Wouter Meuleman
@meuleman.bsky.social
Affiliate Associate Professor @ UW.
Previously @ Altius Institute (Principal Investigator), @csail.mit.edu (postdoc), @nkinl.bsky.social / @tudelfteemcs.bsky.social (PhD).
Loves a good analogy!
Previously @ Altius Institute (Principal Investigator), @csail.mit.edu (postdoc), @nkinl.bsky.social / @tudelfteemcs.bsky.social (PhD).
Loves a good analogy!
All in all, we hope this is a useful tool and resource for the genomics community, providing a valuable functional annotation layer on the (human) genome.
The browser is available here:
epilogos.net
And the preprint here, take a look!
www.biorxiv.org/content/10.1...
The browser is available here:
epilogos.net
And the preprint here, take a look!
www.biorxiv.org/content/10.1...
Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations
Functional genomics data, such as chromatin state maps, provide critical insights into biological processes, but are hard to navigate and interpret. We present Epilogos to address this challenge by of...
www.biorxiv.org
September 10, 2025 at 9:09 AM
All in all, we hope this is a useful tool and resource for the genomics community, providing a valuable functional annotation layer on the (human) genome.
The browser is available here:
epilogos.net
And the preprint here, take a look!
www.biorxiv.org/content/10.1...
The browser is available here:
epilogos.net
And the preprint here, take a look!
www.biorxiv.org/content/10.1...
We've Open Sourced all code, including the genome browser (@alexreynolds.bsky.social):
github.com/meuleman/epi...
...as well as the software to generate epilogos tracks of your own data:
github.com/meuleman/epi...
(or just run `pip install epilogos`)
github.com/meuleman/epi...
...as well as the software to generate epilogos tracks of your own data:
github.com/meuleman/epi...
(or just run `pip install epilogos`)
September 10, 2025 at 9:09 AM
We've Open Sourced all code, including the genome browser (@alexreynolds.bsky.social):
github.com/meuleman/epi...
...as well as the software to generate epilogos tracks of your own data:
github.com/meuleman/epi...
(or just run `pip install epilogos`)
github.com/meuleman/epi...
...as well as the software to generate epilogos tracks of your own data:
github.com/meuleman/epi...
(or just run `pip install epilogos`)
In addition to human data from Roadmap Epigenomics (2015, 127 biosamples) and EpiMap (2021, 833 biosamples), we now also include data from the International Human Epigenome Consortium across a whopping 1698 biosamples:
September 10, 2025 at 9:09 AM
In addition to human data from Roadmap Epigenomics (2015, 127 biosamples) and EpiMap (2021, 833 biosamples), we now also include data from the International Human Epigenome Consortium across a whopping 1698 biosamples:
Visualization of thousands of genome-wide tracks in conventional genome browsers is an absolute pain, so we developed our own on top of higlass.
Our browser provides easy access to the features described above, and offers functionality for exporting figures and data.
Our browser provides easy access to the features described above, and offers functionality for exporting figures and data.
September 10, 2025 at 9:09 AM
Visualization of thousands of genome-wide tracks in conventional genome browsers is an absolute pain, so we developed our own on top of higlass.
Our browser provides easy access to the features described above, and offers functionality for exporting figures and data.
Our browser provides easy access to the features described above, and offers functionality for exporting figures and data.
We observe a lot of stereotypical patterning across the genome, and so we implemented a basic pattern matching and search algorithm.
Think of it as a (rudimentary) genomic recommender system -- given a region of interest, identify others like it:
Think of it as a (rudimentary) genomic recommender system -- given a region of interest, identify others like it:
September 10, 2025 at 9:09 AM
We observe a lot of stereotypical patterning across the genome, and so we implemented a basic pattern matching and search algorithm.
Think of it as a (rudimentary) genomic recommender system -- given a region of interest, identify others like it:
Think of it as a (rudimentary) genomic recommender system -- given a region of interest, identify others like it:
Over the years, we've added many features, including the ability to compare groups of different cell types of biosamples.
For example, shown here for Male versus Female donors (many more examples in the paper and online):
For example, shown here for Male versus Female donors (many more examples in the paper and online):
September 10, 2025 at 9:09 AM
Over the years, we've added many features, including the ability to compare groups of different cell types of biosamples.
For example, shown here for Male versus Female donors (many more examples in the paper and online):
For example, shown here for Male versus Female donors (many more examples in the paper and online):
In this work, we aimed to simplify the interpretation and visualization of large amounts of genome-wide annotation data.
Using simple information theoretic methods, we summarize complex multi-factor data across (thousands of) biosamples into a single interpretable genomic track:
Using simple information theoretic methods, we summarize complex multi-factor data across (thousands of) biosamples into a single interpretable genomic track:
September 10, 2025 at 9:09 AM
In this work, we aimed to simplify the interpretation and visualization of large amounts of genome-wide annotation data.
Using simple information theoretic methods, we summarize complex multi-factor data across (thousands of) biosamples into a single interpretable genomic track:
Using simple information theoretic methods, we summarize complex multi-factor data across (thousands of) biosamples into a single interpretable genomic track:
Grateful to colleagues, collaborators, and mentors who made the journey unforgettable. Let’s stay in touch － our paths may cross again in unexpected ways.
Next up: a few months off to catch my breath and see what sparks my curiosity. Open to ideas － here’s to fresh challenges and new adventures!
Next up: a few months off to catch my breath and see what sparks my curiosity. Open to ideas － here’s to fresh challenges and new adventures!
July 4, 2025 at 12:18 PM
Grateful to colleagues, collaborators, and mentors who made the journey unforgettable. Let’s stay in touch － our paths may cross again in unexpected ways.
Next up: a few months off to catch my breath and see what sparks my curiosity. Open to ideas － here’s to fresh challenges and new adventures!
Next up: a few months off to catch my breath and see what sparks my curiosity. Open to ideas － here’s to fresh challenges and new adventures!
Read all about it!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity
An important and largely unsolved problem in synthetic biology is how to target gene expression to specific cell types. Here, we apply iterative deep …
www.sciencedirect.com
June 19, 2025 at 2:24 PM
Read all about it!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Not only do these exceed the specificity of natural controls, they also use a more condensed sequence grammar.
By iterative retraining we further refine and improve our sequences, and find that their activity is correlated with transcription factor expression in single cells.
By iterative retraining we further refine and improve our sequences, and find that their activity is correlated with transcription factor expression in single cells.
June 19, 2025 at 2:24 PM
Not only do these exceed the specificity of natural controls, they also use a more condensed sequence grammar.
By iterative retraining we further refine and improve our sequences, and find that their activity is correlated with transcription factor expression in single cells.
By iterative retraining we further refine and improve our sequences, and find that their activity is correlated with transcription factor expression in single cells.