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Hirak Das

@hirakdas.bsky.social
109 followers 267 following 4 posts

Marie Curie ESR at Warscheid Lab, University of Würzburg | Mass Spectrometry | Spatial Proteomics and multi-omics | Peroxisomes | Loves playing with MS, Big Data, and AI

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Hirak Das @hirakdas.bsky.social · 05/08/2025
Great work by @dwendscheck.bsky.social from our lab and everyone else involved! This is a collaborative effort from many labs, which led to the identification and characterization a new (and important) Peroxin in more than 20 years!! 👏 Well deserved!
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Hirak Das @hirakdas.bsky.social · 28/04/2025
Happy to share our recent publication where we present the most up to date membrane protein inventory of #Glycosomes and identified the long sought trypanosomal PEX15. Thanks to everyone involved for this amazing collaborative effort to combine #proteomics with #functional #analysis.
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Slavov Laboratory @slavovlab.bsky.social · 25/03/2025
Be courageous to be creative.
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Alexey Nesvizhskii @nesvilab.bsky.social · 04/03/2025
One of the most significant and challenging projects of my career so far. PepCentric: a scalable computational platform utilizing novel 2-D fragment indexing for rapid peptide-centric searches, enabling proteogenomics searches against billions of spectra in seconds. www.biorxiv.org/content/10.1...
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Michael Baym @baym.lol · 17/02/2025
Please don’t stop sharing and posting your science because of the current attack on it, it is still valuable and reminds us what the fight is for
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Hirak Das @hirakdas.bsky.social · 14/02/2025
Had a great time keeping up with the "state-of-the-art" #Thermo #Astral MS instrument and analysis! 👍 Thanks to Michal! We go deeper into the #proteome, faster than ever!! Exciting times ahead.. ☀️
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Nikolai Slavov @slavov-n.bsky.social · 12/02/2025
In 2021, we introduced plexDIA: plexdia.slavovlab.net It enabled many studies, but suitable tags have remained a limitation. Soon, @parallelsq.bsky.social will introduce tags that improve multiplexing, sensitivity & coverage, helping realize huge potential pubs.acs.org/doi/10.1021/... Stay tuned!
plexdia.slavovlab.net
Home
Sensitive, accurate and high-throughput proteomics by multiplexed data-independent acquisition (plexDIA). plexDIA for increasing proteomics throughput Slavov Laboratory and single-cell proteomics cent...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/02/2025
Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com
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Ryan @geekryan.bsky.social · 03/02/2025
Scientists have created an actual treatment for prions, the cause of Creutzfeldt–Jakob disease in humans, chronic wasting disease in deer, & mad cow disease. "Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor". #ShareGoodNewsToo
science.org
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts...
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Itai Yanai @itaiyanai.bsky.social · 08/12/2024
The good idea comes when one person feels comfortable enough to say something that might make them look stupid and their friend is open enough to recognize its potential.
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Rita Strack @ritastrack.bsky.social · 06/12/2024
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
nature.com
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
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Ying Zhu @nanopots.bsky.social · 06/12/2024
After long-time review, #nanoSPLITS is finally published. I am deeply grateful to my colleagues who made this work possible, especially @cajunscience.bsky.social. I am also grateful to the support of our single-cell proteomics community during the peer review on Nature Communication!
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Hirak Das @hirakdas.bsky.social · 06/12/2024
Very important point raised by @rongfan8.bsky.social here: www.nature.com/articles/s41... I think we are slowly getting there. At least one step at a time, thanks to technological feats gained in MS community. For e.g recent nanoSPLITS method by @nanopots.bsky.social The future is exciting!
nature.com
Integrative spatial protein profiling with multi-omics - Nature Methods
Spatial proteomics holds the potential to transform the study of proteins in situ in complex tissues, but it needs to be integrated with other layers of omics data to gain a holistic view of cellular ...
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Oded Rechavi @odedrechavi.bsky.social · 05/12/2024
Scared to share this after 10 freaking years of waiting, but here we go: We found that temperature *perception* can change the biology of the next generations, even when “it’s just in the parents' head”. Read how C. elegans neurons control epigenetic inheritance! www.biorxiv.org/content/10.1...
