Miha Modic
@paraspeckle.bsky.social
Uncovering the beauty of embryonic development with functional RNA biology tools. | TT Prof at @ Carl Zeiss Center for Synthetic Genomics & KIT | http://modiclab.org/
Reposted by Miha Modic
New Tuesday (Oct 28) in Heidelberg and online: kick off event of the Center for Synthetic Genomics: program and link to zoom: www.syn-gen.de/kick-off
Center Kick-Off Event | Center SynGen
www.syn-gen.de
October 24, 2025 at 11:19 AM
New Tuesday (Oct 28) in Heidelberg and online: kick off event of the Center for Synthetic Genomics: program and link to zoom: www.syn-gen.de/kick-off
Beautiful mechanistic story, how QKI by bridging intronic motifs with U6 snRNA ensures inclusion of weak 5’ splice sites that are essential for building sarcomeres. Congrats @kurianlab.bsky.social and @evannostrandlab.bsky.social labs & all involved.
Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites
During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...
www.biorxiv.org
September 8, 2025 at 3:24 PM
Beautiful mechanistic story, how QKI by bridging intronic motifs with U6 snRNA ensures inclusion of weak 5’ splice sites that are essential for building sarcomeres. Congrats @kurianlab.bsky.social and @evannostrandlab.bsky.social labs & all involved.
Reposted by Miha Modic
New paper from the Trcek lab, with Siran Tian as the lead author - congratulations Siran!: www.nature.com/articles/s41...
Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development - Nature Communications
Tian et al. show that RNA folding limits extensive base pairing among mRNAs in Drosophila germ granules. Instead, mRNAs interact via scattered bases exposed on the surface of folded RNAs, which may pr...
www.nature.com
August 30, 2025 at 11:13 PM
New paper from the Trcek lab, with Siran Tian as the lead author - congratulations Siran!: www.nature.com/articles/s41...
Reposted by Miha Modic
Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.
August 6, 2025 at 3:14 PM
Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.
Reposted by Miha Modic
Explore RNA's role in epigenetics, DNA repair, transcription & genome organisation - directly with leaders from academia & industry at #GenReg26!
Remaining talks to be filled from submissions - register & submit by 04 Sep 2025 to join us in Mexico.
Speakers, details & registration➡️ bit.ly/46JQbze
Remaining talks to be filled from submissions - register & submit by 04 Sep 2025 to join us in Mexico.
Speakers, details & registration➡️ bit.ly/46JQbze
July 17, 2025 at 12:14 PM
Explore RNA's role in epigenetics, DNA repair, transcription & genome organisation - directly with leaders from academia & industry at #GenReg26!
Remaining talks to be filled from submissions - register & submit by 04 Sep 2025 to join us in Mexico.
Speakers, details & registration➡️ bit.ly/46JQbze
Remaining talks to be filled from submissions - register & submit by 04 Sep 2025 to join us in Mexico.
Speakers, details & registration➡️ bit.ly/46JQbze
Reposted by Miha Modic
I’m a bit late to the game here, but wanted to highlight this very clever technique from @paraspeckle.bsky.social’s group! Congrats to all authors!!
New method drop:
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...
August 2, 2025 at 6:55 PM
I’m a bit late to the game here, but wanted to highlight this very clever technique from @paraspeckle.bsky.social’s group! Congrats to all authors!!
Reposted by Miha Modic
A day late but STILL IMPORTANT
August 2, 2025 at 4:14 PM
A day late but STILL IMPORTANT
Reposted by Miha Modic
We are hiring! "Researcher in DNA-Based Information Processing Systems" (PhD or postdoc level). Co-supervision by Prof. Ralf Reussner (KIT computer science) and myself (biological systems). Combination of experiments and computational work. Please Apply / Repost!
www.pse.kit.edu/english/karr...
www.pse.kit.edu/english/karr...
July 29, 2025 at 6:24 AM
We are hiring! "Researcher in DNA-Based Information Processing Systems" (PhD or postdoc level). Co-supervision by Prof. Ralf Reussner (KIT computer science) and myself (biological systems). Combination of experiments and computational work. Please Apply / Repost!
www.pse.kit.edu/english/karr...
www.pse.kit.edu/english/karr...
Exited to see SPIDR finally coming out! Congrats to Marko and the team on opening the next multiplexing RNA frontier 💥
Woohoo! So psyched to see this awesome work from the Jovanovic lab out in the world! Congrats to all the authors on this tour-de-force!
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress
SPIDR, a massively multiplexed method that simultaneously maps dozens of RNA-binding
proteins to their RNA targets at single-nucleotide resolution, uncovers new RNA-protein
interactions and provides c...
www.cell.com
July 23, 2025 at 10:47 PM
Exited to see SPIDR finally coming out! Congrats to Marko and the team on opening the next multiplexing RNA frontier 💥
Thrilled to co-advertise this postdoc or PhD position with @erhardtlab.bsky.social!
Join us, if RNP assembly on centromeres, RNA modifications, & bioinformatics are your thing.
More info also on modiclab.org.
Join us, if RNP assembly on centromeres, RNA modifications, & bioinformatics are your thing.
More info also on modiclab.org.
🧪 Open PhD or Postdoc position 🧪
The project is in collaboration with my new collegue Miha Modic. If you are interesed in RNA modification, centromeres and bioinformatics this is for you!
Miha has more positions to fill, infos on his linkedin: linkedin.com/in/miha-modic-9aa8a752.
