David Laub

🎓 Bioinfo PhD @ UCSD | 🤖 Deep Learning | 🧬 Cancer Genomics (he/him)

[James Talwar @jvt_master]

“Hello there!” 👋 A tad late, but worth the wait! GRIEVOUS, your command-line general, is now published in Bioinformatics! Curious how GRIEVOUS can boost your research? Unravel this thread to become a SNP lord. #Bioinformatics #Genomics #GWAS #PRS 1/9 https://t.co/RvKozygUbJ

[David Laub @dvdlaub]

@jmschreiber91 I also wondered whether the mapping array might improve performance, so I implemented a best-of-both-worlds gufunc that used one instead of an alphabet array. I think the results are clear: the mapping array is beneficial so I'll be updating seqpro's implementation soon!

[David Laub @dvdlaub]

@jmschreiber91 Using a gufunc (1) improves the flexibility, enabling broadcasting to work with arbitrary n-dim arrays rather than just 1d arrays. I also benchmarked a multithreaded version of tangermeme, but note that afaik multithreaded Numba functions don't support raising errors.

[Fernan Aguero @fernan_aguero]

Do not use @BioRender. Do not let abusive practices spread!

There is an alternative! Use & Contribute to @simonduerr 's open Bioicons! https://t.co/kNc7l50oft

Illustrations are free to use and reuse, and they are available in SVG vector and PNG format without fees!

[Tae Seok Moon @Moon_Synth_Bio]

My best article @ScienceMagazine. It took ~1 year for me to publish it since its 1st submission. I hope it will positively change the #culture. I hope you will work together with me to make a better world for the next #generations. Please retweet broadly.
https://t.co/EGEC6HC7hg

[Nature Computational Science @NatComputSci]

📢 Out now! @KlieAdam, @CarterCompBio and colleagues present EUGENe, a toolkit for accessible, interoperable, and reusable deep learning analysis in regulatory genomics. https://t.co/TV8Tn2GmbE

[Berk Ustun @berkustun]

📢 Please RT 📢

I am recruiting PhD students to join my group at UCSD!

We develop methods for responsible machine learning - with a focus on fairness, interpretability, robustness, and safety.

Check out https://t.co/dZzD2z5qa1 for more information.

[Kit Curtius @yosoykit]

Never have I been more proud of a title 😁 Check out our N&V out now in @NatureMicrobiol - led by PhD student @c_gucci3 with @KnightLabNews

[Hratch M Baghdassarian @hmbaghdassarian]

We've put together a protocol and set of tutorials to help those interested in cell-cell communication analysis approach it in a generalizable and user-friendly way. Involved work by some awesome people @eagut and @DanielBDimitrov

[Graham McVicker @GrahamMcVicker]

We are excited to share our preprint describing our analysis of enhancer interactions led by @zrcjessica and @somet3000! https://t.co/2lY2KQpB8o

[Bojing Jia @BojingJia]

💃Dancing in the spotlight!🕺Our new paper shows, hidden in plain sight...

...replicated chromosomes, intimately intertwined, in tango!👯‍♀️

Check out the full choreography out today in @NatureBiotech
https://t.co/tyApQQMBrz👈🏼

[Graham McVicker @GrahamMcVicker]

UCSD graduate students are integral to research at the Salk Institute. A group of Salk faculty have signed a letter supporting their effort to obtain fair compensation that allows them to live near the university.
https://t.co/bj4WnvpBx2

[Erick Armingol @eagut]

We continue adding new features to Tensor-cell2cell. In this brief communication we show how concerted temporal dynamics of protein- and metabolite-mediated cell-cell communication can be studied! Check out our latest pre-print!

[Andrea Castro @andrea_b_castro]

So excited to share our latest research! Here we show that accounting for where a peptide comes from within a cell can help improve elution and immunogenicity prediction