Great presentation by Rosa Lozano-Durán @geminiteamlab.bsky.social focusing on geminivirus peptides (sORFs). Also, an important call at the end to increase plant virology at MPMI; there is much more to explore. #2025ISMPMI
July 14, 2025 at 7:21 AM
Great presentation by Rosa Lozano-Durán @geminiteamlab.bsky.social focusing on geminivirus peptides (sORFs). Also, an important call at the end to increase plant virology at MPMI; there is much more to explore. #2025ISMPMI
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!!
August 19, 2025 at 1:19 PM
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!!
But let's start from the beginning www.biorxiv.org/content/10.1...: Lorenzo cloned a library of > 10000 sORFs to performed pooled screens. Subjecting cancer cells to 6-thioguanine, two sORFs conferred increased survival: AltDDIT3 (-> elifesciences.org/articles/27860) ... \2
Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response
Microproteins encoded by short open reading frames (sORFs) of less than 100 codons have been predicted to constitute a substantial fraction of the eukaryotic proteome. However, relevance and roles of ...
www.biorxiv.org
December 9, 2024 at 9:28 PM
But let's start from the beginning www.biorxiv.org/content/10.1...: Lorenzo cloned a library of > 10000 sORFs to performed pooled screens. Subjecting cancer cells to 6-thioguanine, two sORFs conferred increased survival: AltDDIT3 (-> elifesciences.org/articles/27860) ... \2
#Microproteins may be the next frontier in #proteomics. But figuring out the publications can be tough.
If you are looking for some advice about microprotein evidence, check out the latest from our consortium. Lead by @carvunis.bsky.social and Aaron Wacholder!
🧬 💻
#genomics
#RNASky
bit.ly/4bgJSDm
If you are looking for some advice about microprotein evidence, check out the latest from our consortium. Lead by @carvunis.bsky.social and Aaron Wacholder!
🧬 💻
#genomics
#RNASky
bit.ly/4bgJSDm
Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment
Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-ba...
bit.ly
February 24, 2025 at 12:33 PM
#Microproteins may be the next frontier in #proteomics. But figuring out the publications can be tough.
If you are looking for some advice about microprotein evidence, check out the latest from our consortium. Lead by @carvunis.bsky.social and Aaron Wacholder!
🧬 💻
#genomics
#RNASky
bit.ly/4bgJSDm
If you are looking for some advice about microprotein evidence, check out the latest from our consortium. Lead by @carvunis.bsky.social and Aaron Wacholder!
🧬 💻
#genomics
#RNASky
bit.ly/4bgJSDm
📢 PhD Opportunity! 📢
Unlock the power of small genes in big diseases! 🧬🔍 Explore how sORFs in F.hepatica & M.bovis impact host immune responses — revealing potential drug & vaccine targets.
🔗 Apply now ##PhD ##Genomics ##OneHealth ##Parasitology ##LifeSciences
Unlock the power of small genes in big diseases! 🧬🔍 Explore how sORFs in F.hepatica & M.bovis impact host immune responses — revealing potential drug & vaccine targets.
🔗 Apply now ##PhD ##Genomics ##OneHealth ##Parasitology ##LifeSciences
Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions at Aberystwyth University on FindAPhD.com
PhD Project - Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions at Aberystwyth University, listed on FindAPhD.com
www.findaphd.com
December 27, 2024 at 12:00 PM
📢 PhD Opportunity! 📢
Unlock the power of small genes in big diseases! 🧬🔍 Explore how sORFs in F.hepatica & M.bovis impact host immune responses — revealing potential drug & vaccine targets.
🔗 Apply now ##PhD ##Genomics ##OneHealth ##Parasitology ##LifeSciences
Unlock the power of small genes in big diseases! 🧬🔍 Explore how sORFs in F.hepatica & M.bovis impact host immune responses — revealing potential drug & vaccine targets.
🔗 Apply now ##PhD ##Genomics ##OneHealth ##Parasitology ##LifeSciences
I had all sorfs of things I wantedf to do tofay but suddenly I feel a littel aimless. Mayb even in a deeper, philosophical sensef.... buf in teh end, I am jusf a cat.
April 9, 2025 at 5:57 PM
I had all sorfs of things I wantedf to do tofay but suddenly I feel a littel aimless. Mayb even in a deeper, philosophical sensef.... buf in teh end, I am jusf a cat.
Registration is OPEN for the Gordon Research Conference on #Microproteins! Scholarships are available.
Get involved now while spaces are still available.
You won't want to miss this!
🧪
🧬 💻
🔎 microproteins
#darkgenome
#NoncodingGenome
#Cancer
#Proteomics
#sORFs
#Ribose
www.grc.org/decoding-mic...
Get involved now while spaces are still available.
You won't want to miss this!
