Jonathan Froehlich
@jjfroehlich.bsky.social
Postdoc // gene regulation, genomics, synbio, stem cells, c. elegans // with @eddaschulz @molgen.mpg.de previously @n_rajewsky @mdc-bimsb //
Reposted by Jonathan Froehlich
How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/
November 20, 2025 at 9:42 PM
How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/
Reposted by Jonathan Froehlich
(3) Described as “futility theorem” in the 2000s, it’s hard to map functional low-affinity motifs based on low PWM match scores, yet some low-affinity motifs have crucial phenotypic consequences in vivo.
What then makes low-affinity motifs important for enhancer regulation?
What then makes low-affinity motifs important for enhancer regulation?
November 19, 2025 at 8:57 PM
(3) Described as “futility theorem” in the 2000s, it’s hard to map functional low-affinity motifs based on low PWM match scores, yet some low-affinity motifs have crucial phenotypic consequences in vivo.
What then makes low-affinity motifs important for enhancer regulation?
What then makes low-affinity motifs important for enhancer regulation?
Reposted by Jonathan Froehlich
We used model interpretation techniques (DeepLIFT/SHAP & TF-MoDISco) to score the contribution of every nucleotide to accessibility, and discover recurrent patterns of sequences predictive of local chromatin accessibility - and these patterns turned out to primarily resemble TF binding motifs!
May 3, 2025 at 6:27 PM
We used model interpretation techniques (DeepLIFT/SHAP & TF-MoDISco) to score the contribution of every nucleotide to accessibility, and discover recurrent patterns of sequences predictive of local chromatin accessibility - and these patterns turned out to primarily resemble TF binding motifs!