Alexander Sasse
@lxsasse.bsky.social
Learning from algorithms that learn from data about gene regulation.
Reposted by Alexander Sasse
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
Reposted by Alexander Sasse
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
November 10, 2025 at 9:01 PM
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Reposted by Alexander Sasse
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multiple overlapping binding sites determine transcription factor occupancy - Nature
A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...
www.nature.com
October 30, 2025 at 11:04 PM
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alexander Sasse
The low-affinity sites overlap in interwoven ways, making them a sort of selection committee that decides whether or not prospective TFs are granted access to the high-affinity site. Here's how the authors depict it. /6
October 30, 2025 at 11:20 PM
The low-affinity sites overlap in interwoven ways, making them a sort of selection committee that decides whether or not prospective TFs are granted access to the high-affinity site. Here's how the authors depict it. /6
Reposted by Alexander Sasse
Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq [new]
Corrects Tn5 bias in ATAC-seq; improves footprinting, finds elements & reduces false positives.
Corrects Tn5 bias in ATAC-seq; improves footprinting, finds elements & reduces false positives.
October 19, 2025 at 3:36 AM
Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq [new]
Corrects Tn5 bias in ATAC-seq; improves footprinting, finds elements & reduces false positives.
Corrects Tn5 bias in ATAC-seq; improves footprinting, finds elements & reduces false positives.
Reposted by Alexander Sasse
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 16, 2025 at 10:01 PM
Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alexander Sasse
Gene regulatory innovations from transposable elements in mammalian cerebellum development [new]
Cerebellum gene reg. driven by TEs, w/cell-type & sp.-specific expression, esp. primate HERVL in granule cells.
Cerebellum gene reg. driven by TEs, w/cell-type & sp.-specific expression, esp. primate HERVL in granule cells.
October 16, 2025 at 4:32 AM
Gene regulatory innovations from transposable elements in mammalian cerebellum development [new]
Cerebellum gene reg. driven by TEs, w/cell-type & sp.-specific expression, esp. primate HERVL in granule cells.
Cerebellum gene reg. driven by TEs, w/cell-type & sp.-specific expression, esp. primate HERVL in granule cells.
Reposted by Alexander Sasse
Very happy to see this work finally online 🥳
It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝
Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶
5/5
It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝
Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶
5/5
September 30, 2025 at 12:23 PM
Very happy to see this work finally online 🥳
It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝
Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶
5/5
It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝
Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶
5/5
Reposted by Alexander Sasse
Experiment-guided AlphaFold3 resolves accurate protein ensembles [new]
AlphaFold3, by integrating NMR, X-ray, or cryo-EM data, can generate accurate protein conformation ensembles reflecting experimental conditions.
AlphaFold3, by integrating NMR, X-ray, or cryo-EM data, can generate accurate protein conformation ensembles reflecting experimental conditions.
October 12, 2025 at 5:25 AM
Experiment-guided AlphaFold3 resolves accurate protein ensembles [new]
AlphaFold3, by integrating NMR, X-ray, or cryo-EM data, can generate accurate protein conformation ensembles reflecting experimental conditions.
AlphaFold3, by integrating NMR, X-ray, or cryo-EM data, can generate accurate protein conformation ensembles reflecting experimental conditions.
Reposted by Alexander Sasse
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
October 10, 2025 at 4:47 PM
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
Reposted by Alexander Sasse
Which mutations rewire function of regulatory DNA?
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
October 9, 2025 at 12:03 PM
Which mutations rewire function of regulatory DNA?
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Reposted by Alexander Sasse
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Alexander Sasse
Excited to see our review now on arXiv, written together with @fpesce.bsky.social and @lindorfflarsen.bsky.social
doi.org/10.48550/arX...
doi.org/10.48550/arX...
New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴
doi.org/10.48550/arX...
doi.org/10.48550/arX...
September 18, 2025 at 9:44 PM
Excited to see our review now on arXiv, written together with @fpesce.bsky.social and @lindorfflarsen.bsky.social
doi.org/10.48550/arX...
doi.org/10.48550/arX...
