Lisa Baumgartner
@balisa.bsky.social
Fascinated by how specificity is achieved at chromatin!
PhD @IMBA_Vienna #smallRNAs 🪰🦏🔬
Postdoc @FMIscience #TFs 🐁🧫🧬
PhD @IMBA_Vienna #smallRNAs 🪰🦏🔬
Postdoc @FMIscience #TFs 🐁🧫🧬
Reposted by Lisa Baumgartner
anybody looking for exciting opportunities in RNA research, with the goal to use and learn state of the art thinking and experimenting: here is a good starting point. Ulrich is an outstanding scientist and natural leader.
👇👇👇👇
👇👇👇👇
Lastly, I’m excited to join @imbmainz.bsky.social in 2026 to start my own lab. We'll explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology. tinyurl.com/y4x29ctt
Thanks for reading! 20/20
Thanks for reading! 20/20
Research
IMB Mainz
tinyurl.com
November 20, 2025 at 10:31 AM
anybody looking for exciting opportunities in RNA research, with the goal to use and learn state of the art thinking and experimenting: here is a good starting point. Ulrich is an outstanding scientist and natural leader.
👇👇👇👇
👇👇👇👇
Reposted by Lisa Baumgartner
Here is the schedule for the next TriRhena Gene Regulation Club at the FMI @fmiscience.bsky.social in Basel 🇨🇭 next week (5 Nov 2025; 14:00-18:45).
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
October 30, 2025 at 9:17 AM
Here is the schedule for the next TriRhena Gene Regulation Club at the FMI @fmiscience.bsky.social in Basel 🇨🇭 next week (5 Nov 2025; 14:00-18:45).
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
Reposted by Lisa Baumgartner
How are RNAs sorted for export vs. degradation in the nucleus? In collaboration with @heick.bsky.social’s lab we (@clemensplaschka.bsky.social and @juliusbrennecke.bsky.social labs) discovered a direct mechanistic link between the export and decay machineries: www.biorxiv.org/content/10.1... (1/x)
Molecular basis of polyadenylated RNA fate determination in the nucleus
Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs[1][1],[2][2], that are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, in...
www.biorxiv.org
September 22, 2025 at 11:23 PM
How are RNAs sorted for export vs. degradation in the nucleus? In collaboration with @heick.bsky.social’s lab we (@clemensplaschka.bsky.social and @juliusbrennecke.bsky.social labs) discovered a direct mechanistic link between the export and decay machineries: www.biorxiv.org/content/10.1... (1/x)
Reposted by Lisa Baumgartner
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
www.biorxiv.org
September 20, 2025 at 4:10 PM
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
Reposted by Lisa Baumgartner
I am excited to announce that we are looking for a Lab Manager @fmiscience.bsky.social in Basel. If you want to be part of a growing team investigating development and tissue formation, and are enthusiastic about helping set up a new lab, please check out the role:
www.fmi.ch/education-ca...
www.fmi.ch/education-ca...
September 14, 2025 at 11:46 AM
I am excited to announce that we are looking for a Lab Manager @fmiscience.bsky.social in Basel. If you want to be part of a growing team investigating development and tissue formation, and are enthusiastic about helping set up a new lab, please check out the role:
www.fmi.ch/education-ca...
www.fmi.ch/education-ca...
Reposted by Lisa Baumgartner
🚨 Job Alert: we seek a Lab Manager for @juliabatki.bsky.social's new group (start Mar 2026), which will study cell fate regulation during organ development. Join the Batki's group to drive experiments & lab operations! Apply at: www.fmi.ch/education-ca...
September 2, 2025 at 9:03 AM
🚨 Job Alert: we seek a Lab Manager for @juliabatki.bsky.social's new group (start Mar 2026), which will study cell fate regulation during organ development. Join the Batki's group to drive experiments & lab operations! Apply at: www.fmi.ch/education-ca...
Reposted by Lisa Baumgartner
Excited to share our latest preprint. www.biorxiv.org/content/10.1.... Lead by Lukas, we investigated multiple ways of assessing a TF's sensitivity to chromatin based on genome-wide binding profiles. The developed methods allowed us to quantify chromatin sensitivity across tested TFs.
A novel deep learning-based framework reveals a continuum of chromatin sensitivities across transcription factors
The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how...
www.biorxiv.org
August 12, 2025 at 8:32 AM
Excited to share our latest preprint. www.biorxiv.org/content/10.1.... Lead by Lukas, we investigated multiple ways of assessing a TF's sensitivity to chromatin based on genome-wide binding profiles. The developed methods allowed us to quantify chromatin sensitivity across tested TFs.
Reposted by Lisa Baumgartner
I am excited to share that I will join the Friedrich Miescher Institute @fmiscience.bsky.social in Basel as a group leader, starting my lab in March 2026 🎉
We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.
We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.
