Deepak Shilkar
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deepakshilkar.in
Deepak Shilkar
@deepakshilkar.in
58 followers 210 following 100 posts
Academic Editor and researcher in chemical biology and drug discovery. Simultaneously exploring existentialism, nihilism, zen, and advaita.

Profile links + Blog: https://deepakshilkar.in/
Posts Replies Media Videos
Reposted by Deepak Shilkar
richardsever.bsky.social
"We need more institutional experiments for science" makes sense to me @seemaychou.bsky.social. We might not like some of 'em and some'll fail, but given academic science often looks like a feudal system needing an industrial revolution trying things can't hurt.. seemay.substack.com/p/big-experi...
Big experiments are only big if they can fail
Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist
seemay.substack.com
November 6, 2025 at 7:08 PM
deepakshilkar.in
Tried @qedscience.bsky.social by running our published paper through it. It identified 2 issues unknown to us. Amazing work, Dr. @odedrechavi.bsky.social and team. 👌👌👌
November 9, 2025 at 7:32 AM
Reposted by Deepak Shilkar
richardsever.bsky.social
James Watson has died www.nytimes.com/2025/11/07/s...
James Watson, Co-Discoverer of the Structure of DNA, Is Dead at 97
www.nytimes.com
November 7, 2025 at 8:00 PM
Reposted by Deepak Shilkar
richardsever.bsky.social
And another thing: I am far more concerned with data provenance and information/identity verification than peer review right now… 1/2 journals.plos.org/plosbiology/...
November 7, 2025 at 2:30 PM
Reposted by Deepak Shilkar
ebi.embl.org
UniProt is changing its reference proteomes resource.

Reference proteomes will remain in UniProtKB, while others will move to UniParc.

Read more about these changes:
www.ebi.ac.uk/about/news/u...

🧬 🖥️

Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.
Changes to UniProt proteomes
UniProt, the data resource for protein sequence and function information, is making major changes to its proteomes resource and to the UniProt Knowledgebase. UniProt has developed a new workflow that ...
www.ebi.ac.uk
November 4, 2025 at 9:58 AM
Reposted by Deepak Shilkar
tomerullman.bsky.social
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting

I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 3, 2025 at 1:55 PM
Reposted by Deepak Shilkar
acollierastro.bsky.social
but...you shouldn't use a calculator when you are learning elementary math...the whole point is to develop the language of math...

letting elementary math students use a calculator to 'learn math' would be like letting elementary reading students use a voice reader to 'learn to read'
November 3, 2025 at 5:15 PM
Reposted by Deepak Shilkar
ericgreerlab.bsky.social
Excited to share our new work on transgenerational adaptation www.science.org/doi/epdf/10.... out today spearheaded by outstanding former undergraduate @kathleenkim.bsky.social. C. elegans adapt to repeated generational stresses and no longer display altered fertility, fat content, + longevity 1/9
Transgenerational adaptation to hypoxia
You have to enable JavaScript in your browser's settings in order to use the eReader.
www.science.org
October 24, 2025 at 7:32 PM
Reposted by Deepak Shilkar
ewanbirney.bsky.social
This is so good to see - a young baby has had a life changing treatable disease diagnosed early due to broad based (healthy baby) genome sequencing. He has a rare eye cancer gene, and has immediately been put into the effective treatment pathway.
genomicsengland.bsky.social Genomics England @genomicsengland.bsky.social · Oct 17
4 weeks after being born, Freddie was diagnosed with a rare form of eye cancer. He is one of numerous babies born with rare conditions who are receiving earlier diagnoses and treatment as a result of the Generation Study.

Read the full story: ow.ly/YJ7850XcTNk
Text saying 'The Generation Study is looking for more than 200 rare conditions which usually appear in the first few years of life, can be improved if caught early, and can be treated in the NHS.', with a green, a yellow and a pink circle below on a light green background. Text saying 'Four weeks after being born and having his genome sequenced, Freddie was diagnosed with hereditary retinoblastoma, a rare and aggressive form of eye cancer usually diagnosed in very young children.', and a photo of Freddie on a pink background. Text saying 'Very shortly after his diagnosis, Freddie was able to start treatment at Birmingham Children's Hospital. This gives doctors the best chance to minimise the impact on his vision.' and a photo of Freddie, his parents and sibling on a blue, yellow and pink background. Quote from Dr Rich Scott, Chief Executive Officer of Genomics England on a pink and white background saying “We believe genomics can transform healthcare in this country and be used to get ahead of serious illness. It’s been incredibly moving to see the lifechanging impact the Generation Study is having for families like Freddie’s, who have been able to access treatment that makes a world of difference soon after being born.”.
October 18, 2025 at 8:05 AM
Reposted by Deepak Shilkar
harmitmalik.bsky.social
A few alumni have collected in Rochester this weekend to say thank you and happy retirement to my PhD advisor Tom Eickbush, along with three other amazing evolutionary biologists: Allen Orr, John Jaenike, and Jack Werren.

