Vairavan Lakshmanan
@VairavanL
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Postdoctoral Associate at NCCS & @astar_gis | alum @DBT_instem | Fascinated by RNAs. Single-cell genomics, Tumor biology, ncRNAs, 3'UTR & polyA-tails 🎶💻🧬🧪
Singapore
Joined November 2011
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.
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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
cell.com
CRISPR perturbation screens of 42 cleavage and polyadenylation regulators followed by 3′ scRNA-seq (CPA-Perturb-seq) identifies modules of co-regulated polyA sites, their connection with distinct...
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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.
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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!
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/
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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!
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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
pnas.org
Fluorescent proteins (FPs) are ubiquitous tools in research, yet their endogenous functions in nature are poorly understood. In this work, we descr...
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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. 🧵 👇
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🔊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
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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
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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
science.org
RIBOmap enables single-cell in situ profiling of mRNA translation in 3D for thousands of genes in intact cells and tissues.
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Congratulations Dr.Baid ! So happy and proud :) Well deserved and your dissertation talk was phenomenal!
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
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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
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Excited to announce that I recently joined @ccmb_csir as a Senior Scientist. Our lab is interested in deciphering the metabolic basis of cell state transitions in microbes using fungal model systems(Baker’s yeast & Pathogenic fungi)#twitterreentry #fungi
https://t.co/iKUEXK8hSK
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Hello RNA/DNA twitter! Especially postdocs, PhD students and early career researchers! I am organising the Gordon Research Seminar on Nucleic Acids scheduled to take place on June 17th and 18th 2023 at Maine!
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For months I collected data about the representation of Dalit, Adivasi and OBC students and researchers at various levels of academia in some of the elite universities in India. The results were stark. That story for @Nature in 6 charts. 🧵1/n https://t.co/LSOyBfeFaL
nature.com
Data show how privileged groups still dominate many of the country’s elite research institutes.
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Nano3P-seq - method to study polyA tail length ! https://t.co/CT2nFEDooU
nature.com
Nature Methods - Nano3P-seq presents a nanopore-based sequencing tool to profile polyA-tailed and non-polyA-tailed transcripts, as well as capture polyA tail length and composition.
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#PaperAlert Our work on basal lamina maintenance by cathepsin cells & how that affects tissue differentiation is now out on @J_Cell_Sci! This work was led by grad students @Vinay_k_Dubey & @SouradeepSarkar with help from @VairavanL & @RimpleDalmeida
https://t.co/XNQq0doRzs
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Ever wondered how the 'happy pill' Prozac impacts the brain? We did too! Delighted to share our study on the effects of fluoxetine (Prozac) on 27 different rodent brain areas. Paper is out in Molecular Psychiatry & available for free reading. https://t.co/uhGcBT5NeT A thread 👇🏾
nature.com
Molecular Psychiatry - Integrative multi-omics landscape of fluoxetine action across 27 brain regions reveals global increase in energy metabolism and region-specific chromatin remodelling
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Delighted to work with @shyam_lab, @SabineTejpar, Joanito & many talented colleagues on our paper, using insights from single-cell & bulk -omics to propose an update to CMS classification of colorectal cancer, in @NatureGenet 1/ https://t.co/kStHkikbCh
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