August 25, 2025 at 5:21 PM
I am excited to share that I will join the Friedrich Miescher Institute @fmiscience.bsky.social in Basel as a group leader, starting my lab in March 2026 🎉
We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.
We will explore cell fate regulation during organogenesis, with a focus on how cell elimination underlies the emergence of functional tissues.
Reposted by Lisa Baumgartner
1/ How do animals develop immunity against a newly encountered transposable element from scratch? Our study reveals that the mobility of TEs is their Achilles heel, allowing hosts to develop a powerful small RNA-mediated silencing response.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
August 14, 2025 at 5:09 PM
1/ How do animals develop immunity against a newly encountered transposable element from scratch? Our study reveals that the mobility of TEs is their Achilles heel, allowing hosts to develop a powerful small RNA-mediated silencing response.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Lisa Baumgartner
Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....
August 7, 2025 at 4:20 PM
Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....
Reposted by Lisa Baumgartner
It was a great meeting. I hope we can do it again in 2 years. #EMBLsinglemolecule. Single mol omics and imaging is very promising combo to dissect gene regulation.
#EMBLsinglemolecule was a blast! Happy to host the birth of single molecule genomics as a field and to think about the future with the microscopy crowd. Thanks to participants and organizers!
July 19, 2025 at 10:49 AM
It was a great meeting. I hope we can do it again in 2 years. #EMBLsinglemolecule. Single mol omics and imaging is very promising combo to dissect gene regulation.
Reposted by Lisa Baumgartner
📖 Happy to share our recent preprint! www.biorxiv.org/content/10.1... We discovered how SINEs are kept silent: the ChAHP protein complex acts as a molecular brake on POL III transcription retrotransposons. A 🧵:
ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment
Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements derived from RNA polymerase III (POL III)-transcribed short non-coding RNAs. SINEs retain sequence feature...
www.biorxiv.org
July 3, 2025 at 6:18 AM
📖 Happy to share our recent preprint! www.biorxiv.org/content/10.1... We discovered how SINEs are kept silent: the ChAHP protein complex acts as a molecular brake on POL III transcription retrotransposons. A 🧵:
Reposted by Lisa Baumgartner
REFEREE 1: “I conclude with a simple, direct statement - this is the best paper I have read all year!”
#TransparentPeerReview
Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses
@juliusbrennecke.bsky.social et al
www.embopress.org/doi/full/10....
#TransparentPeerReview
Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses
@juliusbrennecke.bsky.social et al
www.embopress.org/doi/full/10....
June 6, 2025 at 2:18 PM
REFEREE 1: “I conclude with a simple, direct statement - this is the best paper I have read all year!”
#TransparentPeerReview
Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses
@juliusbrennecke.bsky.social et al
www.embopress.org/doi/full/10....
#TransparentPeerReview
Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses
@juliusbrennecke.bsky.social et al
www.embopress.org/doi/full/10....
Reposted by Lisa Baumgartner
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
March 17, 2025 at 11:56 AM
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
Reposted by Lisa Baumgartner
Interested in gene expression control? In #singlemolecule approaches? If you like transcription, translation and more please register.
📢 Have you registered for 'Gene regulation: one molecule at a time' yet?
Submit your abstract by 8 April!
👉🏼 s.embl.org/grg25-01-bl
#EMBLSingleMolecule will bring together single molecule genomics and imaging to study mechanisms across the central dogma at molecular resolution 🧬🔍
Submit your abstract by 8 April!
👉🏼 s.embl.org/grg25-01-bl
#EMBLSingleMolecule will bring together single molecule genomics and imaging to study mechanisms across the central dogma at molecular resolution 🧬🔍
February 28, 2025 at 7:59 AM
Interested in gene expression control? In #singlemolecule approaches? If you like transcription, translation and more please register.
Reposted by Lisa Baumgartner
www.sciencedirect.com/science/arti...
I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬
Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌
I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬
Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌
A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin
Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyce…
www.sciencedirect.com
February 26, 2025 at 4:41 PM
www.sciencedirect.com/science/arti...
I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬
Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌
I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬
Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌
Reposted by Lisa Baumgartner
📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...
December 16, 2024 at 11:50 AM
📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...
Reposted by Lisa Baumgartner
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
December 12, 2024 at 11:24 AM
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Reposted by Lisa Baumgartner
We are very excited to share our recent preprint on the nuclear import mechanism of the proteasome, driven by the multivalent adaptor AKIRIN2! www.biorxiv.org/content/10.1... 🧵 1/6
A multivalent adaptor mechanism drives the nuclear import of proteasomes
Nuclear protein homeostasis, including the turnover of transcription factors, critically depends on nuclear proteasomes. After each cell division, proteasomes need to be re-imported into the newly for...
www.biorxiv.org
December 5, 2024 at 8:11 PM
We are very excited to share our recent preprint on the nuclear import mechanism of the proteasome, driven by the multivalent adaptor AKIRIN2! www.biorxiv.org/content/10.1... 🧵 1/6
Reposted by Lisa Baumgartner
1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...
