Bede Portz
@ysptsps.bsky.social
Biotech. Interests: oncology, transcription, RNA, small molecule drug discovery, RNA therapeutics, protein aggregation, phase transitions
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!
bioRxiv Genomics@biorxiv-genomic.bsky.social · 2w agoFormation of an RNA-mediated nuclear compartment https://www.biorxiv.org/content/10.64898/2026.08.20.746005v1
You never forget your first love. www.nature.com/articles/s41...
A tunable CTD grammar governs the spatial programming of the transcription cycle - Nature Communications
The C-terminal domain (CTD) of RNA polymerase II acts as a regulatory platform during the transcription cycle. Here, the authors use a simple tail CTD and reveal how repeating sequence patterns and ch...
nature.com
Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity
Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.
cell.com
www.biorxiv.org/content/10.6...
Physics-guided design of intrinsically disordered proteins
Intrinsically disordered protein regions (IDPs) are found across the tree of life and characterized by the lack of a stable 3D fold, encoding function through a vast ensemble of conformations. This pl...
biorxiv.org
Came across this really cool compendium of AI foundation models of life science curated by @neuromusic.bsky.social and had to share. bio.rodeo
bio.rodeo - The Analyst for Bio AI
Honest evaluations of biological foundation models. We rank and review AI for protein folding, genomics, single-cell analysis, and more.
bio.rodeo
Long wondered if the rules being elucidated in the nucleous apply more broadly to transcriptional condensates? Talked about this with @superscijew.bsky.social over the years. Thoughts? Congrats on paper.
Jon Henninger@jhenninger.bsky.social · 3mo agoSee our handy graphical abstract and article for free here: bit.ly/4vsl845
ft. Katie Copley, Ashleigh Smirnov, Leland Mayne, Miriam Linsenmeier, Jack Rubien, @ysptsps.bsky.social, Bo Lim Lee, Hana Odeh, Longsheng Lai, @yiweichang.bsky.social, Ben Black & James Shorter (BioBio) @science.org www.science.org/doi/10.1126/...
🆕 review with @jpunfried.bsky.social out in Nature SMB. Direct roles of lncRNAs in transcriptional activation. What do we understand about how lncRNAs lure Pol2 and set the stage for RNA production, and what do we still miss? www.nature.com/articles/s41...
Direct roles of long non-coding RNAs in transcription activation - Nature Structural & Molecular Biology
This Review discusses how long noncoding RNAs (lncRNAs) control transcription activation by RNA polymerase II, including how they are produced at active enhancers or chromatin-domain boundaries and ac...
nature.com
If you are interested in mechanistic aspects of transcription regulation and mRNA processing, check out this fantastic EMBO Workshop in Oxford, UK in September 2026. Registration is closing soon!
Can we control cells by forcing TFs to collaborate? Interested? Read our preprint! An awesome collaboration with @cgersbach.bsky.social, @igvfconsortium.bsky.social, Christian McRoberts Amador, @rachel-savage.bsky.social: www.biorxiv.org/content/10.6... 🧵
biorxiv.org
These Chimps Began the Bloodiest ‘War’ on Record. No One Knows Why. www.nytimes.com/2026/04/09/s... fascinating
These Chimps Began the Bloodiest ‘War’ on Record. No One Knows Why.
nytimes.com
i feel like if i was tasked with not starting a war and bringing back US manufacturing jobs, i could have done a better job than this
A raw egg rolled off the counter while cooking tonight and my dog ate it, shell and all. He spent the next 15 minutes excitedly walking laps around the kitchen island hoping to find another.
glam bois gonna glam 2/2
Alex Holehouse@alexholehouse.bsky.social · 7mo agoPleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.
glam bois gonna glam 1 of 2
Alex Holehouse@alexholehouse.bsky.social · 7mo agoPapers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...
Extremely happy to share our latest research on the NELF complex in @emboreports.org done in collaboration with the groups of Dr Takayuki Nojima and Dr Yasukazu Daigaku in Japan. link.springer.com/article/10.1...
NELF prevents transcriptional readthrough into DNA replication zones in cancer cells - EMBO Reports
Regulation of RNA polymerase II (Pol II) transcription is closely associated with cell proliferation. However, it remains unclear how the Pol II transcription program is rewired in cancer to promote u...
link.springer.com
Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology
Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...
nature.com
Alex Holehouse@alexholehouse.bsky.social · 2y agoWe’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...
Papers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...
Accurate predictions of disordered protein ensembles with STARLING - Nature
The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.
nature.com
Borna Novak@bornanovak.bsky.social · 2y agoExcited to announce the newest member of the flock - STARLING (conSTruction of intrinsicAlly disoRdered proteins ensembles efficientLy vIa multi-dimeNsional Generative models). www.biorxiv.org/content/10.1...
I think there was a lot of pressure here to get this to happen. The review needs to be fair and under tremendous scrutiny
Josh Marshall@joshtpm.bsky.social · 7mo agoFDA reverses course, agrees to review Moderna’s flu vaccine www.statnews.com/2026/02/18/f... via @statnews.com
Lutnick Acknowledges Traveling to Epstein’s Island www.nytimes.com/2026/02/10/u...
Lutnick Acknowledges Traveling to Epstein’s Island
nytimes.com
Happy to share this new, very intentional chapter. I have left UCLA after 14 years to join the University of Colorado Anschutz as Professor of Biomedical Informatics and Neurosurgery and the inaugural Marsico Chair in Excellence in Functional Precision Medicine/n news.cuanschutz.edu/dbmi/cu-ansc...
CU Anschutz Recruits National Leader to Launch Functional Personalized Medicine Initiative
CU Anschutz welcomes Alice Soragni to launch a Functional Personalized Medicine Initiative using rapid tumor organoid testing to guide treatment decisions.
news.cuanschutz.edu
www.nature.com/articles/s41...
The role of low-complexity repeats in RNA–RNA interactions and a deep learning framework for duplex prediction - Nature Communications
Interactions between long RNA molecules play essential roles in shaping gene regulation. Here, the authors show that low-complexity repeats drive stable contacts between RNAs and present RIME, a deep ...
nature.com
