Here's a little widget to play with the data across journals (as well as download the raw CSVs).

sashagusev.github.io/Genetics_Pub...

Flow chart of the GENCODE Phase II ORF catalog

We think this reference data set can be used to drive discovery across biomedical science. The sky is the limit for future #DarkProteome science.

Thanks to Sonia Chothani, @jackatierney.bsky.social, Jon Mudge, Owen Rackham, @sebastiaanvheesch.bsky.social and TransCODE!

This is #NIH funded science!

Distribution of quality scores between the Comprehensive set and Primary set of ORFs

We then synthesize this information for a key innovation for the research community: a "gold-standard" set of ~10,000 noncanonical ORFs that we call the Primary set. These have data of equivalent quality to known protein-coding genes.

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Size distribution of noncanonical ORFs in the catalog

With this approach, we confidently assess even the smallest of ORFs, adding a huge abundance of ORFs less than 100 nucleotides to this public catalog.

4/

Metrics for riboseq data analysis

Our approach integrates state-of-the-art quality control metrics to evaluate over 28,000 non-canonical open reading frames found by RiboSeq data.

3/

Global collaboration for the TransCODE Consortium for noncanonical ORFs

Here, we leverage a global collaboration of institutions to consolidate evidence for the most well supported non-canonical ORFs for public dissemination.

Our goal? Simply to help all of your research efforts to make the next breakthrough for patients!

2/

An expanded reference catalog of translated open reading frames for biomedical research Abstract. Non-canonical (i.e. unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidenc

*MANUSCRIPT ALERT*

Today the TransCODE / GENCODE Phase II catalog of #RiboSeq ORFs came out in @narjournal.bsky.social

Check out the most authoritative resource for #DarkProteome discovery.

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academic.oup.com/nar/article/...

from random data to a story, using legos

🌐🧪

🚨 New paper from our lab just published in Nature🚨

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

Discover how 🌱 tumour formation is shaped by tissue context from the very beginning. Cancer is not driven by genetics alone

✨Fantastic team led by Greta Skrupskelyte, Eduardo Rojo, @hariajith.bsky.social

Team ILLUMINE of the Cancer Grand Challenges in New York City in December 2025

So honored to be a part of team ILLUMINE for the new #CancerGrandChallenges for the #DarkProteome.

Excited to crack open this new field in cancer biology!

Full announcement: www.cancergrandchallenges.org/new-teams-an...

All- don't miss the chance to register for the European Association for Cancer Research meeting in Budapest in June.

I'll be there if you want to chat about all things microproteins!

#EACR
#CancerResearch

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

China turns the tables in biotech For at least a century, major scientific research initiatives have reliably occurred in the United States, usually in response to geopolitical competition. This helped establish the country’s status a...

“Success in US science has come from sustained funding and welcoming the best talent from around the world, yet both of these advantages are in decline”

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

Check out the very important topic:
how does poverty influence childhood cancer biology and treatment response?

wonderful work from Birgit Knoechel and Kira Bona!
@huntsmancancer.bsky.social
@danafarber.bsky.social

www.biorxiv.org/content/10.6...

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...

Hallmarks of cancer—Then and now, and beyond Hanahan revisits the evolving framework of cancer hallmarks, synthesizing 25 years of conceptual refinement into a multidimensional view of tumor biology. This review highlights how aberrant capabilit...

Today at Cell: A new #HallmarksofCancer review by Doug Hanahan: www.cell.com/cell/fulltex...
This review marks 25 years since the original seminal Cell review by Hanahan & Robert Weinberg and its impactful follow up in 2011.
@cp-cell.bsky.social @cellpress.bsky.social

From the great @xuebingwu.bsky.social and team!

Highly recommend 👀

A protest about ICE in Ann Arbor

A protest against ICE in Ann Arbor

“The power of the people is greater than the people in power”

Even at 10F.

Ann Arbor this evening.

Systematic Analysis of C-Termini of Small Open Reading Frame-Encoded Peptides in Human Cancer Cell Lines The C-termini often regulate protein biological functions through specific structures or modifications. Small open reading frame-encoded peptides (SEPs) make up a novel class of gene expression products that participate in various biological activities. Their C-termini have also been found to affect their function, but the polymorphism of SEPs’ C-termini has not yet been systematically elucidated. Using C-terminal proteomics, we identified 3636 C-terminal peptides from 2168 proteins in three human cancer cell lines, including 3364 peptides from 1901 classical proteins and 272 peptides from 267 SEPs. Approximately 20% of all of the identified C-terminal peptides had been reported in previous studies, originating from mRNA alternative splicing or protease cleavage, while more than 85% of the C-terminal peptides from SEPs were novel. Bioinformatics analysis revealed that most new SEP C-termini are likely produced by protease cleavage by the KLK, MMP, and CAT protease families. Others without accurately predicted hydrolysis sites may originate from alternative splicing or protein trimming. The intact and hydrolysis products of some SEPs were verified by immunoblotting. Some cleavage occurs in the predicted domain, which might affect SEPs’ function. This study enriches the SEP sequence information, provides experimental evidence for SEP in vivo processing, and supports the subsequent functional analysis of SEP.

Systematic analysis of C-termini of small open reading frame-encoded peptides.

#Riboseq
#proteomics
#darkproteome

pubs.acs.org/doi/10.1021/...

The inside/ outside temperature differential exceeds 75 degrees this morning in Ann Arbor!

Sausage with eggplant with tomato sauce.

Lunch at Cafe du Lys in Geneva today. Magnificent!

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

Congress passes bill to fund U.S. science agencies, rebuffing Trump's requested cuts The Senate voted to provide billions more to NASA, NOAA and the National Science Foundation than the president had asked for.

Nice to see strong support in Congress: “In an 82-15 vote, the Senate approved a minibus budget bill to fund agencies involved in science and the environment, among other issues, through Sept. 30. The bill passed in the House last week by a vote of 397 to 28.” www.nbcnews.com/politics/pol...

Time for some fun!
A lovely paper on mathematical oncology.

🧪

#Math
#Cancer
#CANsky

www.biorxiv.org/content/10.6...

Bus with sign that says AAATA

Ann Arbor- where even the buses love to think about alternative polyadenylation sequences.

#RNAsky

Kids with brain cancer were already in a life and death struggle. Then came Trump The US president vowed to ‘end childhood cancer’. But his administration is dismantling the search for a cure and sending families scrambling for treatment

#ChildhoodCancer advocates-
This is a powerful piece on the negative impact of Trump administration policies on children with brain cancer, written by a spouse who lived this horror.

#DMG/DIPG
#ETMR
#Medulloblastoma
#PEDCAN

www.theguardian.com/us-news/ng-i...

Read our full statement by AAP President Dr. Andrew Racine on today’s HHS announcement about the childhood immunization schedule: www.aap.org/en/news-room...

Introducing you all to @mishamehta.bsky.social who has spent tireless hours advocating for children with brain tumors, supporting researchers doing their work, and building community for other families.

We are indebted to her: www.youtube.com/watch?v=_r_7...

#PEDCan
#CanSky
#CancerSurvivors

Humpback whale genomes reflect the increased efficiency of commercial whaling Humpback whale genomes reflect shifts in whaling practices and their potential impact on the animals’ adaptive capacity.

A new #ScienceAdvances study shows that commercial whaling in the Southern Ocean over the past century reduced the genetic diversity—and possibly the evolutionary fitness—of the region’s humpback whales. https://scim.ag/4anxPpM