Coby Viner

Postdoc, Biology, UPenn

[ClaudeDevs @ClaudeDevs]

We've reset 5-hour and weekly rate limits for all users. Enjoy Fable 5!

[Alec Stapp @AlecStapp]

Just remembered the story about a computer scientist who had his bike stolen and tried to explain binary search to a cop

[Coby Viner @cobyviner]

@arpitrage Agree and surprised to hear there is not usually such an office! At @WesternU we had this, by Faculty. Not everyone knew about it (or always used them), but they did an excellent job in my experience (at least in @westernuScience).

[Coby Viner @cobyviner]

@GallowayLabMIT My pleasure!

[Coby Viner @cobyviner]

@GallowayLabMIT https://t.co/n2wAtWABSe

https://t.co/0nTrckaQay

https://t.co/aU6bI47nxm

https://t.co/ag48LETDmb

https://t.co/JV21VkSUGw

Hope that helps!

[Coby Viner @cobyviner]

@GallowayLabMIT Bit out of my area, but I recall hearing this too. FWIW, I think it's often more complex than just longer vs. shorter, and it seems to often involve cis-acting elements.

I suspect the original notion came from here:
https://t.co/WZeS2agtBW

Some later related work follows:

[Coby Viner @cobyviner]

@TTChelps Except now there was an incident at Rosedale. Just cleared...

[Coby Viner @cobyviner]

@TTChelps An announcement, 2 min prior to this, and again now, claims the delay at Eglinton is clear. Could you please clarify?

[Ewan Birney @ewanbirney]

Very nice paper by @cobvinyer and colleagues in @michaelhoffman's lab. Methylation and Hydroxy-methylation decoding is really starting to be unpicked.

[Princess Margaret Cancer Centre Research @PMResearch_UHN]

Expanded DNA alphabet for gene regulation🧬

Beyond A/C/G/T, a study by @cobyviner and collaborators, led by @michaelhoffman @UHN, added symbols like “m” and “h” to the genetic alphabet as a new way to study epigenetic regulation.

>>https://t.co/YqAfQHijSz

[Michael Hoffman @michaelhoffman.bsky.social @michaelhoffman]

1/Now published @GenomeBiology! Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. By @cobyviner @CharlesIshak @njwalker @HS_HuiShi @marcela_sjoberg @roxs88 @David_J_Adams @AnneF_S @decarvalho_lab @HainerLab et al! https://t.co/uMmkQ9D6y4

[Coby Viner @cobyviner]

@harthouseuoft Just wanted to check back in about this. It would be really nice for the vending machines to come back!

[Coby Viner @cobyviner]

@311Toronto I went to some effort to submit this, only to find it Cancelled earlier today. No explanation was offered without my having to call in. Any chance you might be able to just let me know here. Is this because a work order for this was already enqueued?

[Coby Viner @cobyviner]

⁦@cityoftoronto⁩ There's carrion rotting by Queens Park. Would be great if you could alert the correct city service to have this removed. Thanks!

[Coby Viner @cobyviner]

@311Toronto Okay, thanks. Submitted as Request Number 03206258.

[Michael Hoffman @michaelhoffman.bsky.social @michaelhoffman]

17/This methodology gives us evidence of the epigenetic modification state of the DNA that is actually bound to OCT4. And, as it turns out, OCT4 motifs are indeed preferentially bound when the sequence is hydroxymethylated!

[Michael Hoffman @michaelhoffman.bsky.social @michaelhoffman]

13/For OCT4, our expanded alphabet analysis revealed a potential preference for 5-hydroxymethylcytosine. Unlike some of the other preferences described above, we could not find this described in the literature.

[Michael Hoffman @michaelhoffman.bsky.social @michaelhoffman]

12/FEZF2 appears to have two completely different motifs, one which prefers modified cytosine, and another which prefers unmodified cytosine.