Eclipsed Horizons: Unveiling the Dark Genome Amazon.com: Eclipsed Horizons: Unveiling the Dark Genome eBook : Sudhakaran Prabakaran: Kindle Store

my book is on kindle

📖 View the Kindle edition here: amazon.com/dp/B0GTV3D536/…

#NewRelease #KindleEdition #Genomics #DarkGenome #EclipsedHorizons #ScienceBooks #DarkProteome

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!

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.

1/

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

Five projects share £100m UK-US Cancer Grand Challenges fund Five scientific teams will receive up to £20m each in a new round of funding under the UK and US Cancer Grand Challenges initiative.

#CancerGrandChallenges #CRUK #NCI #UK #USA #oncology #cancer #ATLAS #INSERM #autoantibodies #tumours #REWIRECAN #UCLCancerInstitute #ILLUMINE #NetherlandsCancerInstitute #darkproteome #proteins #immunotherapies #antigenicmarkers #CAUSE #InteroCANCEption #FrancisCrickInstitute
zurl.co/P9eTF

teaching a NEW short course at @PEGSummit Boston on May 12 — "The Dark Proteome: Unlocking Novel Targets for Next-Gen Biologics."
join me → pegsummit.com
#DarkProteome #pegsboston #proteinengineering #antibodydiscovery #biotherapeutics #drugdevelopment #pegsummit

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...

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/...

Giraffe the cat sleeps

Saying goodbye to Giraffe the cat at the conclusion of the first ever #GRC on #microproteins #darkproteome. What a FANTASTIC meeting with worldwide and world class experts on all domains of the dark proteome. Get ready for 2027 because that is when the next of these fantastic meetings will occur!

Day 3 of the #GRC on #microproteins #darkproteome with a lively discussion on mega big data analyses for human #ncORFs #sORFs! What a great group!!

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

Last chance to sign up for the #GordonResearchConference on #Microproteins. Join us to learn about all things #DarkProteome / #RiboSeq!

Poster awards are still available for trainees! Get your abstracts in by July 20!!!

#Proteomics
#RNASky
#GENESky
#Bioinformatics

www.grc.org/decoding-mic...

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

ONE WEEK LEFT TO SIGN UP FOR the GRC on #Microproteins.

Students, trainees, and scientists interested in #darkproteome, #proteomics, #riboseq, #microproteins, #smORFs will not want to miss this.

Submit an abstract now and be eligible for a poster award!

www.grc.org/decoding-mic...

Summary of the ORFs in this catalog

tl;dr
This is a new authoritative catalog of #ncORFs for your #darkproteome research. We have updated many features, and expanded substantially from the original release. You can choose to use either a Comprehensive and Primary set.

This catalog will be supported by #GENCODE in forthcoming updates.

An expanded reference catalog of translated open reading frames for biomedical research Non-canonical (i.e., unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidence of their translation, limiting their incorporation into biomedical research. To address this, in 2022, we initiated the TransCODE consortium and built the first community-driven consensus catalog of human ncORFs, which was openly distributed to the research community via Ensembl-GENCODE. While this catalog represented a starting point for reference ncORF annotation, major technical and scientific issues remained. In particular, this initial catalogue had no standardized framework to judge the evidence of translation for individual ncORFs. Here, we present an expanded and refined catalog of the human reference annotation of ncORFs. By incorporating more datasets and by lifting constraints on ORF length and start-codon, we define a comprehensive set of 28,359 ncORFs that is nearly four times the size of the previous catalog. Furthermore, to aid users who wish to work with ncORFs with the strongest and most reproducible signals of translation, we utilized a data-driven framework (i.e. translation signature scores) to assess the accumulated evidence for any individual ncORF. Using this approach, we derive a subset of 7,888 ncORFs with translation evidence on par with canonical protein-coding genes, which we refer to as the Primary set. This set can serve as a reliable reference for downstream analyses and validation, with a particular emphasis on high quality. Overall, this update reflects continual community-driven efforts to make ncORFs accessible and actionable to the broader research public and further iterations of the catalog will continue to expand and refine this resource. ### Competing Interest Statement J.R.P. has received research honoraria from Novartis Biosciences and Quantum-Si, and is a paid consultant for ProFound Therapeutics. J.L.A. is an advisor to Microneedle Solutions. G.M. is co-founder and CSO of OHMX.bio. P.F. is a member of the scientific advisory board of Infinitopes. A.-R. C. is a member of the advisory board of ProFound Therapeutics. P.V.B. is a cofounder and shareholder of Eirnabio Ltd.

Are you looking to study the #darkproteome but don't know where to start?

Never fear, we've got your back.

Here, we share the latest catalog for #RiboSeq #ORFs.

Thanks to Sonia Chothani and @jruizorera.bsky.social for leading!

🧪
💻 + 🧬
#GENESky
#bioinformatics

www.biorxiv.org/content/10.1...

Webinar: Single-molecule proteome and proteoform analysis Join our webinar to discover how single-molecule proteomic analysis improves scale, sensitivity, and resolution. Learn about measuring 2,048 tau proteoforms in Alzheimer’s disease models.

