@cobyviner

Postdoc & Penn AI Fellow • Computational Biologist

 Philadelphia, PA
cs.toronto.edu/~cviner/
Joined September 2014
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  • Followers341
20Media
Very nice paper by @cobvinyer and colleagues in @michaelhoffman's lab. Methylation and Hydroxy-methylation decoding is really starting to be unpicked.
Michael Hoffman @michaelhoffman.bsky.social@michaelhoffman17 Mar 2023
1/On @biorxivpreprint: revised preprint from my lab: modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. By @cobyviner @CharlesIshak @marcela_sjoberg @roxs88 @David_J_Adams @AnneF_S @decarvalho_lab @HainerLab et al! biorxiv.org/content/10.1101/…

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified...

biorxiv.org
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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. >>genomebiology.biomedcentral.…
Michael Hoffman @michaelhoffman.bsky.social@michaelhoffman17 Mar 2023
1/On @biorxivpreprint: revised preprint from my lab: modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. By @cobyviner @CharlesIshak @marcela_sjoberg @roxs88 @David_J_Adams @AnneF_S @decarvalho_lab @HainerLab et al! biorxiv.org/content/10.1101/…

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified...

biorxiv.org
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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! genomebiology.biomedcentral.…

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Genome Biology - Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between...

link.springer.com
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⁦@cityoftoronto⁩ There's carrion rotting by Queens Park. Would be great if you could alert the correct city service to have this removed. Thanks!
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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!
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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.
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12/FEZF2 appears to have two completely different motifs, one which prefers modified cytosine, and another which prefers unmodified cytosine.
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11/For example, while previous literature reported that JUND is "uniformly inhibited by 5mC", our analysis suggests that a minority of JUND motifs have a slight preference for 5mC.
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4/We developed a method to explicitly model how cytosine modifications on one side of a base pair or the other might affect transcription factor binding. To do this we simply expand the alphabet, adding m for methylcytosine, h for hydroxymethylcytosine, and so on.
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Coby is looking for a postdoc opportunity in the U.S. next and wants to pivot from computational genomics to molecular evolution and has an interest in performant algorithms. If you have any leads I hope you will chat with him! #KSChromatin23 #KSEpigenetics23
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My posters are located next to each-other, with the (fewer) Q8/#KSChromatin23 posters, in the far back of Salon C. Looking forward to chatting about them! #KSChromatin23 #KSEpigenetics23 @KeystoneSymp
Michael Hoffman @michaelhoffman.bsky.social@michaelhoffman15 Mar 2023
My final-year PhD student @cobyviner presents 2 posters #KSchromatin23 #KSepigenetics23 tonight: 2048 Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet 2521 Comparing chromatin accessibility profiles with maximal cliques in temporal graphs
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Stuck in Calgary, due to a long @WestJet delay, on my way to the @KeystoneSymp in Victoria, BC. Looking forward to the conferences! Unfortunately likely to miss tonight's mixer, due to this delay. 😔 Anyone else stuck here too? #KSchromatin23 #KSepigenetics23
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At least we've now boarded. Here's hoping we still make it in time to catch the end of the event!
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Almost every ⁦@WestJet⁩ flight, out of Calgary this evening (YYC) is delayed. The Customer Service lineup, directly below this sign, has a massive line of well over 50 people. What an unfortunate mess.
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Poster #19, this afternoon! #RECOMB2022
Michael Hoffman @michaelhoffman.bsky.social@michaelhoffman23 May 2022
Wish I could be at #recomb2022! I hope you will check out my PhD student @cobyviner's poster "Comparing chromatin accessibility profiles with maximal cliques in temporal graphs" at poster session I today at 2:30p!
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Enjoying #recomb2022 so far. If I know you and you're here, or arriving for the main conference, let me know!
Sources of variation in cell-type RNA-Seq profiles journals.plos.org/plosone/ar…

Sources of variation in cell-type RNA-Seq profiles

Cell-type specific gene expression profiles are needed for many computational methods operating on bulk RNA-Seq samples, such as deconvolution of cell-type fractions and digital cytometry. However,...

journals.plos.org
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An excellent and critically important article: theglobeandmail.com/opinion/…

Opinion: Repeat after me: This is an emergency

As the COVID-19 crisis deepens around the world, I’ve noticed some graphics and dashboards using a subheading: situational awareness

theglobeandmail.com
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By @JillianHortonMD!
Replying to @tina_kesha @SamanthaLWilson
Not quite, but sort of at a higher-level of syntactic sugar. R's `sapply` closest. Map would be the closest Python equivalent in the default library. Pandas has apply, like R. Apply is a functional program concept, and so divisive on those lines. Useful for dataframes and such.
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@AlexBetts How did your bot manage to re-tweet and like this? Some impressive automation there!
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