Arjun Rustagi

STRUCT: a statistical approach to identify RNA secondary structures from raw sequencing data, bypassing multiple sequence alignment 1. STRUCT introduces an innovative MSA-free, assembly-free statistical method to detect RNA secondary structures directly from raw sequencing data, offering unprecedented scalability and accuracy. 2. Unlike traditional methods, STRUCT bypasses the limitations of multiple sequence alignment (MSA), reducing statistical biases and confounding factors associated with evolutionary relationships. 3. STRUCT employs statistical testing for base-pair covariation (BPC) and stem-variation exclusion (SVE), enabling precise identification of conserved RNA structures across diverse datasets. 4. The tool rediscovered key HIV-1 structural RNA elements like the ribosomal frameshift signal, psi packaging signal, and TAR element from longitudinal datasets, demonstrating its accuracy in de novo structure identification. 5. STRUCT’s application to mosquito metatranscriptomics revealed conserved rRNA elements and novel viral RNA structures, including sequences from viruses not present in existing reference databases. 6. By analyzing raw RNA-seq data without requiring a reference genome, STRUCT enables high-throughput discovery of RNA structural motifs crucial for understanding functional RNA elements and viral genome structures. 7. STRUCT sets a new standard in RNA structure prediction, offering a computationally efficient, metadata-independent approach suitable for diverse biological and clinical research applications. @arjunrustagi 💻Code: github.com/juliefrwang/sp… 📜Paper: biorxiv.org/content/10.110… #RNAstructure #Bioinformatics #MachineLearning #StructuralBiology #RNAseq #ComputationalBiology #HIVResearch #Metatranscriptomics

Alex Rodriguez asked a question. Reggie Jackson answered it. (Shouts to the producer and rest of the desk for staying out of Reggie’s way and just letting him talk. I doubt they expected this answer. But it’s a great few minutes of television.)

@pdhsu Yummy Dumplings in the sunset

which restaurant sells the best frozen dumplings in San Francisco? I will try all of them and tell you the correct answer

So excited to see this out! Also a great time to mention the Rustagi Lab is starting up at @UCSF @UCSFDOM and hiring at all levels! Website at previewrustagilab.ucsf.edu

Wu, @KyleTravaglini, @arjunrustagi, @blish_lab, Krasnow et al define cellular tropism & transcriptomic effects of #SARSCoV2 virus. Interstitial #macrophages are a dominant target of viral takeover, #inflammation, & destruction in #COVID19 initiation. hubs.la/Q02sqFTg0

We will miss you Brett. ⁦@BrettLindenbach⁩ legacy.com/us/obituaries/…

⁦@Stanford_ID⁩ is full of superstar fellows and I will forever claim that I helped convince ⁦@arjunrustagi⁩ to do an ID fellowship domannualreports.stanford.edu/renewing-the-f…

@thehitch_md @Stanford_ID Credit deserved!

@nik_krumm @Iberia Ah

@arjunrustagi @Iberia Sorry to hear but your account is locked to followers only, so not sure they will hear you

Trying to get through to @Iberia as need infant ticket number emergency

@JulietaMadridMD - mythbusting - taking a history - social context

Things that we love in ID: source control, cultures pending or better yet resulted, plan for drainage already in place. What else?

ID physicians are highly concentrated in specific areas of the US. We often wonder why our voices in the pandemic are ignored or not heard. This is part of the reason. In many places of the country, no one knows an ID doc. #IDTwitter #AcademicTwitter

@xkcd But was it marinated

Overall, their results matched my answer in the chapter pretty well! The the surface of the steak was cooked by the winds, charred, and blasted away, while the interior stayed cold and raw. Conclusion: This is not a great way to cook steak.

(Thread) In the first What If? book, I answered a question about cooking a steak by dropping it from space. At one point, I commented—jokingly!—that if anyone put a steak in a hypersonic wind tunnel to gather better data, I’d love to see the video. Well, I have good news.

Science Has a Nasty Photoshopping Problem * Unfortunately, many scientific journals and academic institutions are slow to respond to evidence of image manipulation — if they take action at all. My opinion piece @nytimes - #MyGiftArticle nytimes.com/interactive/20…

@drtimothyli Hypermucoid or no?

A case of disseminated klebsiella infection Respect klebsiella pneumoniae It's just like the gram negative cousin of staph aureus

@dadakim @UCRiverside #2

We have an amazing photographer at @UCRiverside and he took photos of me for an upcoming article. I can't pick between these two. Please help.

I'm just going to optimize this one line of code.

JEM welcomes submissions that include reviewer comments from another journal. Transferred manuscripts are four times more likely to be invited for revisions. Just ask Catherine Blish @blish_lab! Take the steps to transfer your paper here: bit.ly/3u4WCc5

@jlsalinas7 Are there infectious diseases in the metaverse? 🤔

Where can one apply for a Chief Metaverse Officer position?