Kandarp Joshi

Presented our work on "Deciphering the dynamic landscape and functional characterization of post-transcriptional modifications in pediatric malignancy medulloblastoma". Had a stimulating discussion on consequences of RNA modifications stoichiometries on downstream regulation.

Fascinating new insights on co-transcriptional m6A deposition - before splicing!

Its purely luck. If the paper gets reviewers not interested in critiquing the work it just passes. Ive reviewed a few papers where i gave major comments for improvement but other reviewer simply wrote "accepted"!

The RMaP challenge of predicting RNA modifications by nanopore sequencing Communications Chemistry, Published online: 12 April 2025; doi:10.1038/s42004-025-01507-0RNA modifications play critical roles in gene expression regulation, RNA stability, and translation efficiency, however, the detection of RNA modifications by various sequencing approaches may present differing results. Here, the authors explore several computational methods for the detection of the most researched mRNA modifications, with a view to improving algorithms’ comparability, reliability, and consistency in RNA modification prediction.

Just out: The RMaP challenge of predicting RNA modifications by nanopore sequencing

The RMaP challenge of predicting RNA modifications by nanopore sequencing - Communications Chemistry RNA modifications play critical roles in gene expression regulation, RNA stability, and translation efficiency, however, the detection of RNA modifications by various sequencing approaches may present...

The RMaP Challenge manuscript has been published in Communications Chemistry. It was a fun challenge and great learning experience.

www.nature.com/articles/s42...

Setdb2 Regulates Inflammatory Trigger-Induced Trained Immunity of Macrophages Through Two Different Epigenetic Mechanisms "Trained immunity" of innate immune cells occurs through a sequential two-step process where an initial pathogenic or sterile inflammatory trigger is followed by an amplified response to a later un-re...

New preprint from @ajaiswal07.bsky.social and @timtocool.bsky.social
www.biorxiv.org/content/10.1...

That depends on whether machine overlords also synthesize emotions. I think no one is safe

I maxed out my credit card, emptied my savings account, and took out a loan to move from Alabama to Bethesda, MD. I don’t even qualify for unemployment since I’ve only worked at NIH for a month. I will be financially and medically devastated.

Seeking suggestions for anywhere that’s hiring!!

Synonymous mutations promote tumorigenesis by disrupting m6A-dependent mRNA metabolism The impact of synonymous mutations remains elusive. Here, the authors demonstrate that synonymous mutations can promote tumorigenesis by disrupting post-transcriptional m6A modification. The findings ...

This is a beautiful, important new paper that forges a link between mRNA epitranscriptomes, cancer variants, and response to therapy.

This should be on everyone's reading list.

#RNAsky
#CANsky
#genomics
#bioinformatics
#GENEsky
🧬 💻
🧪

www.cell.com/cell/fulltex...

Flying pelican

Huh?

#birds #birdsphotography #usbirds

Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promis...

Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump

www.biorxiv.org/content/10.1...

A long time ago in a galaxy far, far away...

#astrophotography #space

Crusing pelican!

#birds #bird #birdsphotography #usbirds

I am an astrophotographer and purse it as a hobby on clear skies.

Yes

My first attempt at #astrophotography back in 2014!

@bot.astronomy.blue signup

Birds of Florida

#addBirder

YTHDF2 promotes ATP synthesis and immune evasion in B cell malignancies YTHDF2 modulates oncogenic transformation and immune evasion across multiple B cell cancers by stabilizing m5C-modified mRNAs and destabilizing m6A-modified mRNAs, thereby serving as a dual reader for...

New study suggests YTHDF2 might have dual reader capacity for m5C and m6A. Would be an interesting read
www.cell.com/cell/fulltex...

Newly discovered mechanism enables precise gene regulation by combining DNA and RNA epigenetics Our genes contain all the instructions our body needs to function, but their expression must be finely regulated to guarantee that each cell performs its role optimally. This is where DNA and RNA epig...

Newly discovered mechanism enables precise gene regulation by combining DNA and RNA epigenetics #rnasky phys.org/news/2025-01...

Hello! We’re the Alex’s Lemonade Stand Foundation Childhood Cancer Data Lab. 👋 We build data and analysis tools and offer workshops designed to accelerate pediatric cancer research. Check us out at ccdatalab.org! We’re excited to connect with the community and share our resources with you.

🚨 We are hiring! We are looking for motivated bioinformatician to join our team “Genomics and Development of Childhood Cancers" at Institut Curie, Paris, France.

The interested candidates should apply by sending an email with their CV and motivation letter

Birds of Florida

Association of polygenic scores for neuropsychiatric traits with self-reported professions based on analysis of 420k individuals from UK Biobank and Million Veteran Program. Look at the 'arts & design' category. Artistic talent comes at a cost--a piece of your mind :)

Selected areas of Human rRNAs showing modification calls in IGV. Samples sequenced by ONT direct RNA sequencing with experimental Remora models calling m6A, m5C, PseudoU, and all 4 2'Ome modifications.

We have been busing working on models to detect all 2'Ome-RNA modified nucleotides on top of PseudoU, m6A, m5C and Inosine using @nanoporetech.com direct RNA sequencing.
This is still very preliminary but here are a few examples of what it looks like on Human #rRNA prepared with standard lib prep 🤩

GitHub - seandavi/awesome-single-cell: Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. - seandavi/awesome-single-cell

Six years on, github.com/seandavi/awe... is still going strong. Contributions welcome. Fastest growing category recently has been spatial transcriptomics.
#compbio #singlecell #transcriptomics #genomics #awesome-list

SPECIAL ISSUE! This month Genome Research publishes a diverse collection of research and review articles in a special issue highlighting advances in long-read sequencing applications in biology and medicine. Full issue links here: tinyurl.com/Genome-Res-3....

Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution RNA polyadenylation is crucial for RNA maturation, stability and function, with polyA tail lengths significantly influencing mRNA translation, efficiency and decay. Here, we provide a step-by-step pro...

Very happy to share our updated #Nano3P-seq protocol, adapted to #nanopore R10 chemistry. After a lot of troubleshooting both in the wet lab protocol but also the computational analysis pipeline, we finally made it! :-) www.biorxiv.org/content/10.1...

🚨 Update for #RNA science fans:
I checked on #Bsky registry, and here is a 'condensate' (😆) of all #RNA #RNAsky starter packs so far:
1. General RNA biology #1
go.bsky.app/RN6HnZp

Action Intent Links | Bluesky Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how:

docs.bsky.app/docs/advance...

#AcademicSky #HigherEd #Altmetrics