Nozomu Saeki
@nozomus.bsky.social
Postdoc with Dr. Carvunis at University of Pittsburgh, Yeast, micro Protein, Enthusiast of systems biology
Reposted by Nozomu Saeki
I am excited to see our performance assessment of the successor of Scanning SWATH on the Zeno TOF7600+ mass spectrometer - ZT Scan DIA - pre-printed (www.biorxiv.org/content/10.1...
Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput
Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in p...
www.biorxiv.org
May 14, 2025 at 8:35 AM
I am excited to see our performance assessment of the successor of Scanning SWATH on the Zeno TOF7600+ mass spectrometer - ZT Scan DIA - pre-printed (www.biorxiv.org/content/10.1...
Reposted by Nozomu Saeki
On this day in 1879, Maud Menten was born in Port Lambton, Ontario.
In her work as a medical researcher, she became a leading expert in histochemistry and enzyme kinetics while fighting against sexism in her field.
Let's learn more about her life!
🧵1/10
In her work as a medical researcher, she became a leading expert in histochemistry and enzyme kinetics while fighting against sexism in her field.
Let's learn more about her life!
🧵1/10
March 20, 2025 at 6:01 PM
On this day in 1879, Maud Menten was born in Port Lambton, Ontario.
In her work as a medical researcher, she became a leading expert in histochemistry and enzyme kinetics while fighting against sexism in her field.
Let's learn more about her life!
🧵1/10
In her work as a medical researcher, she became a leading expert in histochemistry and enzyme kinetics while fighting against sexism in her field.
Let's learn more about her life!
🧵1/10
Reposted by Nozomu Saeki
Our genome encodes > 7000 microproteins that have been previously ignored in genome annotations. How do these microproteins impact tissue function? Here, we use an in vivo single-cell CRISPR screen to systematically explore microprotein function in the mouse epidermis. 1/9
www.biorxiv.org
March 19, 2025 at 3:44 PM
Our genome encodes > 7000 microproteins that have been previously ignored in genome annotations. How do these microproteins impact tissue function? Here, we use an in vivo single-cell CRISPR screen to systematically explore microprotein function in the mouse epidermis. 1/9
Reposted by Nozomu Saeki
#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
Reposted by Nozomu Saeki
Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment https://www.biorxiv.org/content/10.1101/2025.02.19.639069v1
February 23, 2025 at 6:33 PM
Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment https://www.biorxiv.org/content/10.1101/2025.02.19.639069v1
Reposted by Nozomu Saeki
Sometimes the #microprotein field needs to police itself.
I rarely see the point in sharing disapproval for published papers. Let bygones be bygones, I suppose.
Several days ago, however, a new paper came out. My assessment is that it is bogus.
#genomics
🧬 💻
1/
www.nature.com/articles/s41...
I rarely see the point in sharing disapproval for published papers. Let bygones be bygones, I suppose.
Several days ago, however, a new paper came out. My assessment is that it is bogus.
#genomics
🧬 💻
1/
www.nature.com/articles/s41...
Comprehensive discovery and functional characterization of the noncanonical proteome - Cell Research
Cell Research - Comprehensive discovery and functional characterization of the noncanonical proteome
www.nature.com
January 16, 2025 at 12:32 PM
Sometimes the #microprotein field needs to police itself.
I rarely see the point in sharing disapproval for published papers. Let bygones be bygones, I suppose.
Several days ago, however, a new paper came out. My assessment is that it is bogus.
#genomics
🧬 💻
1/
www.nature.com/articles/s41...
I rarely see the point in sharing disapproval for published papers. Let bygones be bygones, I suppose.
Several days ago, however, a new paper came out. My assessment is that it is bogus.
#genomics
🧬 💻
1/
www.nature.com/articles/s41...