🧪
🧬 💻
🔎 microproteins
#darkgenome
#NoncodingGenome
#Cancer
#Proteomics
#sORFs
#Ribose
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.
www.grc.org
November 29, 2024 at 6:35 PM
Registration is OPEN for the Gordon Research Conference on #Microproteins! Scholarships are available.
Get involved now while spaces are still available.
You won't want to miss this!
🧪
🧬 💻
🔎 microproteins
#darkgenome
#NoncodingGenome
#Cancer
#Proteomics
#sORFs
#Ribose
www.grc.org/decoding-mic...
Get involved now while spaces are still available.
You won't want to miss this!
🧪
🧬 💻
🔎 microproteins
#darkgenome
#NoncodingGenome
#Cancer
#Proteomics
#sORFs
#Ribose
www.grc.org/decoding-mic...
PLEASE SHARE: New PhD ALERT...New tools to detect small genes in genomes! Led by Dr Wayne Aubrey Comp Sci AU, myself and Dr Amanda Gibson @aberdlsagb.bsky.social and the wonderful @pauliomcveigh.bsky.social from QUB 🍂 #TeamFluke
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions at Aberystwyth University on FindAPhD.com
PhD Project - Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions at Aberystwyth University, listed on FindAPhD.com
www.findaphd.com
December 17, 2024 at 1:53 PM
PLEASE SHARE: New PhD ALERT...New tools to detect small genes in genomes! Led by Dr Wayne Aubrey Comp Sci AU, myself and Dr Amanda Gibson @aberdlsagb.bsky.social and the wonderful @pauliomcveigh.bsky.social from QUB 🍂 #TeamFluke
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
First up a bioinformatics project with Dr Wayne Aubrey Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions www.findaphd.com/phds/project...
Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions at Aberystwyth University on FindAPhD.com
PhD Project - Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions at Aberystwyth University, listed on FindAPhD.com
www.findaphd.com
December 19, 2024 at 10:57 AM
First up a bioinformatics project with Dr Wayne Aubrey Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions www.findaphd.com/phds/project...
Link to publication: doi.org/10.1093/nar/...
Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response
Abstract. Microproteins encoded by short open reading frames (sORFs) of <100 codons have been predicted to constitute a substantial fraction of the euka
doi.org
November 27, 2025 at 7:55 AM
Link to publication: doi.org/10.1093/nar/...
Twenty-five years after the sequencing of the human genome, scientists are still uncovering hidden layers of the “book of life”.
A team led by CRAG researcher José Luis Riechmann published the first characterization of peptides derived from sORFs during flower development in Arabidopsis thaliana 🌸🔬
A team led by CRAG researcher José Luis Riechmann published the first characterization of peptides derived from sORFs during flower development in Arabidopsis thaliana 🌸🔬
March 17, 2026 at 3:31 PM
Twenty-five years after the sequencing of the human genome, scientists are still uncovering hidden layers of the “book of life”.
A team led by CRAG researcher José Luis Riechmann published the first characterization of peptides derived from sORFs during flower development in Arabidopsis thaliana 🌸🔬
A team led by CRAG researcher José Luis Riechmann published the first characterization of peptides derived from sORFs during flower development in Arabidopsis thaliana 🌸🔬
🧬 SPECIAL ISSUE REVIEW 🧬
Kearly & Nelson discuss historical and modern approaches and their limitations for identifying and characterizing plant short open reading frame-encoded peptides, and how improved techniques are rapidly changing the field 🌱
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
Kearly & Nelson discuss historical and modern approaches and their limitations for identifying and characterizing plant short open reading frame-encoded peptides, and how improved techniques are rapidly changing the field 🌱
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
November 22, 2025 at 9:29 AM
🧬 SPECIAL ISSUE REVIEW 🧬
Kearly & Nelson discuss historical and modern approaches and their limitations for identifying and characterizing plant short open reading frame-encoded peptides, and how improved techniques are rapidly changing the field 🌱
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
Kearly & Nelson discuss historical and modern approaches and their limitations for identifying and characterizing plant short open reading frame-encoded peptides, and how improved techniques are rapidly changing the field 🌱
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
With the explosive growth here at Bluesky, this is just a public service announcement that we have a #Microproteins feed for all things #sORFs. Send a message if you want to join and kick-start this group!
🔎 microproteins
🧬 💻
🧪
#genomics
#bioinformatics
#riboseq
bsky.app/profile/did:...
🔎 microproteins
🧬 💻
🧪
#genomics
#bioinformatics
#riboseq
bsky.app/profile/did:...
November 18, 2024 at 3:21 PM
With the explosive growth here at Bluesky, this is just a public service announcement that we have a #Microproteins feed for all things #sORFs. Send a message if you want to join and kick-start this group!