The project is in collaboration with my new collegue Miha Modic. If you are interesed in RNA modification, centromeres and bioinformatics this is for you!
Miha has more positions to fill, infos on his linkedin: linkedin.com/in/miha-modic-9aa8a752.
July 23, 2025 at 8:25 PM
Thrilled to co-advertise this postdoc or PhD position with @erhardtlab.bsky.social!
Join us, if RNP assembly on centromeres, RNA modifications, & bioinformatics are your thing.
More info also on modiclab.org.
Join us, if RNP assembly on centromeres, RNA modifications, & bioinformatics are your thing.
More info also on modiclab.org.
New method drop:
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...
June 2, 2025 at 10:30 AM
New method drop:
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...
Harnessing the physical properties of peptides to predict their functionality and interactions. 💥
May 24, 2025 at 9:47 AM
Harnessing the physical properties of peptides to predict their functionality and interactions. 💥
Reposted by Miha Modic
Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1...
1/6
1/6
May 19, 2025 at 6:55 PM
Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1...
1/6
1/6
Thank you, Lennart! I'm very excited to join the newly founded Carl Zeiss Center for Synthetic Genomics and KIT with your lab nextdoor! Exciting times ahead!
While it is hard to predict ahead of time *what* the actual discoveries will be that we will make together, it is relatively safe to assume *that* they will happen.
Welcome new T-Track Prof. Miha Modic @paraspeckle.bsky.social to @kit.edu Karlsruhe
I am so very excited to have you with us now!
Welcome new T-Track Prof. Miha Modic @paraspeckle.bsky.social to @kit.edu Karlsruhe
I am so very excited to have you with us now!
April 18, 2025 at 7:25 PM
Thank you, Lennart! I'm very excited to join the newly founded Carl Zeiss Center for Synthetic Genomics and KIT with your lab nextdoor! Exciting times ahead!
Reposted by Miha Modic
I'm excited to share our latest publication on co-transcriptional RNA folding in a eukaryote! Great work by Leo Schärfen with collaboration from Isaac Vock and Matt Simon! @leoschaerfen.bsky.social @mattdsimon.bsky.social
Here is the link that works! authors.elsevier.com/a/1kpxo_Oylr...
Here is the link that works! authors.elsevier.com/a/1kpxo_Oylr...
authors.elsevier.com
March 26, 2025 at 1:07 PM
I'm excited to share our latest publication on co-transcriptional RNA folding in a eukaryote! Great work by Leo Schärfen with collaboration from Isaac Vock and Matt Simon! @leoschaerfen.bsky.social @mattdsimon.bsky.social
Here is the link that works! authors.elsevier.com/a/1kpxo_Oylr...
Here is the link that works! authors.elsevier.com/a/1kpxo_Oylr...
Reposted by Miha Modic
The eternal question: should you focus on one problem for a very long time or is it more productive to bounce and work on many problems? David Baker says that both modes have been important in his career trajectory.
podcasts.apple.com/us/podcast/n... @nightsciencepod.bsky.social
podcasts.apple.com/us/podcast/n... @nightsciencepod.bsky.social
March 26, 2025 at 12:00 PM
The eternal question: should you focus on one problem for a very long time or is it more productive to bounce and work on many problems? David Baker says that both modes have been important in his career trajectory.
podcasts.apple.com/us/podcast/n... @nightsciencepod.bsky.social
podcasts.apple.com/us/podcast/n... @nightsciencepod.bsky.social
Reposted by Miha Modic
📣 Our lab is looking for a PhD student to join us in exploring RNA biology! Details in the announcement. Feel free to reach out with any questions—and please RT!
March 25, 2025 at 8:00 PM
📣 Our lab is looking for a PhD student to join us in exploring RNA biology! Details in the announcement. Feel free to reach out with any questions—and please RT!
Beautiful read from @gabrijelad.bsky.social, outlining what we today know and also have no clue about the exciting world of RNA localisation
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Decoding subcellular RNA localization one molecule at a time - Genome Biology
Eukaryotic cells are highly structured and composed of multiple membrane-bound and membraneless organelles. Subcellular RNA localization is a critical regulator of RNA function, influencing various bi...
genomebiology.biomedcentral.com
March 6, 2025 at 1:16 PM
Beautiful read from @gabrijelad.bsky.social, outlining what we today know and also have no clue about the exciting world of RNA localisation
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Miha Modic
Save the date for the next edition of this wonderful meeting. We look forward to seeing you in Portugal!!
February 28, 2025 at 3:53 PM
Save the date for the next edition of this wonderful meeting. We look forward to seeing you in Portugal!!
Reposted by Miha Modic
"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...
February 6, 2025 at 4:02 PM
"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...
I am thrilled to share the first manuscript from my group on identifying sequence and structural features promoting the condensation of RNAs that are organising highly interconnected RNA networks, thereby expanding our understanding of higher-order transcriptome assemblage.
shorturl.at/pmLIj #RNASky
shorturl.at/pmLIj #RNASky
Integrative profiling of condensation-prone RNAs during early development
Complex RNA–protein networks play a pivotal role in the formation of many types of biomolecular condensates. How intrinsic RNA features contribute to condensate formation however remains unclear. Here...
www.biorxiv.org
February 6, 2025 at 9:44 AM
I am thrilled to share the first manuscript from my group on identifying sequence and structural features promoting the condensation of RNAs that are organising highly interconnected RNA networks, thereby expanding our understanding of higher-order transcriptome assemblage.
shorturl.at/pmLIj #RNASky
shorturl.at/pmLIj #RNASky