iiinova — where your digital self keeps evolving

Reposted by Seema

bioRxiv Genomics @biorxiv-genomic.bsky.social · 23/06/2026

Variation and selection at predicted G-quadruplexes across the human pangenome www.biorxiv.org/content/10.64898/20…

Seema @molbioinfo.bsky.social · 18/02/2026

Visited BioAsia2026 Hyderabad, India. Excited to learn about keynote speakers from my lab's research domain being invited, Howard Y. Chang (lncRNAs) and Pushmeet Kohli (AlphaFold). Happy to meet alongwith my students and discuss all things lncRNAs and AI. #RNA #Computational @alphafold.bsky.social

011

Seema @molbioinfo.bsky.social · 18/02/2026

Delighted and honored to get on board nature.com/npjsba/editors Thanks EiC MK Jolly for the tremendous opportunity and I look forward to working proactively towards being among the ambassadors and contributing to this journal's long-term success. @natureportfolio.nature.com

nature.com

About the Editors | npj Systems Biology and Applications

About the Editors

000

Seema @molbioinfo.bsky.social · 22/01/2026

Thrilled to announce the publication of our latest research: www.sciencedirect.com/science/arti... This entails secondary structural studies on the probable mechanisms of PVT1 binding to multiple mRNAs, common DE coding & non-coding genes across pan-cancer system. #lncRNA #RNA #CancerResearch

sciencedirect.com

Structural basis of long non-coding RNA PVT1 interactions with select mRNAs universal in pan-cancer system: A computational study

PVT1 lncRNA can regulate multi-gene expression through diverse mechanisms, one of which is through binding interactions with mRNAs. Our previous study…

030

Seema @molbioinfo.bsky.social · 08/10/2025

🧪 Thought of the day: Penned by me: "An abstract Abstract doesn't age well". Or does it? #science #NobelPrize #abstract

000

Reposted by Seema

febsopenbio.bsky.social @febsopenbio.bsky.social · 29/09/2025

📣 Don't miss this new Review! Interplay between RNA-protein interactions and RNA structures in gene regulation 🔓 buff.ly/pu6TpVa 🖊️ @rnaminni.bsky.social #RBPs #RNA #RNAbiology #RNAbindingproteins #RNAbinding #RNAstructure

042

Seema @molbioinfo.bsky.social · 02/10/2025

Hello RNA world! Any new news?

100

Seema @molbioinfo.bsky.social · 30/09/2025

MtDNA incorporating ribonucleotides and not deoxyribonucleotides increases inflammation. Interesting article: x.com/davidasincla...

x.com

010

Seema @molbioinfo.bsky.social · 27/07/2025

🧪Intellectuals, Selection for the prestigious National Academy of Sciences (India) Membership is a joy! Yours truly, Ph.D, MNASc 😀 Grateful to everyone who have stood by me rock solid in this scenic and transformative journey. Heartfelt Thank you to The National Academy of Sciences, India...

000

Seema @molbioinfo.bsky.social · 24/07/2025

Happy to share our latest paper using machine-learning-QSAR on ChEMBL dataset. We identified and designed novel inhibitors for Acid Ceramidase inhibition in Glioblastoma using SHAP-based mechanistic interpretations. Thankful to proactive Reviewers and Editors. rdcu.be/exD3a

rdcu.be

An innovative machine learning-based QSAR approach for prediction and structural analysis of novel/repurposed acid ceramidase (ASAH1) inhibitors for glioblastoma therapy

000

Seema @molbioinfo.bsky.social · 03/01/2025

Interesting, so sharing here: x.com/nlarusstone/...

x.com

000

Reposted by Seema

Shah Selbe @shahselbe.bsky.social · 09/12/2024

It is always mind boggling at how massive @agu.org is every year. This is just one session of the poster room, which changes over twice daily for the duration of the conference. #AGU24

722241

Seema @molbioinfo.bsky.social · 28/11/2024

And here I was wondering RNA Capping at the first mention of the word 'cap'...caps impart efficient translation and stability to mRNA... 🤔

000

Reposted by Seema

Armand Sarlangue @armandsarlangue.bsky.social · 26/11/2024

The great Matterhorn in all its glory… A classic shot from the Swiss alps, but the light was too good to not click this one. #bluesky #photography #mountains #nature #landscape #landscapephotography #naturephotography

662796165

Seema @molbioinfo.bsky.social · 21/11/2024

RNA aficianados, Just attended my first seminar series at RNA Collaborative - The RNA Institute, SUNY University at Albany yesterday. It is awesome science and a great way to stay updated in everything RNA. Registration is free: www.rnasociety.org/rna-collabor... #rnabiology #rnasky 🧪

rnasociety.org

RNA Collaborative Seminar Series

022

Seema @molbioinfo.bsky.social · 20/11/2024

Is 108 kb Air the longest lncRNA? Any new champion in this category?🤔 #rnabiology #rnasky 🧪

010

Seema @molbioinfo.bsky.social · 20/11/2024

Molecular dynamics aficionados! Which is the most accurate RNA force-field currently? #rnabiology #computationalbiology #rnasky 🧪

100

Seema @molbioinfo.bsky.social · 18/11/2024

Deers and LncRNAs... www.nature.com/nsmb/volumes... #rna #rnabiology

nature.com

000

Reposted by Seema

Victoria aka Blaze @burrddoh.bsky.social · 13/11/2024

Got birds? Reply or quote this with your pics; we’d love to see them 📷🪶

One of my blue jays standing guard over a piece of dried papaya

117717020502

Reposted by Seema

Igor Ulitsky @igorulitsky.bsky.social · 13/11/2024

Let's make a thread of RNA-related conferences in 2025 🧵 (add missing!)

