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Luay Almassalha

@almassalha.bsky.social
107 followers 113 following 209 posts

Physician-Scientist studying and applying the rules of the physical genome in development, aging, cancer, and inflammation

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Reposted by Luay Almassalha
@PhysGenCenter @physgencenter.bsky.social · 29/09/2026
Just out in Nature Structural and Molecular Biology! CPGE scientists Vadim Backman and Luay Almassalha and colleagues present a framework for understanding how mechanical signals modulate cellular structure, identity and function in the context of cell memory. rdcu.be/wzhynmEQWQaa...
rdcu.be
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Kyle MacQuarrie MD PhD @kylemacquarrie.bsky.social · 28/09/2026
It’s the last days of Childhood Cancer Awareness Month, and our fundraising with Alex’s Lemonade Stand Foundation will soon be coming to an end. Anything from donations, to reposts, to supporting another peds cancer effort is much appreciated! www.alexslemonade.org/2026/macquar...
alexslemonade.org
MacQuarrie Lab
Every day, there are almost 800 new cases of childhood cancer around the world. This adds up to an estimated 300,000 new cases of cancer that affect children under the age of 20 each year worldwide. A...
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Reposted by Luay Almassalha
Richard Lenski @relenski.bsky.social · 22/09/2026
"Philosophy of Biology: The power of theory in the life sciences" elifesciences.org/articles/112... @zdblount.bsky.social shared this thought-provoking paper with the lab group.
elifesciences.org
Philosophy of Biology: The power of theory in the life sciences
Theory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets.
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Nezar Abdennur @nvictus.bsky.social · 19/09/2026
The 4DN Center for 3D Structure and Physics of the Genome proudly presents: "Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation". www.biorxiv.org/content/10.6...
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Harmit Singh Malik @harmitmalik.bsky.social · 11/09/2026
“…the push by AI companies to solve mathematical problems as a benchmark is detrimental to the science of mathematics, and to the mathematical community. The goals of the AI companies and the goals of the mathematical community are severely misaligned.“
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Masa A. Shimazoe @masaashimazoe.bsky.social · 09/09/2026
Our paper on euchromatin and cohesin is now published!!🙌 Euchromatin forms condensed domains, and cohesin constrains their local mixing. This organization maintains transcriptional insulation. This work was truly a team effort, and I’m grateful to everyone who contributed to it.
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Reposted by Luay Almassalha
Cees Dekker @ceesdekker.bsky.social · 09/09/2026
Latest #CDlab paper on BioRxiv: www.biorxiv.org/content/10.6... 1st author Eva Bertosin developed huge DNA origami nanopores that can dilate and constrict in size. With diameters up to 87 nm, they can insert into lipid membranes, showing selective transport when filled with nuclear pore proteins.
biorxiv.org
https://www.biorxiv.org/content/10.64898/2026.09.03.749129v1
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Reposted by Luay Almassalha
Kurianlab @kurianlab.bsky.social · 09/09/2026
Check this exciting study from @gabrijelad.bsky.social and colleagues: www.nature.com/articles/s41...
nature.com
The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis - Nature Cell Biology
Biayna, Baranovskii and colleagues report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the periphery of nuclear speckles and undergo synchronou...
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Reposted by Luay Almassalha
Jackson Hoffman @jxhoffman.bsky.social · 08/09/2026
I'm super excited for our new season of #FragileNucleosome seminars, which kicks off tomorrow with @mpalamin.bsky.social and @robertovn.bsky.social!
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Reposted by Luay Almassalha
Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 08/09/2026
It's worth reading the entire letter. The correct link is here. cims.nyu.edu/~tristanb/st...
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Reposted by Luay Almassalha
Gal Haimovich ☣ 🧪🔬🎗 @grnfluoresceblg.bsky.social · 07/09/2026
my papr was just published! 🧪 #RNABiology #tunnelingnanotubes www.cell.com/cell-reports...
cell.com
Complementation of a human disease phenotype by intercellular mRNA transfer
Intercellular mRNA transfer between mammalian cells in vitro occurs via tunneling nanotubes to express functional proteins upon translation that complement genetic mutation. Complementation via RNA tr...
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Reposted by Luay Almassalha
Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/09/2026
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)
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Prof Chris Jackson @seismatters.bsky.social · 07/09/2026
Has this been discussed here? #AcademicSky #Academia #ECR #HigherEducation www.nature.com/articles/s41...
nature.com
How contemporary academic structures constrain scientific creativity and hold back early-career researchers - Nature Human Behaviour
In this Perspective, Haubrock et al. argue that today’s scientific structures constrain creativity and that strategic conformity is a rational response. They discuss how this holds back early-career r...
