Ankit Sinha
@asinha-yyz.bsky.social
Mass spectrometrist and cancer biologist researching atherosclerosis through the lens of proteomics. Likes and requotes are messages I bookmark for future investigation. YYZ/MUC. 🇨🇦in🇩🇪
Pinned
Ankit Sinha
@asinha-yyz.bsky.social
· Feb 13
Spatially resolved proteomic signatures of atherosclerotic carotid artery disease https://www.medrxiv.org/content/10.1101/2025.02.09.25321955v1
Our draft of proteomes of clinically advanced, #atherosclerosis carotid plaques. We used #proteomics to distinguish between stable and vulnerable plaques. Thanks to the members of @mannlab.bsky.social and Maegdefessel (TUM clinic) labs, as well as the #Cardiology & Surgery departments (TUM clinic).
Reposted by Ankit Sinha
Interpretable machine learning leverages proteomics to improve cardiovascular disease risk prediction and biomarker identification
->Nature | #MachineLearning #Disease #Health | More info from EcoSearch
->Nature | #MachineLearning #Disease #Health | More info from EcoSearch
Interpretable machine learning leverages proteomics to improve cardiovascular disease risk prediction and biomarker identification
The UK Biobank is a large-scale prospective study designed to investigate the impact of biological and environmental factors on human health. It enrolled ~500,000 participants aged 40–69 years old between 2006 and 2010 in England, Scotland, and Wales. In this...
www.nature.com
May 19, 2025 at 3:41 PM
Reposted by Ankit Sinha
Our paper is out in Nature today! We use Deep Visual Proteomics (DVP) to dissect α1-antitrypsin deficiency (AATD) in human liver at single-cell resolution.
Let us take a tour through proteotoxic stress in intact human tissue — one hepatocyte at a time.
www.nature.com/articles/s41...
Let us take a tour through proteotoxic stress in intact human tissue — one hepatocyte at a time.
www.nature.com/articles/s41...
Deep Visual Proteomics maps proteotoxicity in a genetic liver disease - Nature
High-resolution spatial proteomics were used to map molecular events during hepatocyte stress in pseudotime across all fibrosis stages, recapitulating known disease progression markers and revealing e...
www.nature.com
April 16, 2025 at 3:16 PM
Our paper is out in Nature today! We use Deep Visual Proteomics (DVP) to dissect α1-antitrypsin deficiency (AATD) in human liver at single-cell resolution.
Let us take a tour through proteotoxic stress in intact human tissue — one hepatocyte at a time.
www.nature.com/articles/s41...
Let us take a tour through proteotoxic stress in intact human tissue — one hepatocyte at a time.
www.nature.com/articles/s41...
Reposted by Ankit Sinha
Preprint alert ‼️
Excited to share our work investigating liver zonation in human health and disease with our advanced single-cell Deep Visual Peoteomics framework!
Excited to share our work investigating liver zonation in human health and disease with our advanced single-cell Deep Visual Peoteomics framework!
Introducing our single-cell DVP framework combining strategic cell selection with protein gradient mapping algorithms. Analyzing hepatocyte proteomes across 18 human livers, revealing cross-species differences, and mapping disruptions in liver fibrosis.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 14, 2025 at 12:34 PM
Preprint alert ‼️
Excited to share our work investigating liver zonation in human health and disease with our advanced single-cell Deep Visual Peoteomics framework!
Excited to share our work investigating liver zonation in human health and disease with our advanced single-cell Deep Visual Peoteomics framework!
Reposted by Ankit Sinha
🚨NEW PUBLICATION ALERT🚨: In a paper out now in
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
Engineering synthetic phosphorylation signaling networks in human cells
Protein phosphorylation signaling networks have a central role in how cells sense and respond to their environment. We engineered artificial phosphorylation networks in which reversible enzymatic phos...
science.org
January 7, 2025 at 8:24 AM
🚨NEW PUBLICATION ALERT🚨: In a paper out now in
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
Reposted by Ankit Sinha
It's time for individuals and organizations in Europe and other democratic countries to move mission- or life-critical IT services and infrastructure outside the reach of the US government; noting that US tech companies have already largely subordinated themselves.
www.huber.embl.de/group/posts/...
www.huber.embl.de/group/posts/...
