Aakash Grover

Quick plug for our new resource, the Drosophila Species Stock Exchange. This is a database and mailing list that documents species currently in culture and the labs holding them. If you want to know more or sign up then please get in touch. See attached for more info and please share!

#Yeast #Genetics Meeting 2026 is in June - Abstract deadline is TODAY! Submit your abstract, attend the meeting this summer in Pacific Grove, CA at #Asilomar Conference Grounds, a 107-acre protected coastal state park located on the Monterey Peninsula. #Yeast26 #YGM2026 genetics-gsa.org/yeast-2026/

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Three @biorxivpreprint.bsky.social preprints on acute depletion of FACT in ES cells. First, from my colleague at Pitt Sarah Hainer's lab 1/ www.biorxiv.org/content/10.6...

Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar.
Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse.
www.biorxiv.org/content/10.6...

This feels like the fastest February ever🥲

🚨New preprint! We built a cell-free genomics platform (GATO-seq) to probe transcriptional regulation and discovered a “super pause” sequence that triggers a new Pol II active-site conformation. Huge shout-out to @robertovn.bsky.social for pulling off this monster of a project. tinyurl.com/superpause

Cool Stuff!

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n

💻 Networks reveal hidden connections: #Yeast genetic & protein interaction networks share unexpected topological similarities, suggesting genetic epistasis & physical protein binding follow similar organizational rules
🧪 #YeastResearch #SGD #ComputationalBiology
www.yeastgenome.org/reference/S1...

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

Insane!

We've got two exciting chromatin talks coming up on Wednesday next week:

@epijenatics.bsky.social from @jbuenrostro.bsky.social's lab and @ambystoma22.bsky.social!

register and join us: us06web.zoom.us/webinar/regi...

🧬📄 Preprint update (v2): We added new biochemical experiments that clarify how IWS1 associates with the transcription elongation complex and further define competition between IWS1 and RECQL5. 🧪⚙️
www.biorxiv.org/content/10.1...

Structural model is already available in the PDB (9MLC).

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Evolutionary rate covariation across malaria parasite species enables inference of protein interactions https://www.biorxiv.org/content/10.64898/2026.01.29.702598v1

Thanks for sharing!

Join SGD at #Yeast26 for cutting-edge #yeast research, networking opportunities, engaging talks, poster sessions, and workshops, for everyone from early career scientists to experienced researchers! Abstract submission by Mar5, early registration ends Apr16. See you there! @genetics-gsa.bsky.social

🥁 #FragileNucleosome is back on Jan 28! We are very excited to host @au-ho-yu.bsky.social and @gcloner.bsky.social as our first speakers of 2026!
📋Please don't forget to register for our 2026 seminar series: us06web.zoom.us/webinar/regi...

Oh that sounds amazing! I'm preparing to make some sago khichdi (I have no English word for this😂) tomorrow

Daal rice and aloo supremacy🤌

After a short break in our webinars we are delighted to be back up & running this month!

First up, on Jan 30th we will be joined by @lucas.farnunglab.com from @harvardmed.bsky.social 🔬

Shortly after, on Feb 13th we will be hosting @heardlab.bsky.social from @crick.ac.uk 🧬

Registration details 👇

The Vlaming lab continues to grow!
It's an exciting time in the Vlaming lab: we've just had our 2nd PhD student join, and the 3rd is joining in February. Now, we're looking to recruit a postdoc!

Preprints, Peer Review, and Open Access science journals & articles YouTube video by the bumbling biochemist

Pre-prints, open access, peer-review… What’s it to you? youtube.com/watch?v=vTjuDKweQJA

eVGeMdb: a manually curated database for experimentally validated genetic modifiers of neurodegenerative disorders Abstract. Genetic modifiers are genes that, while not directly causing disease, can alter the onset, progression, severity, or specific phenotypes of a dis

First paper from the lab published in NAR Molecular Medicine, led by grad student Subashani. Collaboration work with Dr. Rahul Kumar. Subashani created this database/tool: eVGeMdb. Use it for disease-specific modifiers, mechanisms/hypotheses, and therapeutic targets.
academic.oup.com/narmolmed/ar...

Evolutionary conservation and innovations of RNA polymerase II transcription elongation factors https://www.biorxiv.org/content/10.64898/2026.01.11.698887v1

Yeast Genetics Meeting abstract submission and registration sites are open! Abstract submission and registration for the 2026 Yeast Genetics Meeting are now open! Present at this premier meeting for students, postdoctoral scholars, research staff, principal investigators, and...

#Yeast #Genetics Meeting abstract submission and registration sites are open! Abstracts due March 5!

community.alliancegenome.org/t/yeast-gene...

Software tools and databases for working with proteins YouTube video by the bumbling biochemist

Software tools and databases for working with proteins youtu.be/encoJwuD6Pk

Interpreting AlphaFold predictions AlphaFold uses AI to, based on knowledge gained about the relationship between protein sequences and their corresponding structures (thanks to lots of work by structural biologists!), predict the stru...

In case this is helpful to anyone... thebumblingbiochemist.com/365-days-of-...