🔎 microproteins
🧬 💻
🧪
#genomics
#bioinformatics
#riboseq
bsky.app/profile/did:...
🔎 microproteins
🧬 💻
🧪
#genomics
#bioinformatics
#riboseq
bsky.app/profile/did:...
sORFdb - A database for sORFs, small proteins, and small protein families in bacteria https://www.biorxiv.org/content/10.1101/2024.06.19.599710v1
sORFdb - A database for sORFs, small proteins, and small protein families in bacteria https://www.biorxiv.org/content/10.1101/2024.06.19.599710v1
Small proteins with fewer than 100, particularly fewer than 50, amino acids are still largely unexpl
www.biorxiv.org
June 23, 2024 at 5:49 AM
sORFdb - A database for sORFs, small proteins, and small protein families in bacteria https://www.biorxiv.org/content/10.1101/2024.06.19.599710v1
We are excited to present this paper which has been the brain child of grad student Eric Malekos. He has taken all riboseq data and mass spec data available from immune cells and analyzed and categorized all potential sORFs. He performed 2 CRISPR screens in macrophages to identify functional sORFs.
Integrative multiomics analysis and CRISPR screening identify functional noncanonical translation loci in the mouse immune system. https://www.biorxiv.org/content/10.64898/2026.02.23.707583v1
February 25, 2026 at 3:01 AM
We are excited to present this paper which has been the brain child of grad student Eric Malekos. He has taken all riboseq data and mass spec data available from immune cells and analyzed and categorized all potential sORFs. He performed 2 CRISPR screens in macrophages to identify functional sORFs.
Riboseq identifies 98 alternative ORFs & sORFs beyond HIV-1's canonical CDSs in CD4⁺ T cells. Huge strides in understanding HIV's coding potential! 🌟 #HIVResearch PMID:39966340, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-56773-2 #Medsky #Pharmsky #RNAsky 🧪
Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling | Nature Communications
The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observe that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of people living with HIV, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that a
doi.org
March 11, 2025 at 12:10 PM
Riboseq identifies 98 alternative ORFs & sORFs beyond HIV-1's canonical CDSs in CD4⁺ T cells. Huge strides in understanding HIV's coding potential! 🌟 #HIVResearch PMID:39966340, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-56773-2 #Medsky #Pharmsky #RNAsky 🧪
📝 SPECIAL ISSUE EDITORIAL 📝
"Peptides: powerful, pervasive, and full of potential"
Alyssa Kearly highlights the diversity of plant peptides, the discoveries still ahead and their potential for practical applications and advancing fundamental biology.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
"Peptides: powerful, pervasive, and full of potential"
Alyssa Kearly highlights the diversity of plant peptides, the discoveries still ahead and their potential for practical applications and advancing fundamental biology.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
November 20, 2025 at 1:44 PM
📝 SPECIAL ISSUE EDITORIAL 📝
"Peptides: powerful, pervasive, and full of potential"
Alyssa Kearly highlights the diversity of plant peptides, the discoveries still ahead and their potential for practical applications and advancing fundamental biology.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
"Peptides: powerful, pervasive, and full of potential"
Alyssa Kearly highlights the diversity of plant peptides, the discoveries still ahead and their potential for practical applications and advancing fundamental biology.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
High-throughput selection of human de novo-emerged sORFs with high folding potential https://www.biorxiv.org/content/10.1101/2024.01.22.576604v1
High-throughput selection of human de novo-emerged sORFs with high folding potential https://www.biorxiv.org/content/10.1101/2024.01.22.576604v1
De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo prote
www.biorxiv.org
January 24, 2024 at 9:36 PM
High-throughput selection of human de novo-emerged sORFs with high folding potential https://www.biorxiv.org/content/10.1101/2024.01.22.576604v1
The researchers identified 132 small peptides (SEPs), peptides derived from sORFs, 60 of which are likely involved in flower development. Many of these peptides are conserved across plant species, highlighting their important biological roles 🌿🧪
March 17, 2026 at 3:31 PM
The researchers identified 132 small peptides (SEPs), peptides derived from sORFs, 60 of which are likely involved in flower development. Many of these peptides are conserved across plant species, highlighting their important biological roles 🌿🧪
@fcyucn.bsky.social Hi! Before I start a GitHub issue for FragPipe I thought I'd ask you shortly here. Can a non-specific digest search on dia-pasef data with a custom database of sORFs + Human be run?
#teammassspec
#teammassspec
December 6, 2024 at 8:33 AM
@fcyucn.bsky.social Hi! Before I start a GitHub issue for FragPipe I thought I'd ask you shortly here. Can a non-specific digest search on dia-pasef data with a custom database of sORFs + Human be run?