biorxiv.org
Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance
Can processes occurring in one individuals nervous system influence the physiology of the descendants? Here we explored the provocative hypothesis that parents sensation or perception of environmental...
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Alice Ting @aliceyting.bsky.social · 04/12/2024
Could one envision a synthetic receptor technology that is fully programmable, able to detect diverse extracellular antigens – both soluble and cell-attached – and convert that recognition into a wide range of intracellular responses, from gene expression and real-time fluorescence to modulation..
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Stephan Hacker @stephanhacker2.bsky.social · 03/12/2024
Great to see, that @altmetric.com is now also tracking and reporting on activity on @bsky.app. This is a great further step to make bluesky the key social media network for science. (1/2) www.altmetric.com/de...
altmetric.com
Report for: Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050
In the top 5% of all research outputs scored by Altmetric
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ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · 02/12/2024
Related - there are whole high profile “protein atlases” based on transcript expression that are clearly inaccurate - proteomicsnews.blogspot.com/2024/06/re-r...
proteomicsnews.blogspot.com
Re-revisited the organ specific protein aging study - "organ specificity" is not supported by protein level data!
For anyone unfortunate to visit this blog in the past, you might have seen some of my early analysis and reanalysis of a high profile Natu...
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Walter W. Chen, MD, PhD @walterwchen.bsky.social · 23/11/2024
More recently in @rjdlab.bsky.social, we have discovered a new human peroxisomal biogenesis protein and revealed a new paradigm in peroxisomal protein import (www.biorxiv.org/content/10.1...)
biorxiv.org
PEX39 facilitates the peroxisomal import of PTS2 proteins
Peroxisomes are metabolic organelles essential for human health. Defects in peroxisomal biogenesis proteins (peroxins/PEXs) cause devastating disease. PEX7 binds newly synthesized proteins containing ...
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The Neuron Family @theneuronfamily.bsky.social · 23/11/2024
This diagram was made by Christine Liu, PhD - creator of two photon art @christineliuart.bsky.social I think you’ll love it :) @odedrechavi.bsky.social
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Alejandro Brenes @ajbrenes.com · 22/11/2024
My perspective on CVs for DIA-based #proteomics is out in JPR It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs. doi.org/10.1021/acs....
doi.org
Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics
The coefficient of variation (CV) is a measure that is frequently used to assess data dispersion for mass spectrometry-based proteomics. In the current era of burgeoning technical developments, there ...
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Yasset Perez-Riverol @ypriverol.bsky.social · 22/11/2024
We recently benchmarked multiple packages for #proteomics differential expression analysis. The biggest conclusion is that major differences among tools are only observed in lower-quality datasets. When you see a benchmark, first look into the data that was used. pubs.acs.org/doi/10.1021/...
pubs.acs.org
LFQ-Based Peptide and Protein Intensity Differential Expression Analysis
Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quan...
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PRIDE Database @pride-ebi.bsky.social · 19/11/2024
✨ Exciting news! This year, @pride-ebi.bsky.social introduced a new way to transfer data using the Globus protocol! 🚀 Check out this fantastic 15-minute intro video by @deeptijkundu.bsky.social, PRIDE's lead data curator: 📹 www.youtube.com/watch?v=VRNu... #DataTransfer #Proteomics #Globus #Faster
youtube.com
How to manually upload a proteomics dataset to PRIDE Archive database.
YouTube video by Yasset Perez-Riverol
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 15/11/2024
The Baker lab seems serious about moving into enzyme design. Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory. www.biorxiv.org/content/10.1...
 RFam design methodActivity characterizationCharacterization of A1 activity.
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PastelBio @pastelbio.bsky.social · 17/11/2024
News in Proteomics Research | Get ultralow flow rate nanoLC with ONE pump?? proteomicsnews.blogs... --- #proteomics #prot-other
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PastelBio @pastelbio.bsky.social · 24/01/2024
Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python www.biorxiv.org/cont... --- #proteomics #prot-preprint
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