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Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 03/09/2026
wait, wait, what ????? protein-coding chimeric mRNAs 🤯 www.nature.com/articles/s41...
nature.com
Functional chimeric mRNAs encode proteins in mammalian immunity - Nature
Inflammation induces interchromosomal DNA interactions that bring parent genes into close proximity, facilitating the formation of chimeric mRNAs that encode physiologically relevant, functional prote...
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Jorge Ferreira @jorgeferreira.bsky.social · 03/09/2026
Come and join us in the beautiful city of Porto in April 2027 for what promises to be a great meeting!
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Governor JB Pritzker @govpritzker.illinois.gov · 02/09/2026
A win for our state. NSF’s recognition of Northwestern’s Center for Genome Intelligence Engineering is a validation of the innovation we’re doing here to understand how cells function to prevent decline. We’re fostering the research and science needed to lead in Illinois.
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Teif lab @teiflab.bsky.social · 30/08/2026
AlBawardi et al, 2026. Irregular nucleosome positioning governs a crystalline to liquid-like phase transition and tunes chromatin accessibility www.biorxiv.org/content/10.6... ▶️heterochromatin-like sequences produce compact fibres ▶️positional irregularity (>2-3 bp) triggers a state transition
Abstract: Chromatin must fold tightly enough to protect the genome while being sufficiently accessible for DNA dependent processes such as transcription. The physical rules that balance these competing roles remain unclear, as DNA sequence encodes both biochemical information such as transcription factor binding sites, and biophysical cues that shape chromatin structure. Here, using synthetic chromatin fibres assembled from physiologically relevant DNA sequences, we show that nucleosome positioning dictates the material state of chromatin. Heterochromatin-like sequences produce compact fibres stabilised by nucleosome stacking, whereas euchromatin-like sequences generate irregular nucleosome positioning that yields disrupted, heterogeneous, and mechanically deformable fibres. Quantitative polymer modelling reveals that these irregular arrays are highly dynamic, continually sampling a broad ensemble of conformations as nucleosome stacking breaks down. We identify two previously unrecognised thresholds encoded by nucleosome positioning: minimal positional irregularity (2–3 bp) triggers a transition from an ordered paracrystalline state to a liquid-like phase, whereas an order of magnitude greater irregularity (∼18 bp) is required to generate accessibility and mechanical fragility permissive for transcription factor binding. Euchromatin-like arrays reside at this accessibility threshold. These findings indicate that nucleosome positioning tunes chromatin toward or away from critical structural states that couple genome protection, chromatin dynamics, and transcriptional potential—providing a physical mechanism that helps connect DNA sequence to gene expression.
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@PhysGenCenter @physgencenter.bsky.social · 29/08/2026
The NSF has awarded Northwestern $30 million to launch the Center for Genome Intelligence Engineering (GENIE). By treating the genome as a physical and a computational system, GENIE will harness cellular memory to combat injury, disease, aging and more www.mccormick.northwestern.edu/news/article...
mccormick.northwestern.edu
Northwestern to Launch $30 Million Center to Unlock Genome’s Hidden Code
Led by Northwestern Engineering’s Vadim Backman, the multi-institutional Science and Technology Center will integrate experts in physics, biology, engineering, AI, and medicine to understand how the g...
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Reposted by Luay Almassalha
Surya Nagaraja @snaga13.bsky.social · 26/08/2026
Very happy to announce that I’ll be launching my lab at WashU in 2027! We’ll build on this work to uncover the mechanisms and diversity of epigenetic memory and its role in human disease. Hiring at all levels to start early 2027 — learn more or reach out: nagarajalab.org
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Kate Cavanaugh @katecavanaugh.bsky.social · 25/08/2026
🧵 What if one reason fertility declines with age isn’t just genetic-but mechanical? Thrilled to share our new paper in @NatureCellBio : Elevated contractility drives implantation failure in mouse embryos from aged females… here’s what we found 👇 www.nature.com/articles/s41... 1/11
nature.com
Elevated contractility drives implantation failure in mouse embryos from aged females - Nature Cell Biology
Cavanaugh et al. show that embryos from aged mice have increased contractility and tissue viscosity on embryonic day 4.5, which leads to poor spreading and attachment. Similar age-associated mechanica...