#teammassspec
#teammassspec
Systematic Evaluation of Feature Representations for Cancer-Associated sORF Prediction in Non-coding RNA [new]
...benchmark ML models & feature ext. methods (k-mer, Word2Vec, gLM) to predict cancer sORFs, feature engineering crucial.
...benchmark ML models & feature ext. methods (k-mer, Word2Vec, gLM) to predict cancer sORFs, feature engineering crucial.
June 21, 2026 at 9:21 AM
Systematic Evaluation of Feature Representations for Cancer-Associated sORF Prediction in Non-coding RNA [new]
...benchmark ML models & feature ext. methods (k-mer, Word2Vec, gLM) to predict cancer sORFs, feature engineering crucial.
...benchmark ML models & feature ext. methods (k-mer, Word2Vec, gLM) to predict cancer sORFs, feature engineering crucial.
Our warmest congratulations to #ICREAResearcher José Luis Riechmann and team at @cragenomica.bsky.social!
They discovered tiny peptides that could be key for flower development, conserved across plant species. 🌿🧪
They discovered tiny peptides that could be key for flower development, conserved across plant species. 🌿🧪
CRAG (@cragenomica.bsky.social)
Twenty-five years after the sequencing of the human genome, scientists are still uncovering hidden layers of the “book of life”.
A team led by CRAG researcher José Luis Riechmann published the first characterization of peptides derived from sORFs during flower development in Arabidopsis thaliana 🌸🔬
bsky.app
March 19, 2026 at 8:03 AM
Our warmest congratulations to #ICREAResearcher José Luis Riechmann and team at @cragenomica.bsky.social!
They discovered tiny peptides that could be key for flower development, conserved across plant species. 🌿🧪
They discovered tiny peptides that could be key for flower development, conserved across plant species. 🌿🧪
🧪🌾Book - Would you like to learn more about microproteins?🧬
Naveen Shankar & @microproteins.bsky.social provide a concise overview of microproteins from discovery to biological significance.
Check out their book chapter in @springer.springernature.com Protocols:
link.springer.com/protocol/10....
Naveen Shankar & @microproteins.bsky.social provide a concise overview of microproteins from discovery to biological significance.
Check out their book chapter in @springer.springernature.com Protocols:
link.springer.com/protocol/10....
Microproteins: Uncovering Hidden Layers of the Proteome
Once dismissed as nonfunctional transcriptional noise, small open reading frames (sORFs) and their encoded microproteins have rapidly emerged as key players in diverse biological processes. Ranging fr...
link.springer.com
November 21, 2025 at 2:31 PM
🧪🌾Book - Would you like to learn more about microproteins?🧬
Naveen Shankar & @microproteins.bsky.social provide a concise overview of microproteins from discovery to biological significance.
Check out their book chapter in @springer.springernature.com Protocols:
link.springer.com/protocol/10....
Naveen Shankar & @microproteins.bsky.social provide a concise overview of microproteins from discovery to biological significance.
Check out their book chapter in @springer.springernature.com Protocols:
link.springer.com/protocol/10....
A good starting point to understanding the function of any protein is to look at its structure. In this paper, the groups of @bornberglab.bsky.social and @KlaraHlouchova have designed a #FRET-FACS based assay that estimates the folding propensity of de novo proteins.
🧵 6/9
🧵 6/9
High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential
Abstract. De novo genes emerge from previously noncoding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to ra
academic.oup.com
March 16, 2025 at 5:03 PM
A good starting point to understanding the function of any protein is to look at its structure. In this paper, the groups of @bornberglab.bsky.social and @KlaraHlouchova have designed a #FRET-FACS based assay that estimates the folding propensity of de novo proteins.
🧵 6/9
🧵 6/9
Pitt researchers are raising the bar for microprotein discovery.
By reassessing detection methods, Aaron Wacholder and Anne-Ruxandra Carvunis reveal why standardized protocols are essential for uncovering these elusive proteins' roles in health and disease.
tinyurl.com/NatureWachol...
By reassessing detection methods, Aaron Wacholder and Anne-Ruxandra Carvunis reveal why standardized protocols are essential for uncovering these elusive proteins' roles in health and disease.
tinyurl.com/NatureWachol...
Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics - PubMed
Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identificati …
tinyurl.com
January 21, 2026 at 4:09 PM
Pitt researchers are raising the bar for microprotein discovery.
By reassessing detection methods, Aaron Wacholder and Anne-Ruxandra Carvunis reveal why standardized protocols are essential for uncovering these elusive proteins' roles in health and disease.
tinyurl.com/NatureWachol...
By reassessing detection methods, Aaron Wacholder and Anne-Ruxandra Carvunis reveal why standardized protocols are essential for uncovering these elusive proteins' roles in health and disease.
tinyurl.com/NatureWachol...