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Sandeep Rai

@sandeeprai.bsky.social
62 followers 49 following 0 posts

Postdoc|Flynn lab| @BCHStemCell @HSCRB @SamratLabMohali @IiserMohali @iitdelhi Everything about RNA|Single-molecule biophysics|Super-resolution imaging 🔬.

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Reposted by Sandeep Rai
Ryan Flynn @raflynn5.bsky.social · 06/10/2026
Almost 1 year to the day, now published @cp-molcell.bsky.social, our report of cell surface DNA + csATAC to detect and study it. Jennifer et al have added many new data including proximity network analysis of csDNA on PBMCs and exciting data from SLE patients. www.sciencedirect.com/science/arti...
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Ivan Zanoni @lozanzi.bsky.social · 06/10/2026
#LocationLocationLocation! Excited for a small contribution to the new work @cp-molcell.bsky.social by @raflynn5.bsky.social, Porat &co showing that mitochondrial DNA is exposed on the plasma membrane & can be removed by DNASE1L3, aberrantly accumulating in #lupus patients!
cell.com
DNASE1L3 maintains homeostatic levels of mitochondrial DNA on the mammalian cell surface
Porat et al. develop cell surface ATAC-See, discovering that mitochondrial DNA is a component of the mammalian cell surface. Cell surface DNA (csDNA) on primary human and murine B cells and monocytes ...
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Brett Garabedian, PhD @brettgarabedian.bsky.social · 15/07/2026
www.nature.com/articles/s41...
nature.com
Targeting Siglec-engaging immunosuppressive sialoglycans to suppress prostate cancer bone metastasis - British Journal of Cancer
British Journal of Cancer - Targeting Siglec-engaging immunosuppressive sialoglycans to suppress prostate cancer bone metastasis
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Robert Arkowitz @robertarkowitz.bsky.social · 05/07/2026
www.biorxiv.org/content/10.6...
biorxiv.org
Single-Molecule Dwell Times in Biomolecular Condensates
Biomolecular condensates are dynamic, membrane-free compartments that continuously exchange molecules with their surroundings. The dwell time, defined as the time a molecule remains inside a condensat...
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Ryan Flynn @raflynn5.bsky.social · 29/06/2026
Taking our first steps towards sequencing the extracellular matrix by “Intact and single-molecule analysis of heparan sulfate” from @phristov.bsky.social in the lab, in collaboration with Miten Jain's lab. "HS-nano-seq" www.biorxiv.org/content/10.6...
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David Kuster @rnadavid.bsky.social · 05/06/2026
The E. coli DEAD box helicase CsdA is a NAD+-capped RNA binding protein! With the NAD+-RNA-binding proteome in E. coli! Amazing work by Kaustuv Das, ..., @schraderlab.bsky.social, @childerslab-pitt.bsky.social and @drjeremygbird.bsky.social! www.biorxiv.org/content/10.6...
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Andrew Stern @andrewmstern.bsky.social · 06/06/2026
We found that Aβ fibrils at plaque edges form a complex with the U1 snRNP. U1-70k is the most-correlated insoluble protein with Aβ in AD. Previously thought to be intracellular in tangles, but we find it’s directly bound to Aβ. With @raflynn5.bsky.social. www.biorxiv.org/content/10.6...
biorxiv.org
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Ryan Flynn @raflynn5.bsky.social · 02/06/2026
Eddy, Fardin, and I are happy to share a new review “Defining cell surface and glycosylated RNAs” in an effort to highlight the various sequencing-based tools used to study cell surface RNA biology. @cp-trendsgenetics.bsky.social #glycoRNA
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Thiago Carvalho @cyrilpedia.bsky.social · 31/05/2026
'If a control experiment fails, does that mean that the entire experiment is poorly designed and you must restart from scratch? Often, yes— but not always. I present five examples where failed control experiments triggered entirely new fields of research.' link.springer.com/article/10.1...
link.springer.com
The controls that got out of control - EMBO Reports
EMBO Reports - When experimental controls go wrong, it does not necessarily mean your experiment is flawed. It might well be the first sign of something unexpected.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 23/05/2026
Are you analysing hydrophobicity in disordered proteins and still using the Kyte & Doolittle scale? Maybe instead consider the "stickiness-scale" that Fan & Giulio derived using SAXS data for >100 IDPs doi.org/10.1021/acs....
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Brett Garabedian, PhD @brettgarabedian.bsky.social · 12/05/2026
“Here, we present extrabody, an activatable, modular antibody platform that enables optogenetic or chemical reassembly of split antibody fragments for inducible extracellular antigen recognition”
cell.com
An extracellular, optogenetic antibody platform for stimulus-gated antigen recognition and modulation of cell behavior
Precise control of antigen recognition remains a challenge in engineering cell-cell interactions. Kwon et al. develop extrabody, a split antibody platform that enables optogenetic and chemical control...
