Filip Nemcko

Excited to share VIPerturb-seq! New tech from my lab which aims to improve the cost, data quality, and efficiency of single-cell CRISPR screens so that they are accessible to any lab - even at genome-wide scale Preprint and 🧵 (1/): biorxiv.org/content/10.648…

New preprint on technologies to scale up CRISPR screens. We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells. We also introduce an approach for cloning lentiviral libraries with billions of elements.

Read the full story in our preprint! 👇 biorxiv.org/content/10.648… Excited to share this work with my co-first author Kevin Sabath - a fantastic collaboration between the @AlexanderStark8 and @plaschka_lab labs! 🤝🧪

Using Hcfc1 as a model, we show it functions as a molecular bridge: it connects CGI-bound TFs directly to TFIID. This recruitment overcomes a rate-limiting step unique to CGI promoters, enabling transcription initiation. 🧬🌉

Do transcriptional activators work on any promoter? Our data says no. 🙅‍♂️ Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬

🚀 Excited to share our latest work now on bioRxiv: the computational de novo design of tissue‑specific mammalian enhancers that work in vivo in the mouse embryo. 🐭 We use compact CNNs and transfer learning (pre‑trained on genome‑wide ATAC‑seq and fine‑tuned on validated enhancers from VISTA enhancer browser) to program tissue‑specific enhancers. Transfer learning reveals clear shifts in motif importance between sequence‑to‑accessibility and sequence‑to‑activity models, highlighting the specific features that drive enhancer function. 100% (15/15) of designed enhancers for heart, limb, and CNS are active in their intended tissues in mouse embryos. 🎯 We hope this approach will help enable the design of more versatile and precise synthetic enhancers across mammalian tissues, cell types, and dynamic cell states. Grateful for the amazing guidance from @AlexanderStark8 and @Loubiere20! 🙏 Huge thanks to all co-authors and collaborators, especially Evgeny @evgenykvon and Jacob @jmschreiber91, for making this work possible. 🙏 More details in the preprint and code: bioRxiv: biorxiv.org/content/10.648… #DeepLearning #Genomics #SyntheticBiology

We're looking for a Lab Manager to join our lab @arcinstitute @Stanford! Apply at bit.ly/HornsLabManager

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

Honored to receive the VBC PhD Award!

@vera_manelli @Bonev_Lab Vera, big congrats 😍

Our latest research on position-dependent transcriptional regulatory sequences in plants is now published! 🌿 More details in our preprint tweet and in this thread! 👇 nature.com/articles/s4158… 📄🔍 (1/5)

ORFtag enables protein functional screens by proteome-wide tagging via randomly integrated cassettes. @FilipNemcko @EllingUlrich @juliusbrennecke @AlexanderStark8 @stark_lab @IMBA_Vienna @IMPvienna @MaxPerutzLabs @viennabiocenter nature.com/articles/s4159…

Excited to share our collaborative project at the @viennabiocenter, introducing ORFtag—a new method to advance protein function studies. Learn more in the interview and the linked paper. 🧬

How do enhancers work over distances that sometimes exceed megabases? Excited to share our work led by @gracecbower where we uncover a unique sequence signature globally associated with long-range enhancer-promoter interactions in developing limb buds: biorxiv.org/content/10.110… 1/

@fordycelab @nicole_delrosso @BintuLacra @BintuLab congrats Nicole! 🥳🥳

Super proud of @nicole_delrosso after her amazing PhD thesis defense featuring work done jointly with @BintuLacra and @BintuLab! She is a scientific force and I can't wait to see everything she will accomplish in her career :)

@jb_lalanne congrats!

After a constructive set of reviews, our single-cell reporter work is OUT nature.com/articles/s4159… Check out the briefing if you want the tldr nature.com/articles/s4159… I am particularly fond of some of the new applications. Mini-update.

How do chromatin modifications quantitatively impact gene expression? How do sequence variants or combinatorial marks influence relationships? We developed a modular #EpigenomeEditing toolkit to systematically test these Q, published today 🧵… nature.com/articles/s4158…

🎉Congratulations to @FilipNemcko from @AlexanderStark8's lab for being included in Forbes Slovakia “30 Under 30” list! To earn him the mention is the development of a method that significantly speeds up the understanding of human gene functions. imp.ac.at/news/article/f…

@PauliGroup @TrainingVbc @stark_lab @univienna @IMPvienna @IMBA_Vienna @gmivienna @MaxPerutzLabs thank you Andi!

Congratulations to @FilipNemcko PhD (@stark_lab, IMP), who recently defended his thesis: 'Systematic identification and functional characterization of transcriptional regulators' - Well done Filip! 🥂🍾 @univienna @IMPvienna @IMBA_Vienna @gmivienna @MaxPerutzLabs

Just earned my PhD! 👨‍🎓 Huge thanks to all who helped me reach this milestone.