1211846

Seema @molbioinfo.bsky.social · 13/11/2024

@ijayas.bsky.social please add me to Biophysics starter pack. Thanks.

000

Seema @molbioinfo.bsky.social · 12/11/2024

I am struck by a moment of sonder as I gaze around the @bluesky #bluesky

000

Reposted by Seema

Zid Lab @zidlab.bsky.social · 09/11/2024

🎯 Our focus: TIM50, a mitochondrial import receptor with 7 consecutive prolines. When eIF5A is depleted, ribosomes get seriously stuck here - creating a traffic jam up to 300 base pairs long!

Ribosomes start to build up ~300bps upstream of a stretch of 7 proline residues and then do not seem to make it through the ribosome stall.

121

Reposted by Seema

Thiago Carvalho @cyrilpedia.bsky.social · 29/10/2024

'On the evolutionary timescale, accumulation of L1 & SINEs occurred via multiple “explosions” when, during rather short evolutionary times, numerous insertions of retroelements entered genomes of our ancestors creating structurally distinct subfamilies of L1s & SINEs.' www.pnas.org/doi/10.1073/...

pnas.org

The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of “retrobiome” in naked mole rat | PNAS

Approximately half of mammalian genomes are occupied by retrotransposons, highly repetitive interspersed genetic elements expanded through the mech...

011

Seema @molbioinfo.bsky.social · 30/10/2024

I know there are prediction tools for MHC and T cell Binding. Any computational tools for predicting T cell response? 🧪

000

Reposted by Seema

Zen Faulkes @doctorzen.net · 29/10/2024

Two high school students wanted the cash prize 🏆 for a math contest. They discovered new profs of the Pythagorean theorem, presented it at conferences, and published it in a journal - which has an awesome “Conclusion” section with the backstory: www.tandfonline.com/doi/full/10....

tandfonline.com

Five or Ten New Proofs of the Pythagorean Theorem

We present five trigonometric proofs of the Pythagorean theorem, and our method for finding proofs (Section 5) yields at least five more.

47331

Reposted by Seema

Mark Peifer (He, him) @peiferlabunc.bsky.social · 29/10/2024

If you are interested in biological evolution in its many guises and aren't following Will, you're REALLY missing out 🧪

1185

Reposted by Seema

RCSB Protein Data Bank @rcsbpdb.bsky.social · 10/10/2024

PDB depositors provided an enormous wealth of open access 3D structure data that helped drive breakthroughs in protein structure prediction More at Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction www.cell.com/structu...

033

Seema @molbioinfo.bsky.social · 07/10/2024

Delighted are we too!! Our studies on lncRNA actions on gene regulation in pan-cancer system.... 1.RNPS1 among others: doi.org/10.7717/peer... 2. MALAT1 among others:https://doi.org/10.1038/s41598-022-11214-8 3. MALAT1-RNPS1 complex in alternative splicing:http://dx.doi.org/10.1021/acsomega.4c04467

010

Reposted by Seema

Karolin Luger @nucleosomepolice.bsky.social · 17/09/2024

New function for an 'old' chromatin remodeler: great collaboration with @nitikataneja.bsky.social and others. Fantastic work from our own @nhoitsma.bsky.social. Check out how SMARCAD1 contributes to resolving R-loops during replication, before they become a problem. www.biorxiv.org/content/10.1...

11810

Reposted by Seema

Adam Phillippy @aphillippy.bsky.social · 16/09/2024

"Epigenetic control and inheritance of rDNA arrays" New preprint from the T2T acrocentrics team! We find a tight link between methylation and transcription of the rDNAs, including the occasional silencing of entire arrays www.biorxiv.org/content/10.1...

3189

Seema @molbioinfo.bsky.social · 16/09/2024

Bluesky now has over 10 million users, and I was #8,673,690! Arrived at last! 😄

000

Reposted by Seema

John Prensner @johnprensner.bsky.social · 10/09/2024

5/ This work is a definitive statement on the capacity for small ORFs to produce the highest quality evidence in mass spectrometry data. In collaboration with GENCODE and PeptideAtlas, these ORFs and peptides will be supported for public view and public research resources.

023

Reposted by Seema

Stephen Turner @stephenturner.us · 12/09/2024

Multi-pass, single-molecule nanopore reading of long protein strands www.nature.com/articles/s41586-024-… 🧬🖥️ github.com/uwmisl/PASTOR-sequencing

01212

Reposted by Seema

The Interactive Fly @interactivefly.bsky.social · 12/09/2024

Pollex, T., Marco-Ferreres, R., Ciglar, L., Ghavi-Helm, Y., Rabinowitz, A., Viales, R. R., Schaub, C., Jankowski, A., Girardot, C., Furlong, E. E. M. (2023).. Chromatin gene-gene loops support the cross-regulation of genes with related function. Mol Cell. www.cell.com/molecular-ce...

cell.com

Chromatin gene-gene loops support the cross-regulation of genes with related function

023

Reposted by Seema

Joanna Masel @joannamasel.bsky.social · 06/09/2024

Our latest paper doi.org/10.7554/eLif... directly measures the "effective population size" that matters to nearly neutral / drift barrier theory, as the degree to which codon bias differs from expectations from GC content. Surprisingly, stronger natural selection -> more disordered proteins 1/

doi.org

The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

Proteins evolve more intrinsic structural disorder under more effective selection, with selection assessed via a novel metric of codon adaptation.

11511

Reposted by Seema

Mark Peifer (He, him) @peiferlabunc.bsky.social · 10/09/2024

The fruit fly Drosophila has been and continues to be a place where exciting new discoveries are made in all areas of biology. For example, we now have the entire "connectome" of its brain, with all neurons and neural connections identified. 1/n 🧪 www.science.org/doi/10.1126/...

Figure from link showing the 3016 neurons in the central brain and the synaptic connections revealed

23124