Can a function grow gradually?
rdcu.be/d5vRC
rdcu.be/d5vRC
The gradational nature of biological functions: lessons from genome biology
rdcu.be
January 7, 2025 at 9:22 PM
Can a function grow gradually?
rdcu.be/d5vRC
rdcu.be/d5vRC
Reposted by Nozomu Saeki
He said he realized that the protein didn’t do anything.
The RNAs evolved to regulate themselves in an appropriate way, taking advantage of a protein whose structure changed depending on the cellular iron status.
22/n
The RNAs evolved to regulate themselves in an appropriate way, taking advantage of a protein whose structure changed depending on the cellular iron status.
22/n
a man in a suit and bow tie is sitting at a desk with his arms outstretched in front of a globe .
ALT: a man in a suit and bow tie is sitting at a desk with his arms outstretched in front of a globe .
media.tenor.com
December 31, 2024 at 1:29 PM
He said he realized that the protein didn’t do anything.
The RNAs evolved to regulate themselves in an appropriate way, taking advantage of a protein whose structure changed depending on the cellular iron status.
22/n
The RNAs evolved to regulate themselves in an appropriate way, taking advantage of a protein whose structure changed depending on the cellular iron status.
22/n
Reposted by Nozomu Saeki
Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
December 31, 2024 at 1:09 PM
Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight
Reposted by Nozomu Saeki
Excited to share our review article "Finding functional microproteins", published in @TrendsGenetics. It was fun writing it together with Alex and @FeiyueYang1 in the lab. #microprotein authors.elsevier.com/a/1kNCscQbJB...
January 2, 2025 at 9:55 PM
Excited to share our review article "Finding functional microproteins", published in @TrendsGenetics. It was fun writing it together with Alex and @FeiyueYang1 in the lab. #microprotein authors.elsevier.com/a/1kNCscQbJB...
Reposted by Nozomu Saeki
"GENETICS, the flagship journal of the Genetics Society of America, is calling for papers for a Special Issue on Experimental & Computational Methods."
Eds: Stan Fields (UW Seattle), Maria Chikina (U Pittsburgh), Konrad Lohse (U Edinburgh).
Deadline Mar 1, 2025.
click.skem1.com/click/bbu3-2...
Eds: Stan Fields (UW Seattle), Maria Chikina (U Pittsburgh), Konrad Lohse (U Edinburgh).
Deadline Mar 1, 2025.
click.skem1.com/click/bbu3-2...
Methods: a call for papers
The journal GENETICS is calling for submission of papers for a Special Issue on Experimental and Computational Methods.
click.skem1.com
December 20, 2024 at 3:07 AM
"GENETICS, the flagship journal of the Genetics Society of America, is calling for papers for a Special Issue on Experimental & Computational Methods."
Eds: Stan Fields (UW Seattle), Maria Chikina (U Pittsburgh), Konrad Lohse (U Edinburgh).
Deadline Mar 1, 2025.
click.skem1.com/click/bbu3-2...
Eds: Stan Fields (UW Seattle), Maria Chikina (U Pittsburgh), Konrad Lohse (U Edinburgh).
Deadline Mar 1, 2025.
click.skem1.com/click/bbu3-2...
Reposted by Nozomu Saeki
We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...
Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains | PNAS
The current “consensus” order in which amino acids were added to the genetic code
is based on potentially biased criteria, such as the absence of s...
www.pnas.org
December 12, 2024 at 3:43 PM
We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...
Reposted by Nozomu Saeki
Register by Dec. 17 (11:59pm MST) for the Microproteins conference and save $200! Join organizer @thomasmartinez.bsky.social, Keynote Speaker @Jonathan W. Yewdell, and other experts to explore microproteins' roles in health and disease in Massachusetts! keysym.us/KSMicroprote... #KSMicroproteins25
December 5, 2024 at 6:17 PM
Register by Dec. 17 (11:59pm MST) for the Microproteins conference and save $200! Join organizer @thomasmartinez.bsky.social, Keynote Speaker @Jonathan W. Yewdell, and other experts to explore microproteins' roles in health and disease in Massachusetts! keysym.us/KSMicroprote... #KSMicroproteins25
Reposted by Nozomu Saeki
Can a single small molecule rescue the stability of nearly all mutations in a protein?