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Reposted by Sandeep Rai
Ritu Raman @rituraman.bsky.social · 11/05/2026
New preprint! Biohybrid #robots powered by skeletal muscle have historically relied on 3D tissue. Here we show that 2D skeletal muscle thin films can be 20X more efficient than their 3D counterparts - producing significantly larger forces from smaller tissue volumes: www.biorxiv.org/content/10.6...
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Keri Backus @keribackus.bsky.social · 03/05/2026
Super excited to launch POCAxOMAP with @dschweppe.bsky.social and @oligopain.bsky.social and led by Eli Biletch, Conor Herlihy and Lidan Li. If you’ve ever wanted to do proximity labeling on DNA, RNA, or protein without genetic engineering, look no further. www.biorxiv.org/content/10.6...
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adamjrubin.bsky.social @adamjrubin.bsky.social · 30/04/2026
Excited to share our paper out today in @science.org! We directed high-content, single-cell genetic screens to ask how a disordered adapter protein orchestrates the complex process of T cell activation. (1/4) www.science.org/doi/10.1126/...
science.org
Disordered protein LAT encodes relative levels of signaling pathways in T cell activation
The disordered adapter protein linker for activation of T cells (LAT) propagates T cell receptor signaling. To interrogate how LAT coordinates multiple downstream pathways, we developed a single-cell ...
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Ritu Raman @rituraman.bsky.social · 23/03/2026
Excited to see our MagMix platform on the cover of Device! MagMix is a modular, compact, material-agnostic in situ mixing platform for 3D bioprinters that actively + safely homogenizes cell-laden bioinks with no printer hardware/software mods: www.cell.com/device/fullt... @cellpress.bsky.social
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Priya R Banerjee @priya-r-banerjee.bsky.social · 02/01/2026
What physical principles actually govern whether stress granules promote or suppress amyloid formation? Check out our new preprint led by an outstanding collaborative team comprising our group and Tanja Mittag’s group at St. Jude CRH. www.biorxiv.org/content/10.6...
biorxiv.org
Viscoelasticity and interface properties of multi-component condensates govern protein sequestration and suppression of amyloid formation
Stress granules (SGs) are multi-component protein–RNA condensates widely viewed as crucibles for fibril formation in neurodegenerative diseases such as amyotrophic lateral sclerosis. Here, we test thi...
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Ritu Raman @rituraman.bsky.social · 02/02/2026
New #3Dbioprinting paper out today in Device @cellpress.bsky.social! Presenting MagMix: a compact modular platform for active in situ bioink mixing during bioprinting. MagMix uses a magnetic propellor to prevent cell settling, enabling consistent fabrication of large tissues: doi.org/10.1016/j.de...
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Vincent Graziano @vinnieviruses.bsky.social · 28/01/2026
Huge advance in glycoRNA biology. Congrats to @raflynn5.bsky.social and all of the wonderful authors! Can’t wait to see what you guys do next!
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 28/01/2026
New #glycotime discovery from @raflynn5.bsky.social’s lab @bostonchildrens.bsky.social @harvard.edu, cell surface glycoRNA-RBP complexes organized by heparan sulfate PG nanoclusters that modulate VEGF signaling www.nature.com/articles/s41...
nature.com
GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling - Nature
Heparan sulfate proteoglycans facilitate the assembly of clusters of glycoRNAs and cell surface RNA-binding proteins, which negatively modulate VEGF-A signalling and angiogenesis.
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Ryan Flynn @raflynn5.bsky.social · 28/01/2026
Science update from my postdoc Peiyuan Chai - his work “glycoRNA complexed with heparan sulfate regulates VEGF-A signaling” is now published @nature.com uncovering a new layer or glycoRNA-regulation of growth factor mediated control physiological processes rdcu.be/e1bBX
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Ritu Raman @rituraman.bsky.social · 28/01/2026
Out today in Nature - our collaborative work with Ryan Flynn's lab, led by Dr. Peiyuan Chai with support from Dr. @sinakheiri.bsky.social and @shahjess.bsky.social from our group. Exciting findings showcasing how glycoRNAs can modulate angiogenesis!
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bioRxivpreprint @biorxivpreprint.bsky.social · 15/12/2025
The vault associates with membranes in situ www.biorxiv.org/content/10.64898/20…
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Ritu Raman @rituraman.bsky.social · 16/12/2025
Excited to share our new paper on high-throughput #optogenetic #exercise assays for tissue engineered skeletal muscle! We leverage a multi-well stimulation apparatus to study how exercise regimen of various durations + frequencies impact muscle gene expression: doi.org/10.1002/btm2... #myoblue
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Olivier Duss @olivierduss.bsky.social · 07/11/2025
The story of how multiple RBPs cooperate to repress translation is now out in @cp-cellreports.bsky.social by @marcopayr.bsky.social and in a great collaboration with @hennig-lab.bsky.social! www.cell.com/cell-reports...