Digital sovereignty – Huber Group @ EMBL
The US is now a mafia-style extortionist you want to stay away from
www.huber.embl.de
March 8, 2025 at 9:15 AM
It's time for individuals and organizations in Europe and other democratic countries to move mission- or life-critical IT services and infrastructure outside the reach of the US government; noting that US tech companies have already largely subordinated themselves.
www.huber.embl.de/group/posts/...
www.huber.embl.de/group/posts/...
What an outstanding study! This majorly expands our understanding by showing that glycosylated RBPs are not only present but also organized into specialized clusters. New avenues for cellular communication and therapeutic delivery strategies! Many congratulations @raflynn5.bsky.social and team.
RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry
Mammalian cells present RNA-binding proteins on the cell surface that form clustered
domains containing glycoRNAs.
www.cell.com
February 28, 2025 at 7:40 AM
What an outstanding study! This majorly expands our understanding by showing that glycosylated RBPs are not only present but also organized into specialized clusters. New avenues for cellular communication and therapeutic delivery strategies! Many congratulations @raflynn5.bsky.social and team.
Reposted by Ankit Sinha
Mindblowing new study by @raflynn5.bsky.social @bostonchildrens.bsky.social, cell surface RNA-binding proteins form nanoclusters with #glycoRNA and mediate cell-penetrating peptide entry into cells 👏
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry
Mammalian cells present RNA-binding proteins on the cell surface that form clustered
domains containing glycoRNAs.
www.cell.com
February 27, 2025 at 11:58 PM
Mindblowing new study by @raflynn5.bsky.social @bostonchildrens.bsky.social, cell surface RNA-binding proteins form nanoclusters with #glycoRNA and mediate cell-penetrating peptide entry into cells 👏
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
Reposted by Ankit Sinha
Out today in Nature Genetics: Using MS-based proteomics, we mapped 1,200+ plasma proteins in 2,100+ children, showing how genetics & development shape blood protein levels during childhood.
nature.com/articles/s41588-025-02089-2
#PediatricProteomics #pQTL
First author @liliniu.bsky.social explains ⬇️
nature.com/articles/s41588-025-02089-2
#PediatricProteomics #pQTL
First author @liliniu.bsky.social explains ⬇️
Plasma proteome variation and its genetic determinants in children and adolescents - Nature Genetics
This mass spectrometry-based proteomic study profiles the plasma proteome in 2,147 children and adolescents and reveals its association with age, sex, puberty, body mass index and genetics.
nature.com
February 19, 2025 at 10:44 AM
Out today in Nature Genetics: Using MS-based proteomics, we mapped 1,200+ plasma proteins in 2,100+ children, showing how genetics & development shape blood protein levels during childhood.
nature.com/articles/s41588-025-02089-2
#PediatricProteomics #pQTL
First author @liliniu.bsky.social explains ⬇️
nature.com/articles/s41588-025-02089-2
#PediatricProteomics #pQTL
First author @liliniu.bsky.social explains ⬇️
Reposted by Ankit Sinha
My favorite books, 2024
December 28, 2024 at 6:31 PM
My favorite books, 2024
Our draft of proteomes of clinically advanced, #atherosclerosis carotid plaques. We used #proteomics to distinguish between stable and vulnerable plaques. Thanks to the members of @mannlab.bsky.social and Maegdefessel (TUM clinic) labs, as well as the #Cardiology & Surgery departments (TUM clinic).
Spatially resolved proteomic signatures of atherosclerotic carotid artery disease https://www.medrxiv.org/content/10.1101/2025.02.09.25321955v1
February 13, 2025 at 3:32 AM
Our draft of proteomes of clinically advanced, #atherosclerosis carotid plaques. We used #proteomics to distinguish between stable and vulnerable plaques. Thanks to the members of @mannlab.bsky.social and Maegdefessel (TUM clinic) labs, as well as the #Cardiology & Surgery departments (TUM clinic).
