Lukas Frank

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

Screenshot of Essay from Martin Schwartz on 'Why would anyone want to be a scientist'. An anniversary article from The Company of Biologists published in Journal of Cell Science. The first few lines are: It is difficult to fathom why anyone intelligent enough to be a scientist would actually choose to be one. Doing good science requires the utmost exertion of body, mind and spirit, yet is consistently filled with failure and rejection. But, strange even to myself, I not only don't question the unfavorable risk-to-reward ratio but consider myself astonishingly lucky to be a scientist. There are three fundamental pleasures that have sustained me through 50 years of this madness.

Why would anyone want to be a scientist?

Check out our new Essay from Martin Schwartz: journals.biologists.com/jcs/article/...

Delving into LLM-assisted writing in biomedical publications through excess vocabulary Large language models (LLMs) like ChatGPT can generate and revise text with human-level performance. These models come with clear limitations, can produce inaccurate information, and reinforce existing biases.

The appearance of large language models caused a drastic shift in the vocabulary of academic writing, according to an analysis in #ScienceAdvances of more than 15 million biomedical abstracts published from 2010 to 2024.

Learn more:

Honoured to be awarded
Young Investigator Neuroscience Award from CHS Foundation together with my dearest David Brito for our paper in Molecular Psychiatry!

Curios about the work
⬇️⬇️⬇️ check out our paper & my 🧵 below
www.nature.com/articles/s41...

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...

Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)

Congrats!! Happy to see it published. 🙂 We need more of such user-friendly, fast and threshold-agnostic tools for bioimage analysis

YouTube video by Amanpour and Company Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company

David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏

youtu.be/8YhJM6zxYDw?...

Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...

🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...

From enhancer hijacking to ecDNA and onco-condensates – we review how changes in nuclear architecture drive oncogenic gene expression by disrupting enhancer–promoter communication. doi.org/10.1002/ijc..... Kudos to Isabelle Seufert, @claire-vrgs.bsky.social and Sina Wille 👏

Finally in its nice looking journal style 🤩🥳🍾

Check out our paper about DNA methylation, engram maturation and systems consolidation.

You can find a 🧵 on my previous link
bsky.app/profile/jani...

Thanks to all people involved and the journal for awarding it "Priority Communication"

🧬🌟We're excited to add an Extrachromosomal Circular DNA conference to our 2025 calendar!🧬🌟
Chairs Birgitte Regenberg (Univ. of Copenhagen) & Zhao Zhang (Duke Univ.) are bringing a fantastic line up of speakers together in Mexico this year. More details➡️https://bit.ly/4az0PbV #ecDNA25 #eccDNA #ecDNA