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Thiago Carvalho @cyrilpedia.bsky.social · 26/08/2026
Blood of Crom! "It is clear that many of these vendors are using the same images as one another for their own versions of the same product. For instance, this HAS1 antibody from Thermo Fisher uses the same Western blot image as similar products from Millipore Sigma, Novus (R&D Systems) & Boster Bio"
reeserichardson.blog
At least 15 companies are selling antibodies using faked validation data
Popular vendors’ catalogs feature more than 18,000 manipulated images
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Seth Trueger @mdaware.org · 26/08/2026
we all have mental rolodexes of patients we never forget as an ER doc, I've taken care of quite a few patients where we found new -- almost always advanced -- pancreatic cancer this is great news and a nice reminder of why we all chip in and hire the best scientists to find new & better tools
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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...
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Job Dekker @jobdekker.bsky.social · 24/08/2026
How do nuclear compartments form inside cell nuclei? We show RNA glues certain loci together to form a nuclear compartment. This involves special GC-rich regions of highly expressed genes that also associate with nuclear speckles, but interactions between these loci are independent of speckles!
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Konrad Kording @kordinglab.bsky.social · 24/08/2026
Hiring for research scientists in expansion chemistry and optical physiology at mindspan.org with @eboyden3.bsky.social, Yongxin Zhao, Xue Han. We will build tools to analyze the human brain. We are into compiling arxiv.org/abs/2603.25713. We are into cutting edge technology.
mindspan.org
Mindspan Institute
A non-profit creating and applying tools to characterize the molecules and wiring of the human brain, as well as to interpret how they contribute to brain functions and dysfunctions, openly sharing to...
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Eric Topol @erictopol.bsky.social · 19/08/2026
mRNA vaccines vs cancer success —melanoma (Phase 3, RCT, definitive, announced today) —triple negative breast cancer —pancreatic cancer —non-small cell lung cancer —glioblastoma
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Bas van Steensel lab (NKI) @basvansteensellab.bsky.social · 18/08/2026
Inferring transcription factor activity: use ATAC-seq, reporter assays, or both? link.springer.com/article/10.1...
link.springer.com
Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays - Molecular Systems Biology
Transcription factors (TFs) are central to gene regulation and play critical roles in development, cellular homeostasis and disease. The ability to accurately measure TF activity is essential to under...
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Reposted by Luay Almassalha
Evgeny Kvon @evgenykvon.bsky.social · 18/08/2026
“Super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting” www.cell.com/cell-genomic...
cell.com
Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting
Super-enhancers have been proposed to cluster in the nucleus when compared to other genomic elements. Le et al. found that super-enhancer clustering was rare and driven by non-specific interactions. P...
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Harmit Singh Malik @harmitmalik.bsky.social · 18/08/2026
www.nsf.gov/news/foundat...
nsf.gov
August 2026 Notices of Funding Opportunity for Foundational Research
Learn about new NSF funding opportunities prioritizing foundational research across the sciences and engineering.
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Luay Almassalha @almassalha.bsky.social · 15/08/2026
I wonder if a White Sox starting pitcher will make it through the 3rd inning this weekend
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@PhysGenCenter @physgencenter.bsky.social · 14/08/2026
Just published in Advanced Science: "Chromatin Packing Domain Engineering Through the Manipulation of Nuclear Cationic States" "We may soon be able to engineer chromatin packing states to influence cell function” postdoctoral fellow Cody Dunton said. www.mccormick.northwestern.edu/news/article...
mccormick.northwestern.edu
Study Reveals New Way Cells Organize Their Genomes
Professor Vadim Backman’s group showed that changing the nucleus’s ionic environment can rapidly reshape chromatin and alter how cancer cells respond to chemotherapy.
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Randall Munroe @xkcd.com · 06/08/2026
I really recommend the 2022 documentary “It’s Quieter in the Twilight,” which profiles the scientists working in relative obscurity to keep the Voyager spacecraft operating—many of them past retirement age, but unwilling to quit until the Voyagers do. It was very sweet and thought-provoking.
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Simon Gaudin @simongaudin.bsky.social · 02/08/2026
Now out from Bintu lab: compaction following transient KRAB recruitment tracks long-term epigenetic memory. But K9me3 decays after KRAB release and is replaced by DNA methylation. Does compaction help maintain K9me3, or slow its loss enough to facilitate the handoff to DNAme? tinyurl.com/ycay4mrh
tinyurl.com
Single-cell chromatin state transitions during epigenetic memory formation
Large-scale chromatin compaction quantitatively predicts the percentage of cells with durable epigenetic memory of gene silencing.
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Geoff Faulkner @faulknerlab.bsky.social · 30/07/2026
Our study published today @science.org shows that X-chromosome inactivation (XCI) attracts L1 mutations to the human X chromosome: doi.org/10.1126/scie... With outstanding Perspective from @aurelien-doucet.bsky.social & @retrogenomics.bsky.social: doi.org/10.1126/scie...
