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Nozomu Saeki

@nozomus.bsky.social
241 followers 534 following 5 posts

Postdoc with Dr. Carvunis at University of Pittsburgh, Yeast, micro Protein, Enthusiast of systems biology

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Reposted by Nozomu Saeki
Ludwig Sinn @lrsinn.bsky.social · 14/05/2025
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...
biorxiv.org
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...
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Canadian History Ehx @cdnhistoryehx.bsky.social · 20/03/2025
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
A black-and-white photo shows a woman in a patterned dress with a lace collar and pearl necklace, sitting in a chair. The background features shelves with bottles and a wire basket, suggesting an early 20th-century setting, possibly a pharmacy or study.
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Sendoel Lab @sendoellab.bsky.social · 19/03/2025
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
biorxiv.org
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John Prensner @johnprensner.bsky.social · 24/02/2025
#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
bit.ly
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...
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bioRxivpreprint @biorxivpreprint.bsky.social · 23/02/2025
Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment www.biorxiv.org/content/10.1101/202…
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John Prensner @johnprensner.bsky.social · 16/01/2025
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...
nature.com
Comprehensive discovery and functional characterization of the noncanonical proteome - Cell Research
Cell Research - Comprehensive discovery and functional characterization of the noncanonical proteome
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Nozomu Saeki @nozomus.bsky.social · 07/01/2025
Can a function grow gradually? rdcu.be/d5vRC
rdcu.be
The gradational nature of biological functions: lessons from genome biology
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Jeremy Berg @jeremymberg.bsky.social · 31/12/2024
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
media.tenor.com
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 .
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Jeremy Berg @jeremymberg.bsky.social · 31/12/2024
Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight
media.tenor.com
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
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Xuebing Wu @xuebingwu.bsky.social · 02/01/2025
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...
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Fritz Roth @fritzroth.bsky.social · 20/12/2024
"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...
click.skem1.com
Methods: a call for papers
The journal GENETICS is calling for submission of papers for a Special Issue on Experimental and Computational Methods.
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Reposted by Nozomu Saeki
Joanna Masel @joannamasel.bsky.social · 12/12/2024
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/...
pnas.org
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...
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Keystone Symposia @keystonesymposia.bsky.social · 05/12/2024
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
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Ben Lehner @benlehner.bsky.social · 03/12/2024
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...
biorxiv.org
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...
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Reposted by Nozomu Saeki
Anthony Amend @fungaloha.bsky.social · 26/11/2024
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...
A researcher on a boardwalk in a DANK hawaiian forest on Molokai.
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John Prensner @johnprensner.bsky.social · 26/11/2024
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 🧬 💻
science.org
‘Dark proteome’ survey reveals thousands of new human genes
Database confirms that overlooked segments of the genome code for a multitude of tiny proteins
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Joachim Goedhart @joachimgoedhart.bsky.social · 25/11/2024
The dark side of fluorescent protein tagging: the impact of protein tags on biomolecular condensation www.biorxiv.org/content/10.1...
Figure 4. Position and type of fluorescent tag affect protein expression and P-body numbers in vivo.
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Frances Yap @ribo1214.bsky.social · 23/11/2024
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
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Fritz Roth @fritzroth.bsky.social · 22/11/2024
🧪 #AcademicSky #AcademicJobs #SciJobs #ScienceJobs #STEMJobs #FacultyPosition
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John Prensner @johnprensner.bsky.social · 20/11/2024
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...
biorxiv.org
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...
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Reposted by Nozomu Saeki
John Prensner @johnprensner.bsky.social · 15/11/2024
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
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PastelBio @pastelbio.bsky.social · 17/11/2024
News in Proteomics Research | Astral vs TIMSTOF Ultra on real single cells? Just about evenly unreal numbers! proteomicsnews.blogs... --- #proteomics #prot-other
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Isaac Yellan @downbythebayes.bsky.social · 15/11/2024
(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....
doi.org
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...
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Reposted by Nozomu Saeki
Nikolai Slavov @slavov-n.bsky.social · 14/11/2024
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...
biorxiv.org
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....
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Alex Holehouse @alexholehouse.bsky.social · 10/11/2024
We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
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