We have just posted our most recent research on alternative splicing on bioRxiv. We show that more than 100 ancient dual coding regions that derived from frame changing alternative splicing events may be under selection constrains. In each case the selection pressure is apparent in both frames:
Gleichschaltung. bsky.app/profile/alex...
Alex Wild@alexwild.bsky.social · 3mo agotl,dr; Scientists no longer allowed to use federal funding to publish, attend meetings, or talk to the public. They cannot collaborate internationally. Grants can be cancelled for any reason, at any time, political appointees have a final say over what gets funded, and who gets funded.
The scope of these terminations is unprecedented. At RFK Jr's HHS alone, 77 advisory boards were disbanded in 2025 — more than a quarter of all the panels. For context: in 2024, HHS terminated just two. Among the casualties: panels on organ transplantation, dietary guidelines, and long COVID.
"No to war." - Spain's PM Pedro Sanchez “You can’t respond to one illegality with another because that’s how humanity’s great disasters begin.” www.theguardian.com/world/2026/m...
‘No to war’: Sánchez doubles down after Trump threat to cut off trade with Spain
PM says his country will not be complicit in growing conflict in Middle East ‘simply out of fear of reprisals from someone’
theguardian.com
Spanish PM Pedro Sánchez on the Iran War. "Spain's position at this juncture is clear and forceful. It is the same position we have maintained in Ukraine and also in Gaza. No to the breaking of international law that protects us all, especially the most defenceless - the civilian population."
Over the weekend, Molecular Genetics and Genomics published our most recent paper. Upstream start codons can produce alternative proteins with novel N-terminal amino acids that block signal peptides. These proteins are translated but not found in any proteomics experiments. rdcu.be/eUi7o
The degradation of extended protein isoforms points to a misfiring translation initiation process
rdcu.be
Finally managed to write a thread to go with our new paper ...
Michael Tress@michaeltress.bsky.social · 9mo agoA new paper out this weekend in which we analysed PeptideAtlas peptides in search of coding genes novel to the Ensembl/GENCODE reference set, The peptides suggested another 35 potential new coding genes, but the devil is in the detail. Thread shortly: bmcgenomics.biomedcentral.com/articles/10....
A new paper out this weekend in which we analysed PeptideAtlas peptides in search of coding genes novel to the Ensembl/GENCODE reference set, The peptides suggested another 35 potential new coding genes, but the devil is in the detail. Thread shortly: bmcgenomics.biomedcentral.com/articles/10....
An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs - BMC Genomics
Background The human genome has been the subject of scrutiny for more than two decades, yet new protein coding genes are still being uncovered and recently ribosome profiling experiments have provided...
bmcgenomics.biomedcentral.com
Our 2025 State of the Climate Report was just published in BioScience by scientists from around the world including @michaelemann.bsky.social @petergleick.bsky.social This video (2 minutes) shows the key highlights: doi.org/10.1093/bios...
🚨 Earth's vital signs are flashing red. 🌡️ 2024 was the hottest year in recorded history. Read the latest Climate report from @williamripple.bsky.social and Christopher Wolf's team, published in BioScience. oxford.ly/47i6K5j
We have recalculated APPRIS principal isoforms for GENCODE v48 / Ensembl 114 human. GENCODE added loss of function genes to this version and we discovered that this caused the TRIFID scores to change, affecting some of the PRINCIPAL:2 -> PRINCIPAL:5 isoforms. Our fault, we asked for the change!
So, our definitive paper on the human reference gene set is out this week in Database (Oxford). We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies. Details of what we found in the thread ...
There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd. It's not just budgets but research, institutions, expertise, and training the next generation.
The latest human GENCODE releases for Human (48) and Mouse (M37), have just been released. They're available via gencodegenes.org and visible in @ensembl.bsky.social genome browser as part of Ensembl 114 ensembl.org
GENCODE - Home page
gencodegenes.org
As I reported, ALL research abroad - especially if under a subaward - is in danger. “I don’t know how to make this clearer.. If a study has a foreign site, we need to start closing it down or finding a different way to fund it that can be tracked properly,” Matthew Memoli wrote to staff.
Overseas grants could be ‘closed down’ by NIH under new policy, internal email suggests
A NIH policy change on funding of foreign scientists is far more sweeping than described in a Thursday announcement
statnews.com
Max Kozlov@maxkozlov.bsky.social · last yr.NIH is ending billions of dollars in foreign subawards, jeopardizing thousands of projects on infectious diseases, cancer and more. Unless foreign researchers secure funding directly from NIH by October — a tall order for any researcher — clinical trials abroad and other research will shut down.
Per source, NIH has been instructed to hold off from issuing ALL awards to Harvard, Cornell, Columbia, Brown, and Northwestern (including med schools) Agency staff have also been instructed to not speak about this funding freeze to grantees and applicants
This week's dump takes the cancelled HHS grants and programs from 42 pages to 51. New this week: NIH has begun terminating projects about misinformation. This comes after the agency sent out a data call on March 26. One cancelled grant: "Cancer misinformation on social media and its correction"
taggs.hhs.gov
Max Kozlov@maxkozlov.bsky.social · last yr.🚨 NIH sent out another data call, this time for projects "related to any form of censorship at all or directing people to believe one idea over another related to health outcomes… e,g., any contracts to promote COVID vaccine uptake," I'm told. These data calls have recently preceded terminations.
