Julius Judd

@manvendr7 Thanks Manu!

Congratulations @judd_julius , you deserve nothing less than the best. All the best and do the best! #ProudLabMate :)

So proud of @judd_julius who became Dr. Judd today! Julius was co-advised by John Lis so we had to have a PRO-seq cake! 🍰 Julius ate a piece of his own beautiful data and John was content with a slice of paused polymerase! 🎉CONGRATS Julius!!🍾

I'm giving my thesis seminar tomorrow at noon EST! There will be a zoom option that's open to anyone who would like to attend, DM me for the link!

In this issue of @NatRevMCB, our review on transposable elements in mammalian cis-regulation. A joint effort with @judd_julius, @CedricFeschotte, and Joanna Wysocka. We have already seen our figures used in conference talks, so the work was worth it! rdcu.be/cQEF0

@SomePaddy @paul_m_orwin This is not true. Trizol followed by ethanol precipitation absolutely will recover RNAs smaller than 200nt. Even 20nt RNAs are fine.

@paul_m_orwin Not for RNA <200nt though... But that may not matter to you.

I was today years old when I discovered that Trizol is really great for RNA extraction. I wasted a lot of $$ and time not using it :(

@marcotrizzino I have some qPCR primers for LTR5HS and LINE1 (multiple subfamily specificity), dm me your email and I’ll send you the sequences and references.

TE community: we have to do some RT-qPCRs for LINEs and ERVs. At this stage pretty much any LINE or ERV would be fine. Where can I find good resources for already validated primers? (Human genome). Thanks and please RT!

@aaronquinlan @ryanlayer It’s banker’s aka half-even rounding, the default round function in R does the same thing

@ryanlayer That's..............odd

PSA for everyone out there using Python 3 to help aggregate their final grades. 🚨🚨🚨 round() ROUNDS TO THE NEAREST EVEN NUMBER 🚨🚨🚨 If that doesn't mean anything to you, let me give some examples: round(1.5)==2 round(2.5)==2 round(3.5)==4 round(4.5)==4 🤬

@GuertinLab I always just explicitly specify using the contrast argument to results, less potential for confusion IMO

@rnaErin pybedtools will get you a lot of the functionality. Not a drop in replacement but can do a lot

@rohmanoabdur @RPuggaardRode @AnthonyTeacher @tmalsburg I mean that when used within a function = only assigns the variable within the scope of that function. This is useful when you specifically want this, but if you don’t can produce unexpected results.

@judd_julius @RPuggaardRode @AnthonyTeacher @tmalsburg Do you mean by "scope" is like `sum(x <- 1:5)` vs `sum(x = 1:5)` or something else?

99% of all R criticism: 1. R is different from my favorite programming language (usually Python or JavaScript). 2. I didn't bother to learn R and I'm upset that it doesn't behave the way I expected. 3. R is bad for task X, where X is something for which R was never designed.

@AnthonyTeacher @tmalsburg It’s literally less keystrokes than the space-equal-space you’d use in most other languages

@AnthonyTeacher @tmalsburg These people need to learn about option/minus in Rstudio

@RPuggaardRode @AnthonyTeacher @tmalsburg Bad idea if you ever intend to write functions or otherwise need to think about scope.

@AnthonyTeacher @tmalsburg Just use = instead of <- #ChaoticEvil

@pastramimachine @lucksmith @evornithology At least it has a distinct sound!

What’s your favorite lab reagent? I’ll start. Proteinase K.

Rare glimpse into the office of the reviewer who requests qPCR validation of RNA seq data

Check out now our new #Review led by @CedricFeschotte and Joanna Wysocka on roles of #transposons in the regulation of mammalian #transcription @Stanford @StanfordMed @ChemSysBio @FueyoRaquel @Cornell @CornellCALS @CornellMBG @judd_julius 👉go.nature.com/3tstHxq

Super excited to share this review that I wrote with @FueyoRaquel @CedricFeschotte and Joanna Wysocka!! This was a lot of fun to write and I hope you all enjoy it! nature.com/articles/s4158…

PhD rejections (1st cycle right after undergrad): UW Madison Stanford Harvard Et al (n=12) No acceptances, not even an interview. Acceptances after 2 years as a tech: UAlbany Cornell Yale MIT No rejections this time. Experience makes a huge difference!

Can't resist sharing this fig preview of an upcoming review on transposons & gene reg @judd_julius and I had great fun writing with @FueyoRaquel & Joanna Wysocka. Seeing these proofs put a big smile on my face! #ThursdayTease

@GuertinLab @rnaErin Just resuspend the powdered agarose in water and transform new bacteria with it, if anyone was wondering how.