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Laura Howes @laurahowes.bsky.social · 29/07/2026
Alas poor AlphaFold, we knew you well... This is not entirely surprising to me, as it wasn't clear what more AF could do outside of what Hassabis is trying to build with Isomorphic. But I am interested in people's thoughts here #chemsky #biotech 🧪 www.ft.com/content/61b2...
ft.com
Google DeepMind dismantles Nobel-winning AlphaFold team in strategy shift
Landmark project that solved protein folding gives way to a wider race to build AI systems for scientific discovery
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Casey Drottar @caseydrottar.bsky.social · 28/07/2026
Detroit Squirrel update: The Tigers' entire grounds crew went out on the field to try to get that thing out of there and all that's missing is the Benny Hill theme
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Jeremy Berg @jeremymberg.bsky.social · 24/07/2026
@dereklowe.bsky.social lets loose again (and I am still here for it). www.science.org/content/blog... 1/2
science.org
The Assault On Science Funding Continues
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Alejandro Montenegro @aemonten.bsky.social · 15/07/2026
Interesting. Full deletion of all introns in yeast was actually my project in the Staley lab, *20 years ago*. I actually found a bunch of phenotypes. We did this in collaboration with the Guthrie lab. www.cell.com/cell/abstrac...
cell.com
A spliceosome-independent eukaryote generated by complete intron removal
Elimination of all spliceosomal introns reveals a spliceosome-independent eukaryote.
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Jan Philipp Kreysing @jpkreysing.bsky.social · 13/07/2026
Delighted that our story on chromatin architecture inside human cells is now published — the last chapter of my PhD. It was a pleasure working with @sergiocruzleon.bsky.social, @johannesbetz.bsky.social, and everyone involved. #teamtomo www.nature.com/articles/s41...
nature.com
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells - Nature Communications
The 3D organisation of chromatin inside a human cell is still not fully resolved. Here the authors reveal that in situ cryo-ET resolves individual nucleosomes and predicts DNA linkers, thus showing th...
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Luay Almassalha @almassalha.bsky.social · 12/07/2026
Goooooooal!!!!! Go Jude!!!
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Luay Almassalha @almassalha.bsky.social · 10/07/2026
www.biorxiv.org/content/10.6...
biorxiv.org
Direct visualization of Na,K-ATPase clustering by 3D DNA-PAINT MINFLUX nanoscopy
Direct validation of the nanoscale structural organization of membrane proteins requires localization precision that matches their molecular dimensions. The sodium-potassium pump, or the Na,K-ATPase i...
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Luay Almassalha @almassalha.bsky.social · 03/07/2026
Watching Messi, incredible! I cannot believe how fortunate I have been to get to watch sports in this era. All time greats across every major sport
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Luay Almassalha @almassalha.bsky.social · 02/07/2026
Tillman!!!
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Jason Tan @yjtan.bsky.social · 30/06/2026
Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...
biorxiv.org
Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers
Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...
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Konrad Chudzik @konrad-chudzik.bsky.social · 30/06/2026
My first PhD paper is out in Nucleic Acids Research! We describe "Ab-trapping" - an antibody artifact that distorts assays relying on antibody diffusion (microscopy, CUT&Tag, CUT&RUN). The revisions made the story much stronger. Check it out! doi.org/10.1093/nar/...
doi.org
Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus
Abstract. Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome’s most essential functions. Many microscopy and geno
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Anders Sejr Hansen @andersshansen.bsky.social · 30/06/2026
Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates
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Jan Lammerding - Lab @lammerdinglab.bsky.social · 30/06/2026
Interested in a faculty career in biomedical engineering #BME? Apply for the Rising Stars in Engineering in Health workshop for postdocs and PhD students interested in engineering, medicine & health: be.engineering.upenn.edu/home/rising-... Applications are open until July 31, 2026. Please share!
Image depicting stars rising from the bottom with comet trails and the words "Rising Starts in Engineering in Health"
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Luay Almassalha @almassalha.bsky.social · 27/06/2026
What's with all the NBA trades this year centered around second round picks? Is there some big change to the salary cap coming?
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Genes & Development @genesdev.bsky.social · 25/06/2026
🆕 ADVANCE ONLINE 🆕 RESEARCH PAPER: The competition between splicing and 3′ processing shapes the human transcriptome By Soles et al. and Yongsheng Shi ➡️ ow.ly/bXG150ZachI UC Irvine UC Irvine School of Medicine #RNAprocessing #splicing #mRNA #transcription
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