"Peshkin said that Petrova was a highly skilled researcher and had a visa that enabled her to travel abroad freely. In February, when on vacation, her boss asked her to pick up frog embryo samples from colleagues in France." Starting to see a pattern here ... www.theguardian.com/us-news/2025...
Russian scientist working at Harvard detained by Ice at Boston airport
Kseniia Petrova was returning to the US from a trip to France when officials revoked her visa and detained her
theguardian.com
Yesterday when I talked to @maxkozlov.bsky.social about this, I wondered which of my NIH-funded colleagues would have their grants cut. All of them. Research on pandemic viruses has now ground to a screeching halt in the US. www.nature.com/articles/d41...
Exclusive: NIH to cut grants for COVID research, documents reveal
Studies on climate change and South Africa are also on the latest list of grants to be terminated, according to updated documents obtained by Nature.
nature.com
"Since its establishment in 1898, the US National Plant Germplasm System and the scientists who support it have maintained the agricultural plant species that undergird our food system. Food security depends on the availability of diverse plant genetic resources." www.nytimes.com/2025/03/22/o...
Opinion | Why Did Elon Musk Go After Bunkers Full of Seeds? (Gift Article)
Gene banks are like a survivalist cache: our nation’s safeguard against all future challenges to growing the food we need.
nytimes.com
“My overall concern is whether this is a sensible use of resources rather than spending the money on trying to prevent species becoming extinct,” “As it is, we have some cute-looking hairy mice, and we have learned little biology.” www.theguardian.com/science/2025...
Scientists aiming to bring back woolly mammoth create woolly mice
Genetically modified mice have traits geared towards cold tolerance, in step towards modifying elephants
theguardian.com
An outgoing NIH director: "I think if Republicans in Congress don’t act soon ... we are damn near Trump realizing his dream of Putinizing America. I honestly, 100% believe if he’s not removed from office soon, 2024 will be our last free and fair election." golikehellmachine.com/doge-is-four...
Nate Brought | Maryland
I am the Director of the Executive Secretariat at the National Institutes of Health until COB Friday, February 28.
golikehellmachine.com
Users of APPRIS may have noticed that there is a new category of principal isoforms, Principal:M. These principal isoforms are exclusive to the human gene set and are principal isoforms that have been manually corrected. In GENCODE v47 there were 45 genes with Principal:M isoforms. Here is DCD:
APPRIS has updated to GENCODE v47 and mouse M36. Danio rerio has also been updated to Ensembl 113. in this release 80.7% of human coding genes have a PRINCIPAL:1 isoform. Also, we have begun the manual curation of principal isoforms. More soon. @gencodegenes.bsky.social @ensembl.bsky.social
Our paper analysing the protein coding genes added as part of the new T2T-CHM13 assembly of the human genome was officially published over the holidays. In particular it shows that what was previously thought to be the human WASH1C gene is actually a pseudogene. bsky.app/profile/mich...
Michael Tress@michaeltress.bsky.social · 2y agoWe find that 12 of the 13 WASHC1 paralogues are likely to be pseudogenes, and that the only functional WASHC1 gene is on chromosome 20, not on chromosome 9 as was previously thought. This goes some way to explaining why so little is known about this vital gene, an integral part of the WASH complex.
This week's paper (well, last week's paper, but it took time to process) returns to the theme of reference protein coding genes. We wanted to know if the human proteome was more streamlined after we merged RefSeq, @gencodegenes.bsky.social and UniProtKB back in 2018. www.biorxiv.org/content/10.1...
More than 2,500 coding genes in the human reference gene set still have unsettled status
In 2018 we analysed the three main repositories for the human proteome, Ensembl/GENCODE, RefSeq and UniProtKB. They disagreed on the coding status of one of every eight annotated coding genes. The ana...
biorxiv.org
So, this week's paper is about signal peptides and what they reveal about the function of N-terminally extended protein isoforms and other upstream translation such as uORFs. www.biorxiv.org/content/10.1...
The rapid degradation of translated upstream regions points to an inefficient translation initiation process
Large-scale experimental analyses find ever more abundant evidence of translation from start codons upstream of the canonical start site. This translation either generates entirely new proteins (from ...
biorxiv.org
ARHGAP36, a gene overexpressed in hair follicles in Bazex-Dupre-Christol syndrome in humans, is the gene behind orange fur and calicos and tortoiseshells in cats. Fascinating. www.science.org/content/arti...
Gene behind orange fur in cats found at last
After 60 years, scientists know why gingers, calicos, and tortoiseshells look the way they do
science.org
By the way, I totally disown the AI-generated rubbish that accompanies the paper we published today. I don't know what that gains apart from sensationalism. www.biorxiv.org/content/10.1...
A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation
The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have been proposed from large-scale RNASeq, ribosom...
biorxiv.org