In the article, you'll also find a link to our upcoming webinar (also linked below) where Parag and Taylor Bertucci will discuss exciting new proteoform data generated on the Nautilus Platform and its implications.

www.selectscience.net/webinar/brin...

#Proteomics #DarkProteome #Neuroscience

Single-molecule proteomics platform reveals biology’s hidden players Scalable single-molecule analysis could uncover low-abundance proteins and proteoforms critical for understanding complicated disease networks and therapeutic response

The dark proteome is mysterious and important and we're working to bring it into the light. Learn how in this article by Cameron Smith-Craig at Select Science:

www.selectscience.net/article/sing...

#Proteomics #DarkProteome #Proteoform #Proteoforms #Biotech #Biotechnology

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

Looking to come to the #GordonConference on #Microproteins / #DarkProteome, but missed the abstract deadline?

NO WORRIES. Late breaking abstracts are now accepted until July 20. Be eligible for a #BestPoster award!

#RNAsky
#Genomics
#Bioinformatics
#Proteomics
#RiboSeq

www.grc.org/decoding-mic...

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

Final reminder, folks.

Get your abstracts in for the first-time-ever #GordonConference on #microproteins and the #darkproteome. Deadline is June 1 if you want to be eligible for a selected oral abstract!

#GENEsky
#bioinformatics
#genomics
#RNAsky
🧪
💻 + 🧬

www.grc.org/decoding-mic...

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

LISTEN UP
You have until June 1 to be competitive for a travel award or short talk at the #GordonConference on #microproteins #darkproteome

Get your abstracts in soon!

You will not want to miss this event.

🧪
💻 + 🧬
#genomics
#bioinformatics
#RNAsky
#GeneSKY

www.grc.org/decoding-mic...

Dark Proteome | Illuminating the Dark Proteome Exploring the dark proteome & why it represents a critical, underexplored frontier in understanding and treating disease.

What is the 𝐝𝐚𝐫𝐤 𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐞 & what role does it plays in the manifestation & progression of diseases like #cancer?

See recent findings that reinforce why the #darkproteome is a critical new frontier to explore as part of #drugdevelopment: bit.ly/4drNGCZ

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

*LESS THAN 1 MONTH TO SUBMIT ABSTRACTS*

Sign up for the #GordonResearchConference on #microproteins and the #darkproteome now!

Scholarships are available for students. Apply by June 1 to be eligible!!!

www.grc.org/decoding-mic...

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

ONE MONTH LEFT if you want to be considered for a selected oral abstract & scholarship to attend the AMAZING Gordon Research Conference on #microproteins and the #darkproteome.

Students & Post-docs: Submit by June 1 to be eligible for a travel award!

www.grc.org/decoding-mic...

Hey #AACR2025 if you think #microproteins and the #darkproteome might be cool, come check out my session at 12:30pm today room S406!

2025 Decoding Microproteins Across Evolution and Disease Conference GRC The 2025 Gordon Research Conference on Decoding Microproteins Across Evolution and Disease will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.

ALERT: Time to turn your research to the #darkproteome.

The deadline is approaching for abstracts for the AMAZING Gordon Research Conference on 🔎 #microproteins.

Sign up now while space is available!

#RiboSeq
#RNASky
#Cancer
#Genomics
#Bioinformatics
#Proteomics

www.grc.org/decoding-mic...

Could blocking ‘jumping genes’ help fight disease and aging? The first clinical trials are testing inhibitors of transposons, DNA sequences that hop around the genome on their own

Great article in @science.org highlighting our efforts to target the #darkproteome!

Nice to see our colleagues David Ting, Daniel De Carvalho, and Marty Taylor highlighted along with the amazing work of @rometx.bsky.social👇👇👇

www.science.org/content/arti...

If you are interested in the #darkproteome and how this can impact diseases like #cancer and new #immunotherapy options, this is the conference for you!

If you are interested in #smallORF translation and #bigdata methodologies for RNA translation, this conference is for you!

Where else will you get access to the leaders and best in #RiboSeq, #Immunopeptidomics, and the #DarkProteome?

It's a once-a-year chance to get into this new field and don't miss out!

Alert to the #darkproteome community 👇

Here's a great article to get you fast-tracked into the world of #microproteins.

Such a pleasure to work on this piece with @nature.com, @sebastiaanvheesch.bsky.social, Marie Brunet, Jonathan Weissman and Jon Mudge.

#genomics
#bioinformatics
🧬 💻
#proteomics

Looks exciting for everyone jazzed about 🔎 microproteins and the #darkproteome!

I’m going to put it on my calendar.

Sign up below!

#proteomics
#RNAsky
#genomics
#bioinformatics
#microproteins

Speaker list for the 2025 Gordon Research Conference on Microproteins

If you are excited about the #darkproteome. If you want to delve into #ncORFs and #RiboSeq, then this is the meeting for you!

Check out the speaker list. 🤩

Come to the dark side! Join the #darkproteome team to work on plant functional annotation within our OSCARS
@HorizonEU
project FAIRFUN4Biodiversity. Great project, great advisor, great city and great team! 👇👇