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

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

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....

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

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.

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"

"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...

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...

"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...

“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...

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...

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...

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...

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...

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...

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 www.biorxiv.org/cont... --- #proteomics #prot-preprint

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...

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#/

#nmdar #nmda receptors #sorfs #uorfs #GRIN2B #GluN2B #regulation

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-...

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

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

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...