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Sina Kheiri @sinakheiri.bsky.social · 21/11/2025
What if we could “nudge” blood vessels to grow where we want them, in 3D and over time? We show that mechanical strain can guide new vessel sprouts in 3D as they grow. Thanks to my co-authors @shahjess.bsky.social Shah, Shashaank Venkatesh, Roger Kamm, and @rituraman.bsky.social
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Ritu Raman @rituraman.bsky.social · 20/11/2025
Preprint alert: Our latest study shows that "4D" force patterning enables spatial control of angiogenesis! Check out how we use Magnetic Matrix Actuation to precisely fabricate of 3D microvascular networks: www.biorxiv.org/content/10.1... Led by @sinakheiri.bsky.social @shahjess.bsky.social!
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Subhabrata Maiti @subhachem.bsky.social · 16/11/2025
www.nature.com/articles/s41... Happy to share our latest article published in Nature Communications. #ReactionDiffusion system with Local inhibition Distal Activation..Potential to develop synthetic systems mimicking natural biological pathways with precise spatial and temporal control of signals.🧵
nature.com
A chemoenzymatic reaction-diffusion system with local inhibition and distal activation - Nature Communications
Achieving spatiotemporal gating of signals is desirable for mimicking of biological processes, but is challenging to achieve in synthetic systems. Here, the authors report a multicomponent chemoenzyma...
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Ryan Flynn @raflynn5.bsky.social · 31/10/2025
Lab organized a pretty good costume
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Molecular Cell @cp-molcell.bsky.social · 20/10/2025
Sugar coats shield immunogenic RNA modification:A new function for RNA glycosylation
dlvr.it
Sugar coats shield immunogenic RNA modification:A new function for RNA glycosylation
A new function of glycosylated RNAs has been discovered by Graziano et al. in which the glycosylation of RNA molecules shields acp³U RNA modification from triggering innate immune responses.
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Jerelle Joseph @jerelleaj.bsky.social · 08/10/2025
Is there a way to directly connect microstructural dynamics of condensates to their mechanical response? In his new pre-print, Pablo presents a “condensate Deborah number” that does just that! www.biorxiv.org/content/10.1...
biorxiv.org
Biomolecular condensate viscoelasticity is dictated by the interplay between single-molecule shape memory and mesh reconfigurability
Biomolecular condensates are membraneless organelles that compartmentalize biological functions in living cells. Formed by the phase separation of biomolecules, condensates possess a wide range of mec...
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Ryan Flynn @raflynn5.bsky.social · 07/10/2025
We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...
biorxiv.org
DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells
The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...
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Ryan Flynn @raflynn5.bsky.social · 06/10/2025
Lead by postdoc in the lab Ruiqi Ge and in collaboration with Bob Coffey’s lab, we are happy to share rPAL-seq for rapid and sensitive sequencing based profiling of glycoRNAs @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
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Nazlican Yürekli @nazlicanyurekli.bsky.social · 02/10/2025
🍬🔬Proteins are so sweet under the microscope .. 🍬🔬 As Möckl RG, for the first time, we image the single-protein glycosylation in native cell state with super-resolution microscopy, map cell-surface glycoproteins, and uncover their spatial organization. #MöckIRG #glycotime #glycoprotein #dnapaint
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SFG @sfglycobiology.bsky.social · 13/08/2025
4/5 The Glycobiology Significant Achievement Award: Dr. Ryan Flynn @raflynn5.bsky.social, Harvard University, 👏👏🥂
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Trends in Biochemical Sciences @cp-trendsbiochem.bsky.social · 11/07/2025
Available online - the Technology of the Month "Tools for illuminating the cell surface glycoRNA landscape" from Yuan Ma et al. #glycoRNA #RNABindingProteins #RBP #ARPLA #HieCo2 #MDEM #drFRET Read it here: authors.elsevier.com/a/1lOie3S6Gf...
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CrowDsourcing COndensate Database & Encyclopedia @cdcode.bsky.social · 11/06/2025
☀️summer is here - and so is CD-CODE v1.10 release!🤩 💡CD-CODE has now 719 manually curated #condensates (and ~40% are #human associated!) 💡Check out new #condensates and updated #protein - condensate connections at cd-code.org #Bioinformatics #DatabaseUpdate #IDR #RNP #RBP #cdcode
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CrowDsourcing COndensate Database & Encyclopedia @cdcode.bsky.social · 11/06/2025
The latest release was supported by the #condesathon joined by @mpi-cbg.de condensate community🤩 Big #thankyou to all the participants from @hymanlab.bsky.social, @tothpetroczylab.bsky.social and von Appen labs for your support and enthusiasm!💜
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Samrat Mukhopadhyay @samratmukhopadhyay.bsky.social · 07/06/2025
Happy to share our latest paper published in Science Advances @aaas.org. Congratulations to my incredible students, Sandeep @sandeeprai.bsky.social, Roopali @roopsiek.bsky.social (co-first author), Anusha @anushasarbahi.bsky.social & Ashish @ashishjoshi.bsky.social. www.science.org/doi/10.1126/...
science.org
Chaperone-mediated heterotypic phase separation regulates liquid-to-solid phase transitions of tau into amyloid fibrils
A chaperone tasked with protein quality control tunes the phase behavior of tau and prevents its pathological phase transitions.
