique shows DNA binding domains are not central to transcription factor targeting in human cells, unlike in bacteria
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Ivan Ferreira @ptychodera.bsky.social · 24/04/2026
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