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...
A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
Reduced protein stability is the most frequent mechanism by which rare missense variants cause disease. A promising therapeutic avenue for treating destabilizing variants is pharmacological chaperones...
www.biorxiv.org
December 3, 2024 at 9:40 AM
Can a single small molecule rescue the stability of nearly all mutations in a protein?
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...
Reposted by Nozomu Saeki
#Proteomics must be one of the few fields where people still think that a long list of authors & the phrase "high-quality" will boost the credibility of a phenomenon that has been well-known (& ignored) for years. doi.org/10.1101/2024...
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins
A major scientific drive is to characterize the protein-coding genome as it provides the primary basis for the study of human health. But the fundamental question remains: what has been missed in prio...
doi.org
November 29, 2024 at 7:06 PM
#Proteomics must be one of the few fields where people still think that a long list of authors & the phrase "high-quality" will boost the credibility of a phenomenon that has been well-known (& ignored) for years. doi.org/10.1101/2024...
Reposted by Nozomu Saeki
RP PLS! Iʻm hiring 3 postdocs at U Hawaiʻi to study yeast diversity and evolution, marine fungi, and the genomics of microbiomes in experimental foodwebs. All of these projects have existing datasets and LATITUDE to pursue individual interests and "blue sky" ideas www.dropbox.com/scl/fi/5d7u4...
November 26, 2024 at 7:19 PM
RP PLS! Iʻm hiring 3 postdocs at U Hawaiʻi to study yeast diversity and evolution, marine fungi, and the genomics of microbiomes in experimental foodwebs. All of these projects have existing datasets and LATITUDE to pursue individual interests and "blue sky" ideas www.dropbox.com/scl/fi/5d7u4...
Reposted by Nozomu Saeki
Do you want to go further with your proteomics? Looking for something new in cancer?
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
‘Dark proteome’ survey reveals thousands of new human genes
Database confirms that overlooked segments of the genome code for a multitude of tiny proteins
www.science.org
November 26, 2024 at 6:05 PM
Do you want to go further with your proteomics? Looking for something new in cancer?
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
Check out microproteins!
Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social
www.science.org/content/arti...
🔎 microprotein
🧬 💻
Reposted by Nozomu Saeki
The dark side of fluorescent protein tagging: the impact of protein tags on biomolecular condensation
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 25, 2024 at 12:19 PM
The dark side of fluorescent protein tagging: the impact of protein tags on biomolecular condensation
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nozomu Saeki
Wonderful tools for Ribosome profiling (Ribo-seq) within a web browser. Check out riboseq.org and academic.oup.com/nar/advance-... 🧪 #RNASky #ribosome
RiboSeq.Org
riboseq.org
November 23, 2024 at 12:23 AM
Wonderful tools for Ribosome profiling (Ribo-seq) within a web browser. Check out riboseq.org and academic.oup.com/nar/advance-... 🧪 #RNASky #ribosome
Reposted by Nozomu Saeki
Calling all systems and computational biologists in search of a faculty position:
We have Assistant and Associate Professor positions! 🚀
Pittsburgh is beautiful, and we are doing amazing science here.
cfopitt.taleo.net/careersectio...
cfopitt.taleo.net/careersectio...
Please apply by Dec 2!
We have Assistant and Associate Professor positions! 🚀
Pittsburgh is beautiful, and we are doing amazing science here.
cfopitt.taleo.net/careersectio...
cfopitt.taleo.net/careersectio...
Please apply by Dec 2!
Faculty.Professor.Assistant - Full-Time
Click the link provided to see the complete job description.
cfopitt.taleo.net
November 22, 2024 at 1:14 AM
Reposted by Nozomu Saeki
Once upon a time, FFPE was considered a death knell for studying molecular biology in archived cancer samples.