Reposted by Alexander Sasse
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...
www.biorxiv.org
August 28, 2025 at 12:16 PM
Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alexander Sasse
New preprint alert!
Corgi imitates cellular gene regulation and integrates DNA sequence and trans-regulator information.
This allows Corgi to make accurate predictions in unseen cell types. Also, it can simulate trans-regulator perturbations in silico.
Corgi imitates cellular gene regulation and integrates DNA sequence and trans-regulator information.
This allows Corgi to make accurate predictions in unseen cell types. Also, it can simulate trans-regulator perturbations in silico.
June 26, 2025 at 7:46 AM
New preprint alert!
Corgi imitates cellular gene regulation and integrates DNA sequence and trans-regulator information.
This allows Corgi to make accurate predictions in unseen cell types. Also, it can simulate trans-regulator perturbations in silico.
Corgi imitates cellular gene regulation and integrates DNA sequence and trans-regulator information.
This allows Corgi to make accurate predictions in unseen cell types. Also, it can simulate trans-regulator perturbations in silico.
Reposted by Alexander Sasse
Wow, maybe genomic imprinting as we know it is just the tip of then iceberg. Hopefully this helps usher in a wave of mechanistic studies www.nature.com/articles/s41...
Parent-of-origin effects on complex traits in up to 236,781 individuals - Nature
A novel multistep strategy reveals how parent-of-origin effects shape complex traits in large-scale biobanks.
www.nature.com
August 23, 2025 at 11:06 AM
Wow, maybe genomic imprinting as we know it is just the tip of then iceberg. Hopefully this helps usher in a wave of mechanistic studies www.nature.com/articles/s41...
Reposted by Alexander Sasse
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
August 18, 2025 at 1:00 PM
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
Reposted by Alexander Sasse
Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development [new]
Hi-C jointly decmp. samples: captures cell states, improves gene pred.
Hi-C jointly decmp. samples: captures cell states, improves gene pred.
August 8, 2025 at 7:52 AM
Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development [new]
Hi-C jointly decmp. samples: captures cell states, improves gene pred.
Hi-C jointly decmp. samples: captures cell states, improves gene pred.
Reposted by Alexander Sasse
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 Alexander Sasse
www.sciencedirect.com/science/arti...
Check this: A scar-free strategy enables seamless editing of multi MB regions without residual sequences
Check this: A scar-free strategy enables seamless editing of multi MB regions without residual sequences
Iterative recombinase technologies for efficient and precise genome engineering across kilobase to megabase scales
Genome editing technologies face challenges in achieving precise, large-scale DNA manipulations in higher organisms, including inefficiency, limited e…
www.sciencedirect.com
August 6, 2025 at 5:35 AM
www.sciencedirect.com/science/arti...
Check this: A scar-free strategy enables seamless editing of multi MB regions without residual sequences
Check this: A scar-free strategy enables seamless editing of multi MB regions without residual sequences
Reposted by Alexander Sasse
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Reposted by Alexander Sasse
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Alexander Sasse
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader - Genome Biology Unit
Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...
embl.wd103.myworkdayjobs.com
July 30, 2025 at 1:41 PM
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Alexander Sasse
In a new Perspective article, Josh Morgan discusses how progress in cell biology is hindered by significance testing and the need for a shift to effect size estimation. rupress.org/jcb/article/...
#Technology #Reproducibility #CellCycle #CellDivision #Statistics
#Technology #Reproducibility #CellCycle #CellDivision #Statistics
July 23, 2025 at 5:15 PM
In a new Perspective article, Josh Morgan discusses how progress in cell biology is hindered by significance testing and the need for a shift to effect size estimation. rupress.org/jcb/article/...
#Technology #Reproducibility #CellCycle #CellDivision #Statistics
#Technology #Reproducibility #CellCycle #CellDivision #Statistics
Reposted by Alexander Sasse
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.