David Laub

16 posts

David Laub

David Laub

@dvdlaub

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

San Diego, CA Katılım Mayıs 2021
287 Takip Edilen57 Takipçiler
David Laub retweetledi
James Talwar
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 doi.org/10.1093/bioinf…
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David Laub
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!
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David Laub
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.
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Jacob Schreiber
Jacob Schreiber@jmschreiber91·
Added a super-fast one-hot encoding function to `tangermeme` last Friday, and I'm still surprised by how fast it is. Timings are encoding chr1. for-loop: ~40s numpy-vectorized: ~12s new: ~1s Thought I'd share some intuition for why it works so well. #L189" target="_blank" rel="nofollow noopener">github.com/jmschrei/tange…
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Fernan Aguero
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! bioicons.com Illustrations are free to use and reuse, and they are available in SVG vector and PNG format without fees!
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Berk Ustun
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 berkustun.com/join/ for more information.
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Hratch M Baghdassarian
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
Saez-Rodriguez Group@saezlab

1/ 📢 New protocol paper for #CellCellCommunication! Our manuscript presents a pipeline for robust and generalizable cell-cell communication analysis of complex single-cell datasets, combining the best of LIANA & Tensor-cell2cell! 💥🔬 #CompBio #SingleCell doi.org/10.1101/2023.0…

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Bojing Jia
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 nature.com/articles/s4158…👈🏼
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Graham McVicker
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. docs.google.com/document/d/1hV…
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Andrea Castro
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
The EMBO Journal@embojournal

Which tumor-derived peptides can serve as #neoantigens for #immunotherapy? Andrea Castro, Hannah Carter et al @UCSDHealthSci @UCSanDiego find that subcellular location matters for MHC elution and can lead to improved prediction embopress.org/doi/10.15252/e…

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Keşfet

@jmschreiber91 @BioRender @simonduerr @ScienceMagazine @CarterCompBio @NatureMicrobiol @c_gucci3 @KnightLabNews