November 27, 2024 at 5:58 PM
1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...
Reposted by Lisa Baumgartner
Hundreds of genome's off-switches were just mapped by Alexander Starks lab at the IMP.
Using the new method 'silencer-seq', they identified more than 800 silencers in fruit flies.
🧬Now published in Molecular Cell!
Read more: imp.ac.at/news/article...
Paper: cell.com/molecular-ce...
Using the new method 'silencer-seq', they identified more than 800 silencers in fruit flies.
🧬Now published in Molecular Cell!
Read more: imp.ac.at/news/article...
Paper: cell.com/molecular-ce...
November 21, 2024 at 9:09 AM
Hundreds of genome's off-switches were just mapped by Alexander Starks lab at the IMP.
Using the new method 'silencer-seq', they identified more than 800 silencers in fruit flies.
🧬Now published in Molecular Cell!
Read more: imp.ac.at/news/article...
Paper: cell.com/molecular-ce...
Using the new method 'silencer-seq', they identified more than 800 silencers in fruit flies.
🧬Now published in Molecular Cell!
Read more: imp.ac.at/news/article...
Paper: cell.com/molecular-ce...
Reposted by Lisa Baumgartner
Sevi Durdu from @schubelerlab.bsky.social presents extensive work on how different tissue-specific TFs bind and open chromatin depending on exact motif composition and co-binding
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Chromatin-dependent motif syntax defines differentiation trajectories
Transcription factors recognizing short DNA sequences within gene regulatory regions are crucial drivers of cell identity. Despite recent advances, their specificity remains incompletely understood. H...
www.biorxiv.org
November 21, 2024 at 9:12 AM
Sevi Durdu from @schubelerlab.bsky.social presents extensive work on how different tissue-specific TFs bind and open chromatin depending on exact motif composition and co-binding
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Lisa Baumgartner
Pls share 🌟Join the IMP as a Group Leader
We are 👀 for a colleague, ready to lead a groundbreaking research program. Enjoy generous funding, outstanding facilities & a vibrant scientific community in one of the world's most livable cities @impvienna.bsky.social
👉https://tinyurl.com/impgl2025
November 20, 2024 at 10:46 AM
Pls share 🌟Join the IMP as a Group Leader
We are 👀 for a colleague, ready to lead a groundbreaking research program. Enjoy generous funding, outstanding facilities & a vibrant scientific community in one of the world's most livable cities @impvienna.bsky.social
👉https://tinyurl.com/impgl2025
Reposted by Lisa Baumgartner
New conference that will explore gene regulation mechanisms at molecular resolution. We bring bring together a fine crowd that uses microscopy, genomics and theory to chart the future of the booming fields of #singlemoleculegenomics and #singlemoleculemicroscopy. Join us July 15-18th 2025 at EMBL
November 14, 2024 at 8:43 AM
New conference that will explore gene regulation mechanisms at molecular resolution. We bring bring together a fine crowd that uses microscopy, genomics and theory to chart the future of the booming fields of #singlemoleculegenomics and #singlemoleculemicroscopy. Join us July 15-18th 2025 at EMBL
Reposted by Lisa Baumgartner
🧬 New PAN Lab Preprint Alert! 🧬
1/ Genome defence pathway genes are crucial for animal fertility yet often evolve rapidly. We investigated the molecular basis of such rapid evolution in the fly piRNA pathway
TL;DR: protein-protein interaction innovation 💡🤝
🧵👇
www.biorxiv.org/content/10.1...
1/ Genome defence pathway genes are crucial for animal fertility yet often evolve rapidly. We investigated the molecular basis of such rapid evolution in the fly piRNA pathway
TL;DR: protein-protein interaction innovation 💡🤝
🧵👇
www.biorxiv.org/content/10.1...
Recurrent innovation of protein-protein interactions in the Drosophila piRNA pathway
Despite being essential for fertility, genome defence pathway genes often evolve rapidly. However, little is known about the molecular basis of this adaptation. Here, we characterize the evolution of ...
www.biorxiv.org
October 30, 2024 at 1:57 PM
🧬 New PAN Lab Preprint Alert! 🧬
1/ Genome defence pathway genes are crucial for animal fertility yet often evolve rapidly. We investigated the molecular basis of such rapid evolution in the fly piRNA pathway
TL;DR: protein-protein interaction innovation 💡🤝
🧵👇
www.biorxiv.org/content/10.1...
1/ Genome defence pathway genes are crucial for animal fertility yet often evolve rapidly. We investigated the molecular basis of such rapid evolution in the fly piRNA pathway
TL;DR: protein-protein interaction innovation 💡🤝
🧵👇
www.biorxiv.org/content/10.1...