Vairavan Lakshmanan

Postdoctoral Associate at NCCS & @astar_gis | alum @DBT_instem | Fascinated by RNAs. Single-cell genomics, Tumor biology, ncRNAs, 3'UTR & polyA-tails 🎶💻🧬🧪

[The Nobel Prize @NobelPrize]

BREAKING NEWS
The 2024 #NobelPrize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun for the discovery of microRNA and its role in post-transcriptional gene regulation.

[Rahul Satija @satijalab]

Interested in 3' UTR changes in scRNA-seq? Check out our:
* CPA-Perturb-seq paper
* UCSC Perturb-seq tracks (see who regulates your favorite 3’ UTR!)
* Seurat extension for polyA site analysis (PASTA)
* Deep neural perturbation network (APARENT-Perturb)
https://t.co/XXYEBHV1iG

[Vairavan Lakshmanan @VairavanL]

@VirajDoddihal Thanks Viraj !

[Vairavan Lakshmanan @VairavanL]

We propose ctQC(https://t.co/hm2OfLoDqs), a data-driven method to filter low-quality cells from scRNA & spatial omics data! Apart from empty droplets it efficiently eliminates soup/debris & damaged cells improving downstream biological inferences. Comments & suggestions welcome!

[Shyam Prabhakar Lab @shyam_lab]

We finally wrote up our cell type-specific QC (ctQC) protocol for scRNA (and spatial)-seq data: https://t.co/KLDzc77ZH9 . Comments welcome! In a nutshell: we show that sc QC cutoffs should be strict, cell type-specific and data-driven. 1/

[Vairavan Lakshmanan @VairavanL]

@sayanb08 Thanks @sayanb08 !

[Vairavan Lakshmanan @VairavanL]

Check out the tweetorial for more details - https://t.co/Y7DWyPk5i7 ! Huge thanks to Shyam for all the discussions throughout this work and special thanks to @iaintan_mdphd for co-supervising! I would like to thank all @shyam_lab members, @astar_gis & NCCS.

[Matthias Lutolf @TheLutolfLab]

Have you ever seen real-time footage of a tumor developing outside a living organism? We are thrilled to announce a new paradigm in ex vivo cancer modelling https://t.co/N619EGEFgc. Let’s have a quick look!

[nat clarke @natclarke8]

Many of us use GFP all the time in lab, but have you ever wondered what fluorescent proteins do in nature? I’m delighted to share our paper (https://t.co/0KPvBbNQHV), hot off the presses, where we uncover new roles for FPs in intertidal sea anemones.

Curious? Read on: 🧵1/n

[Shyam Prabhakar Lab @shyam_lab]

1. BANKSY is out! https://t.co/uy8myuVA5p
Our spatial clustering algo applies to any spatial RNA/protein/... assay, scales to 2M cells, detects both cell typing and spatial domains and facilitates spatial batch correction.
🧵 👇

[Vairavan Lakshmanan @VairavanL]

@shivaprasad_pv @NCBS_Bangalore @TIFRScience Congratulations Shiva 😁 well deserved !

[Vairavan Lakshmanan @VairavanL]

@AcharyaAchyuth @centuri_ls @IBDMmarseille @lai Congratulations dude 🎉

[The Academinist @theacademinist]

🔊Start the week right with a fresh episode! 🔊This month @BaidSrishti joins us, sharing her insight & tips on navigating an international career move 🇮🇳✈️🇺🇸We also discuss how some of the challenges of a big
move can intersect with being #womeninSTEM ⬇️
Don't miss it! 🧵1/2

[Vairavan Lakshmanan @VairavanL]

@Palakodeti_Lab @Vinay_k_Dubey @DPalakodeti @DBT_inStem @MAHE_Manipal Congratulations Dr. Dubey Ji 🎉🎉 well deserved !

[Vairavan Lakshmanan @VairavanL]

@varmaalok22 @VatsalaT @NCBS_Bangalore Congratulations aalok 😁 well deserved and good luck for your next adventure!

[Vairavan Lakshmanan @VairavanL]

@shivaprasad_pv Congratulations shiva and Vivek 😎 very interesting work !

[Felix Horns @FelixHorns]

Want to sequence RNA from cells without killing them or deliver RNA programs from cell to cell? Today in Cell, we present RNA exporters, which package and secrete cellular RNA, for non-destructively monitoring cell dynamics by sequencing and delivering RNA https://t.co/JG1mzYvLgb

[Xiao Wang @WangXiaoLab]

RIBOmap for spatially resolved single-cell translatomics is published today! Congrats to the whole team and thanks so much for the constructive feedback and great suggestion from the editor, reviewers, colleagues, and friends!
https://t.co/Dmxbe7atn5

[Vairavan Lakshmanan @VairavanL]

@shivaprasad_pv @genomeresearch @CSHLPress Congratulations shivaprasad and @VivekHariSunda1 !👏 Excellent work !

[Vairavan Lakshmanan @VairavanL]

Congratulations Dr.Baid ! So happy and proud :) Well deserved and your dissertation talk was phenomenal!

[P. Scott Hefty @pshefty]

Congratulations Dr. Srishti Baid!!! Fantastic (and incredibly energetic) dissertation defense - on to post-doc at University of Michigan with David Ginsburg - so very proud of her!! ⁦@KUbiology⁩ ⁦@kuhotZmicro⁩ ⁦@KUMolBio⁩ ⁦@DyanMorgan⁩ ⁦@BaidSrishti⁩

[Feng Zhang @zhangf]

Delivery of therapeutic molecules is a major bottleneck for treating a wide range of diseases. Today we describe a new modality for delivering proteins based on an engineered contractile injection system @nature https://t.co/eIAn8MW6jN