iiinova — where your digital self keeps evolving

Michael Tress @michaeltress.bsky.social · 10/06/2026

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:

dN/dS analysis of two sections of the dual coding region in DCLK1
A. A representation of the two transcripts involved in the dual coding region annotated in DCLK1. The position of the red and purple lines corresponds to the image in panels B and C, stop codons are marked in yellow and blue. B. A representation of the cross-species alignment for transcript ENST00000359142 over the region corresponding to the final coding exon of ENST00000360631; dN/dS was calculated over codons that are indicated by the red horizontal line for this reading frame. C. A representation of the cross-species alignment for the final coding exon of ENST00000360631; dN/dS was calculated over codons indicated by the horizontal purple line for this frame. In panels B and C, codons are coloured by variant type, fluorescent green codons are synonymous with the human sequence, dark green and red codons are non-synonymous changes and stop codons are marked in yellow or blue (or purple).

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Michael Tress @michaeltress.bsky.social · 30/05/2026

Gleichschaltung. bsky.app/profile/alex...

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Max Kozlov @maxkozlov.bsky.social · 29/04/2026

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.

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Kevin Maguire @kevmag.bsky.social · 04/03/2026

"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...

theguardian.com

‘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’

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Adam Schwarz @adamjschwarz.bsky.social · 04/03/2026

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."

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Michael Tress @michaeltress.bsky.social · 15/12/2025

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

rdcu.be

The degradation of extended protein isoforms points to a misfiring translation initiation process

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Michael Tress @michaeltress.bsky.social · 24/11/2025

Finally managed to write a thread to go with our new paper ...

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Michael Tress @michaeltress.bsky.social · 24/11/2025

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....

bmcgenomics.biomedcentral.com

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...

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Prof William Ripple @williamripple.bsky.social · 02/11/2025

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...

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Oxford Academic @academic.oup.com · 31/10/2025

🚨 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

The 2025 state of the climate report: A planet on the brink

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APPRIS database @appris.bsky.social · 15/10/2025

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!

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Michael Tress @michaeltress.bsky.social · 30/09/2025

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 ...

Counts of the merged Ensembl/GENCODE, RefSeq and UniProtKB coding genes with the most likely explanations for the outliers for each gene set. For example, most Ensembl/GENCODE singletons are readthrough genes.

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Peter Gleick @petergleick.bsky.social · 31/05/2025

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.

Graphs showing 25 years of budgets for the National Institute of Health, NASA, and the NSF. In all cases, the proposed budget for next year is far, far below any year of the previous quarter century.

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Gencode Genes @gencodegenes.bsky.social · 08/05/2025

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

gencodegenes.org

GENCODE - Home page

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Max Kozlov @maxkozlov.bsky.social · 02/05/2025

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.

statnews.com

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

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Max Kozlov @maxkozlov.bsky.social · 18/04/2025

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

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Max Kozlov @maxkozlov.bsky.social · 04/04/2025

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

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Michael Tress @michaeltress.bsky.social · 28/03/2025

"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...

theguardian.com

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

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Angie Rasmussen @angierasmussen.bsky.social · 26/03/2025

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...

nature.com

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.

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Michael Tress @michaeltress.bsky.social · 25/03/2025

"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...

nytimes.com

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.

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Michael Tress @michaeltress.bsky.social · 04/03/2025

“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...

theguardian.com

Scientists aiming to bring back woolly mammoth create woolly mice

Genetically modified mice have traits geared towards cold tolerance, in step towards modifying elephants

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Michael Tress @michaeltress.bsky.social · 24/02/2025

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...

golikehellmachine.com

Nate Brought | Maryland

I am the Director of the Executive Secretariat at the National Institutes of Health until COB Friday, February 28.

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APPRIS database @appris.bsky.social · 24/02/2025

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 web page screenshot showing the new Principal:M annotation for the gene DCD

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APPRIS database @appris.bsky.social · 22/01/2025

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

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Michael Tress @michaeltress.bsky.social · 07/01/2025

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...

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Michael Tress @michaeltress.bsky.social · 10/12/2024

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...

biorxiv.org

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...

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Michael Tress @michaeltress.bsky.social · 27/11/2024

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...

science.org

Gene behind orange fur in cats found at last

After 60 years, scientists know why gingers, calicos, and tortoiseshells look the way they do

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PastelBio @pastelbio.bsky.social · 16/11/2024

A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation www.biorxiv.org/cont... --- #proteomics #prot-preprint

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Michael Tress @michaeltress.bsky.social · 18/11/2024

So, we have posted a new paper at BioRxiv. We carried out a deep manual curation of the human peptides identified in PeptideAtlas. This allowed to fill in some of the blanks in the @gencodegenes.bsky.social human gene set, including 16 novel protein coding genes. www.biorxiv.org/content/10.1...

biorxiv.org

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...

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APPRIS database @appris.bsky.social · 03/07/2024

APPRIS has new annotations for GENCODE human v46 and mouse M35. The human reference set now has 16,483 genes with Principal:P1 isoforms and mouse has 18,782 genes. Agreement with MANE Select transcripts in human (no MANE Select in mouse) has risen slightly to 17,661 genes. appris.bioinfo.cnio.es#/

appris.bioinfo.cnio.es

{APPRIS} - Annotating principal splice isoforms

Explore and download data on alternative splicing annotations and principal isoforms with the APPRIS Database, WebServer and WebServices.

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Michael Tress @michaeltress.bsky.social · 03/07/2024

We have just published a paper in which we take an in depth look at translation of 5' UTR regions. The key takeaways are that it is common and that most translation from 5' UTR is in-frame, so the effect at the protein level is to extend the N-terminal. academic.oup.com/nar/advance-...

academic.oup.com

Evidence for widespread translation of 5′ untranslated regions

Abstract. Ribosome profiling experiments support the translation of a range of novel human open reading frames. By contrast, most peptides from large-scale

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APPRIS database @appris.bsky.social · 26/03/2024

APPRIS has annotated principal and alternative isoforms and TRIFID functional isoform scores for Ensembl Bos taurus version e111: appris.bioinfo.cnio.es#/

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Arang Rhie @arhie.bsky.social · 12/03/2024

Congrats!! 👏👏 👏 This is an important piece demonstrating paralogous genes newly found in T2T-CHM13 better represents the coding form while the version in hg38 that was conceived as protein coding turned out to be a pseudogene. Also supported by the #HPRC assemblies. #T2Tgenomes

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Michael Tress @michaeltress.bsky.social · 12/03/2024

Finally published. Our paper on the fascinating recent history of human genes WASH1C and GPRIN2, uncovered as part of the T2T-CHM13 assembly. @arhie.bsky.social academic.oup.com/bioinformati...

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