Anand

Bioengineering/bioinformatics researcher at @ucsd_sbrg focusing on #machinelearning and #omics analysis

[Miles Gander @milesgander]

Excited to announce our recent paper at @abscibio developing deep learning-based codon optimization. Using LLMs we learn natural patterns of codon usage, predict expression levels and use our models to design high expressing CDSs on proteins outside our training set. Thread (1/N)

[Absci @abscibio]

Today, we announce a breakthrough in AI drug design: we are the first to design AND validate new therapeutic antibodies with zero-shot #generativeAI. De novo antibodies are here!

Read our preprint: https://t.co/3eI1N8FGfr

#JPM23

[Joshua Meier @joshim5]

🚨We are releasing a new #manuscript highlighting how our AI-based drug discovery platform can rapidly optimize parameters critical to drug development.

‍🔬Wet-lab data shows that our AI-generated protein drugs exhibit their designed qualities.

Paper: https://t.co/NFUWw9y9RY

[Anand @asastry1]

It's been exciting working with all the different teams at @abscibio to make this preprint happen. Huge shoutout to @RobSpreafico for driving this effort forward!

[Tomás Gomes (@tomsgoms.bsky.social) @tomsgoms]

Research can be hard, but there are ways to make it simpler.

Here are some tips for working in the lab

🧵⬇️

[mSphere @mSphereJ]

@asastry1 and @Nick_Dillon_PhD present a machine learning approach to dissect microbial responses to antibiotics. @ucsd_sbrg #RNA-seq #transcriptome https://t.co/ckaA9GOil7 @ASMicrobiology #mSphere

[ᐯIᑕTOᖇ ᑎIᘔET @victornizet]

new in @mSphereJ from Anand Sastry @asastry1 Nick Dillon @Nick_Dillon_PhD we apply machine learning and iModulon analysis to bacterial RNAseq datasets to understand the roots of environment-dependent changes in antibiotic susceptibility

FEAR vs. GREED

https://t.co/DqswnktWnq

[arnavm.bsky.social @arnavm1]

I hadn't seen a version for genomics yet.

[Anand @asastry1]

New paper out! Independent component analysis is key to understanding transcriptomics data

[UC San Diego Systems Biology @ucsd_sbrg]

In a new publication, @asastry1 and colleagues show that a common structure underlies all E. coli gene expression datasets, and predict three novel regulons for the bacteria. https://t.co/opiSvlsXeK @DTUBiosustain

[XKCD Comic @xkcdComic]

mRNA Vaccine https://t.co/ngCtNfxpTq https://t.co/FTzTqNflvD

[Jeremy Howard @jeremyphoward]

Our paper, "An evidence review of face masks against COVID-19", written by a cross-disciplinary team of 19 international experts, was published in the Proceedings of the National Academy of Sciences today.

No time for the paper? Then read this thread!
https://t.co/bx65CtkTva

[Jahir Gutiérrez-Bugarín, Ph.D @GutierrezJahir]

Should you take the COVID-19 vaccine or not? Pascal’s wager might help you decide ⁦@NautilusMag⁩ (spoiler: you should take it) https://t.co/pKNCXSTOmo

[Anand @asastry1]

A suite of powerful multi-omics data analysis tools, accompanied by jupyter notebooks. Excited to try it out!

[Laura Cantini @cantinilab]

Our work benchmarking joint multi-omics dimensionality reduction approaches in cancer is finally out on @NatureComms !

https://t.co/DKhOcYOoJs

Thanks to all those who contributed @BaudotAnais
@CelHern
Denis Thieffry, Elisabeth Remy, Aurelien Naldi, Pooya Zakeri

[Nature Communications @NatureComms]

.@KRychel27 and @asastry1 from @ucsd_sbrg present the systems-level regulatory structure underlying gene expression in Bacillus subtilis.

https://t.co/1fJ75FhxCN

[UC San Diego Systems Biology @ucsd_sbrg]

Our iModulon decomposition of Bacillus subtilis reveals evidence for 5 putative relationships between metabolic, lifestyle, and stress functions, plus a data-driven summary of sporulation. https://t.co/LHMurovnTu @DTUBiosustain @UCSDJacobs @NatureComms

[Anand @asastry1]

iModulons are data-driven co-regulated gene sets. Explore them for E. coli, B. subtilis, and S. aureus here!

[UC San Diego Systems Biology @ucsd_sbrg]

iModulonDB (https://t.co/Y7m1sVGEA2) is a new knowledgebase
of prokaryotic transcriptional regulation
computed from high-quality transcriptomic datasets
using ICA. https://t.co/yQykotiWCc @DTUBiosustain @UCSDJacobs

[Nathan Lewis @Nathan_E_Lewis]

Exciting new postdoc opening at UCSD https://t.co/z5gtiIZdFw to analyze large amounts of diverse data re: #autism (e.g., genetics, RNA-seq, clinical data, imaging). Building off of our recent exciting work https://t.co/v0VhzfsaPo https://t.co/87cUmyG4hw
https://t.co/Nusvincbbx

[Anand @asastry1]

@GraingerLab Awesome work by @KRychel27. Stay posted for his complete B subtilis manuscript coming soon!

[Anand @asastry1]

Meet my quarantine project! From left to right: Lydia the Clostridia, Colin the E. coli, and Steph aureus (aka Mrs.A). I forgot to put eyes when making the E. coli, so I guess he's technically Coln

[UC San Diego Systems Biology @ucsd_sbrg]

The i-modulon structure of the Bacillus transcriptome is now available, with 63 i-modulons associated with a known transcription factor. https://t.co/Q1WCPnEb9a @biorxiv_sysbio