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Anton Petrov @antonipetrov.bsky.social · 23/05/2025
🤯 Implications for OLE RNA as a natural integral membrane RNA from Ron Breaker's lab rnajournal.cshlp.org/content/earl...
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Trends in Biochemical Sciences @cp-trendsbiochem.bsky.social · 01/05/2025
Other articles include: - a Feature Review on cell surface glycoRNAs and RBPs (@raflynn5.bsky.social) - a Review on the ETC of methanogens - an Opinion on transcription factor dynamics - a Review on the repertoire of RNA-catalyzed reactions - a Review on Mps1 kinase in chromosome segregation
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 25/04/2025
Check it out - amazing new work by @raflynn5.bsky.social and Kostas Tzelepis labs, discovery of a cell surface RNA/glycoRNA binding protein that is also a cancer antigen, new target for antibody therapy! www.nature.com/articles/s41...
nature.com
Treatment of acute myeloid leukemia models by targeting a cell surface RNA-binding protein - Nature Biotechnology
An RNA-binding protein on leukemia cells provides an effective target in mouse models.
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Ryan Flynn @raflynn5.bsky.social · 25/04/2025
“Cell surface RNA biology: new roles for RNA binding proteins” Jennifer Porat and I discuss this new cellular topology on which to study RNA–RBP interactions and consider how changes in the csRBPs may drive autoimmune responses. @cp-trendsbiochem.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
Cell surface RNA biology: new roles for RNA binding proteins
Much of our understanding of RNA–protein interactions, and how these interactions shape gene expression and cell state, have come from studies looking…
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Ritu Raman @rituraman.bsky.social · 23/04/2025
Happy to share the latest in 2.5D and 3D biohybrid robots from our lab with a packed room at RoboSoft! Thanks to all the organizers for putting together an exciting workshop on "Soft Robotic Actuation and Sensing Based on Functional Materials"! robosoft2025.org
robosoft2025.org
IEEE Robosoft 2025 - IEEE RoboSoft 2025
Celebrating Interdisciplinarity in Soft Robotics The theme for the 8th IEEE-RAS International Conference on Soft Robotics (RoboSoft 2025) centers on “Interdisciplinarity and Widening Horizons”, emphas...
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Ryan Flynn @raflynn5.bsky.social · 23/04/2025
Excited to share Benson’s and Maria’s work in collab w/Kostas Tzelepis: we found the nucleolar protein NPM1 is a marker of AML and can be targeted therapeutically connecting ‘cell surface RNA biology’ to cancer biology @natbiotech.nature.com www.nature.com/articles/s41...
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Leonhard Möckl @lmoeckl.bsky.social · 23/04/2025
A wonderful study, published today in Nature Biotech.: NPM1 is a marker of AML and can be targeted for efficient therapy! @karimalmahayni.bsky.social created the first SR reconstructions of NPM1 on the cell surface. Great collaborative work, spearheaded by @raflynn5.bsky.social and Kostas Tzelepis!
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Ritu Raman @rituraman.bsky.social · 18/04/2025
Excited to help organize a session on "Dynamic Extracellular Matrices to Control Cell Signaling" at #TERMISAM2025! The deadline for abstract submissions is April 28 - please consider joining our session and sharing your work in this space: am2025.termis.org/abstract-ins... @termisam.bsky.social
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Ryan Flynn @raflynn5.bsky.social · 27/02/2025
www.sciencedirect.com/science/arti... for fast readers
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Ryan Flynn @raflynn5.bsky.social · 27/02/2025
Excited to share the work of Jonathan Perr where he uncovered a surprisingly common feature of cell surfaces - the presentation and clustering of RNA binding proteins with #glycoRNA. Critically support by #NIH @cp-cell.bsky.social www.cell.com/cell/abstrac...
cell.com
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.
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Nikolai Slavov @slavov-n.bsky.social · 27/02/2025
Biological systems find ingenuous solutions. Almost anything that can happen, happens. Still, I would not have guessed a role of RNA-binding proteins on the cell surface. @raflynn5.bsky.social and his team are boldly investigating glycoRNAs and following their leads.
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