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue
Formalin-fixed paraffin-embedded FFPE patient tissues are a valuable resource for proteomic studies with the potential to associate the derived molecular insights with clinical outcomes. Here we prese...
www.biorxiv.org
November 20, 2024 at 8:20 PM
Once upon a time, FFPE was considered a death knell for studying molecular biology in archived cancer samples.
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.
Check out this new gem. 💎
#proteomics
#genomics
www.biorxiv.org/content/10.1...
Reposted by Nozomu Saeki
We will feature many of your favorite BlueSky scientists!
@carvunis.bsky.social
@thomasmartinez.bsky.social
@sebastiaanvheesch.bsky.social
@microproteins.bsky.social
@nickywhiffin.bsky.social
@uweohler.bsky.social
@luispedrocoelho.bsky.social
@slavofflab.bsky.social
@carvunis.bsky.social
@thomasmartinez.bsky.social
@sebastiaanvheesch.bsky.social
@microproteins.bsky.social
@nickywhiffin.bsky.social
@uweohler.bsky.social
@luispedrocoelho.bsky.social
@slavofflab.bsky.social
November 15, 2024 at 12:23 PM
We will feature many of your favorite BlueSky scientists!
@carvunis.bsky.social
@thomasmartinez.bsky.social
@sebastiaanvheesch.bsky.social
@microproteins.bsky.social
@nickywhiffin.bsky.social
@uweohler.bsky.social
@luispedrocoelho.bsky.social
@slavofflab.bsky.social
@carvunis.bsky.social
@thomasmartinez.bsky.social
@sebastiaanvheesch.bsky.social
@microproteins.bsky.social
@nickywhiffin.bsky.social
@uweohler.bsky.social
@luispedrocoelho.bsky.social
@slavofflab.bsky.social
Reposted by Nozomu Saeki
News in Proteomics Research | Astral vs TIMSTOF Ultra on real single cells? Just about evenly unreal numbers! proteomicsnews.blogs...
---
#proteomics #prot-other
---
#proteomics #prot-other
November 17, 2024 at 10:00 PM
News in Proteomics Research | Astral vs TIMSTOF Ultra on real single cells? Just about evenly unreal numbers! proteomicsnews.blogs...
---
#proteomics #prot-other
---
#proteomics #prot-other
Reposted by Nozomu Saeki
(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....
Extensive binding of uncharacterized human transcription factors to genomic dark matter
Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...
doi.org
November 15, 2024 at 7:02 PM
(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....
Reposted by Nozomu Saeki
We report many proteins not predicted by the genetic code.
They are stable & abundant O( 10³ ) copies / cell.
Generative mechanisms include codon-anticodon mismatches & RNA modifications.
Their abundance depends on codon frequency & protein stability.
www.biorxiv.org/content/10.1...
They are stable & abundant O( 10³ ) copies / cell.
Generative mechanisms include codon-anticodon mismatches & RNA modifications.
Their abundance depends on codon frequency & protein stability.
www.biorxiv.org/content/10.1...
Alternate RNA decoding results in stable and abundant proteins in mammals
Amino acid substitutions may substantially alter protein stability and function, but the contribution of substitutions arising from alternate translation (deviations from the genetic code) is unknown....
www.biorxiv.org
November 14, 2024 at 9:33 AM
We report many proteins not predicted by the genetic code.
They are stable & abundant O( 10³ ) copies / cell.
Generative mechanisms include codon-anticodon mismatches & RNA modifications.
Their abundance depends on codon frequency & protein stability.
www.biorxiv.org/content/10.1...
They are stable & abundant O( 10³ ) copies / cell.
Generative mechanisms include codon-anticodon mismatches & RNA modifications.
Their abundance depends on codon frequency & protein stability.
www.biorxiv.org/content/10.1...