Luke Funk

@CajalNeuro. Former: @BlaineyLab, @broadinstitute, @MIT_HST. Opinions my own.

[Luke Funk @lukebfunk]

If the subject line includes the word "synergies" it's going straight to the trash

[Mohamad Ali Najia @MohamadNajia]

Excited to share how @jacobborrajo Anna Le and I are enabling the future of profiling dynamic cellular processes! We built a synthetic RNA export pathway for cells to "self-report" their transcriptional states in real-time. Big thanks to the entire team!
https://t.co/KWHzp8fRtt

[Luke Funk @lukebfunk]

@markkitti @manorlaboratory I'm here. Tried to use h5 for a while, but I think zarr is the future.

[Luke Funk @lukebfunk]

Closest I have found to what I am looking for is MolArt (https://t.co/fhPEFHroN0), but doesn't seem to allow custom annotations.

[Luke Funk @lukebfunk]

Is there something like genome browser for protein structures? I would like an easy way to make custom annotations on specific amino acids and then see where those are in the 3D structure.

[Luke Funk @lukebfunk]

@mike_tilapia @DrAnneCarpenter Awesome work! I might be missing it, but I am not seeing the supplementary table on bioRxiv...is it posted somewhere?

[Steph Sansbury @stephsansbury]

I'm really excited to present work from @ophirshalem’s group with my outstanding co-first author Yevgeniy Serebrenik @YSereb to tag and manipulate proteins at scale, which we use to study the #proteome and #proteostasis https://t.co/USXPgZR5Ju

[Luke Funk @lukebfunk]

@stephsansbury @ophirshalem @YSereb Congrats on getting this out @stephsansbury; excited to read in detail!

[Jan Funke @janfunkey]

How can machine learning help you to analyze your microscopy images?

Find out at the "Deep Learning for Microscopy Image Analysis" course at the @MBLScience in Woods Hole from Aug 21-Sep 5!

Applications are due 🚨 May 18 🚨

Read on for more! 👇

https://t.co/zuPyW4LbOh

[Luke Funk @lukebfunk]

@benjaminbarad @OHSUSOM Great news, congrats!

[Seth Bannon @sethbannon]

Entrepreneur AI anxiety is real. Everything is moving so fast that many feel the ground is shifting under their feet. A 10x product of last month may be obsolete today. Many are asking the same question:

Where is defensibility in the age of AI?

👇

[Wallace Marshall @WallaceUcsf]

Sci Twitter help - why does differentiation of cells entail both cell fate determination AND arrest of division? Is continued division somehow incompatible with locking in a specific cell fate? Like by erasing chromatin state or something? Sorry if this is a dumb question

[Luke Funk @lukebfunk]

@FrankwithHank

[Luke Funk @lukebfunk]

Had conversations with two separate people this weekend who had never heard of CRISPR...I guess I am sufficiently getting out of my bubble?

[Luke Funk @lukebfunk]

@jonesr18 @nika_shakiba I see, thanks for the clarification! Are the supplementary figures available?

[Luke Funk @lukebfunk]

@nika_shakiba Also, in the experiments in Fig. 4c & d, did you compare to a control without the miR casette? Wondering if the v4 miR-Oct4e with many mismatches is actually producing any repression? Or if the high & tight Oct4 distribution is driven primarily by the high MOI?

[Luke Funk @lukebfunk]

@nika_shakiba In the final trajectory controller designs in Fig. 4a, it looks like the miR-Oct4e variants will target both the endogenous and exogenous OCT4 mRNA? Did you have a way to separately control and “overwrite” Oct4 levels in these experiments like earlier in the paper?

[Luke Funk @lukebfunk]

@RecursionChris Also, how were the labeled genes chosen? Random subset? Intentionally selected for specific properties? What properties?

[Luke Funk @lukebfunk]

Can't decide if this is a useful dataset release for external users

[Chris Gibson @RecursionChris]

Big day for open-science at Recursion! Releasing a 2.2M image, 100TB genome-spanning CRISPR KO dataset* in primary human cells alongside a demo of one of our internal apps. Kudos to the team for getting this ready! Can’t wait to see what the community finds/builds on top of it!

[Luke Funk @lukebfunk]

@RecursionChris Totally agreed! Just not sure what to think of the 16k anonymized genes without any specific plans to de-anonymize in the future.