Reposted by Ankit Sinha
🚀 Robust and high sensitivity #proteomics: Our Nature protocol demystifies #PASEF workflows and provides ready-to-use dia-PASEF & synchro-PASEF methods. Find out how to achieve 7,000 protein groups or 29,000 phosphosites in 21min. Let's explore! #TeamMassSpec #Bruker doi.org/10.1038/s415... 1/🧵
https://doi.org/10.1038/s41596-024-01104-w1/🧵
January 20, 2025 at 8:49 PM
🚀 Robust and high sensitivity #proteomics: Our Nature protocol demystifies #PASEF workflows and provides ready-to-use dia-PASEF & synchro-PASEF methods. Find out how to achieve 7,000 protein groups or 29,000 phosphosites in 21min. Let's explore! #TeamMassSpec #Bruker doi.org/10.1038/s415... 1/🧵
Reposted by Ankit Sinha
Our mipDVP workflow integrates 22-marker imaging with Deep Visual Proteomics to spatially map cell-type proteomes in hot/cold tumors, revealing distinct immune landscapes, macrophage barriers, T cell adaptations to hypoxia & tumor heterogeneity. Online in Molecular Cell.
doi.org/10.1016/j.mo...
doi.org/10.1016/j.mo...
January 14, 2025 at 4:24 PM
Our mipDVP workflow integrates 22-marker imaging with Deep Visual Proteomics to spatially map cell-type proteomes in hot/cold tumors, revealing distinct immune landscapes, macrophage barriers, T cell adaptations to hypoxia & tumor heterogeneity. Online in Molecular Cell.
doi.org/10.1016/j.mo...
doi.org/10.1016/j.mo...
Reposted by Ankit Sinha
Looking for rapid, deep & reproducible proteomics? Follow our @Nature protocol to get 7k proteins & 29k phosphosites in just 21 min! Complete #PASEF workflow using optimal dia-PASEF, synchro-PASEF & py_diAID. From method development to analysis. #TeamMassSpec @patiskowronek.bsky.social explains 👇
🚀 Robust and high sensitivity #proteomics: Our Nature protocol demystifies #PASEF workflows and provides ready-to-use dia-PASEF & synchro-PASEF methods. Find out how to achieve 7,000 protein groups or 29,000 phosphosites in 21min. Let's explore! #TeamMassSpec #Bruker doi.org/10.1038/s415... 1/🧵
https://doi.org/10.1038/s41596-024-01104-w1/🧵
January 22, 2025 at 11:40 AM
Looking for rapid, deep & reproducible proteomics? Follow our @Nature protocol to get 7k proteins & 29k phosphosites in just 21 min! Complete #PASEF workflow using optimal dia-PASEF, synchro-PASEF & py_diAID. From method development to analysis. #TeamMassSpec @patiskowronek.bsky.social explains 👇
Reposted by Ankit Sinha
Our Deep Visual Proteomics workflow maps protein networks in bladder, prostate, seminal vesicle & lymph node Signet Ring Cell Carcinoma, revealing DNA damage response alterations & immune signatures that could guide therapy choice. Out now in NPJ Precision Oncology! rdcu.be/d8KyK
Deep visual proteomics reveals DNA replication stress as a hallmark of signet ring cell carcinoma
npj Precision Oncology - Deep visual proteomics reveals DNA replication stress as a hallmark of signet ring cell carcinoma
rdcu.be
February 6, 2025 at 8:06 AM
Our Deep Visual Proteomics workflow maps protein networks in bladder, prostate, seminal vesicle & lymph node Signet Ring Cell Carcinoma, revealing DNA damage response alterations & immune signatures that could guide therapy choice. Out now in NPJ Precision Oncology! rdcu.be/d8KyK
Reposted by Ankit Sinha
A universal spectrum annotator for complex peptidoforms in mass spectrometry-based proteomics www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
January 26, 2025 at 10:40 AM
A universal spectrum annotator for complex peptidoforms in mass spectrometry-based proteomics www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
Reposted by Ankit Sinha
I would frame it another way. Science is a method to answer questions. We have drifted away from asking questions, or at least from asking good, focused questions, framing testable hypotheses and then testing with good experiments. Big datasets can be very useful, but we need good questions.
February 9, 2025 at 5:36 PM
I would frame it another way. Science is a method to answer questions. We have drifted away from asking questions, or at least from asking good, focused questions, framing testable hypotheses and then testing with good experiments. Big datasets can be very useful, but we need good questions.
For a good positive start, just a reminder that Claire Patterson was one of the greatest mass spectrometrist. It is very possible that most of us are alive because of him, and his will and determination to fight uphill. #proteomics #teamMassSpec
February 10, 2025 at 12:29 AM
For a good positive start, just a reminder that Claire Patterson was one of the greatest mass spectrometrist. It is very possible that most of us are alive because of him, and his will and determination to fight uphill. #proteomics #teamMassSpec