My heart is filled with gratitude for having trained with them.
October 4, 2025 at 3:14 AM
Reposted by Deepak Shilkar
charlottewright.bsky.social
How many chromosomes can an animal have?

In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...
tinyurl.com
September 11, 2025 at 3:22 PM
Reposted by Deepak Shilkar
prosanta.bsky.social
Our department @lsu.bsky.social LSU Biological Sciences is hiring an Assistant Professor in Neurobiology.

Our department is amazing - come join us...

lsu.wd1.myworkdayjobs.com/LSU/job/0202...
Assistant Professor-Neurobiology
All Job Postings will close at 12:01a.m. CST (1:01a.m. EST) on the specified Closing Date (if designated). If you close the browser or exit your application prior to submitting, the application progre...
lsu.wd1.myworkdayjobs.com
September 12, 2025 at 10:44 PM
Reposted by Deepak Shilkar
chemjobber.bsky.social
cc: old time chemtwitter friends

@alexgoldberg.ca
August 4, 2025 at 1:54 AM
Reposted by Deepak Shilkar
soreklab.bsky.social
We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology

www.nature.com/articles/s41...

Was fun to write this piece with Dina Hochhauser!

Here is a thread to explain the premises

1/
Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology
Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...
www.nature.com
July 30, 2025 at 6:05 AM
Reposted by Deepak Shilkar
labfame.bsky.social
How does the brain 🧠 change around the clock 🕰️? Can this inform treatments?

Learn more in a new review from the lab 'Harnessing the #circadian nature of the choroid plexus and cerebrospinal fluid' ➡️ npj Biological Timing & Sleep | #Nature @natureportfolio.nature.com
www.nature.com/articles/s44...
A The major components of the CSF system include CSF, choroid plexus, and circumventricular organs. These systems change their properties across time of day, including those listed below each component. B Multiple inputs affect the CSF system across time of day.
May 26, 2025 at 9:25 PM
Reposted by Deepak Shilkar
biorxiv-genomic.bsky.social
Malaria parasite population genomics during an elimination program in Eastern Myanmar https://www.biorxiv.org/content/10.1101/2025.05.21.655408v1
May 26, 2025 at 9:33 PM
Reposted by Deepak Shilkar
dbikard.bsky.social
I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!
May 18, 2025 at 3:20 PM
Reposted by Deepak Shilkar
alana-m-vincent.net
FOR A STUDENT WHO USED AI TO WRITE A PAPER Now I let it fall back in the grasses. I hear you. I know this life is hard now. I know your days are precious on this earth. But what are you trying to be free of? The living? The miraculous task of it? Love is for the ones who love the work.
May 5, 2025 at 5:10 PM
Reposted by Deepak Shilkar
ashjogalekar.bsky.social
One of the most useful tables for a chemist to remember, and it illustrates why computational chemistry and drug design are hard: even a 1.3 kcal/mol error in calculating an equilibrium conformational or binding free energy difference will essential translate into a 90:10 estimation error
April 24, 2025 at 5:20 PM
deepakshilkar.in
Please repost and amplify the reach.
scott-delaney.bsky.social Scott Delaney @scott-delaney.bsky.social · Apr 22
If your NIH grant has been terminated, please let us know as soon as possible using this link ⤵️

forms.gle/cgEyj7gRjGWg...

Unless we know which grants have been cancelled, where, and when, we can't organize and advocate.
April 22, 2025 at 2:33 PM
Reposted by Deepak Shilkar
jay.bsky.team
The future is a web of branching paths, and each choice opens up new possibilities as it closes others. This is as true for a civilization as it is for an individual. The more our collective intelligence can inform each choice, the better our chances of finding paths through to a beautiful future.
graphic of branching lifelines, with the path taken traced through it. past paths no longer in play are greyed out, possible future paths spread out like a network of roots in front
March 31, 2025 at 6:22 AM
Reposted by Deepak Shilkar
manu-lera.bsky.social
🚀 #ShareYourCloning rebrands to #OpenCloning 🧫

An Open Source web application to plan and document molecular cloning 🧬 and genome engineering 🦠.

Latest version adds support for WekWikGene 🔍 as a plasmid source, and UI improvements.

👉 Check it out here: opencloning.org 🌍
February 6, 2025 at 1:29 PM
Reposted by Deepak Shilkar
londonsynbio.bsky.social
Join us Apr. 24th, 6pm @ Imperial Royal School of Mines

🦠 Microbial consortia for plastic upcycling
Javier Molpeceres (CIB-CSIC)

🧑‍🔬‍🔬 OpenCloning: a credible Open Source alternative to SnapGene and Benchling that supports automation
Dr. Manuel Lera Ramirez (UCL)

events.humanitix.com/copy-of-lond...
London SynBio Network 8
London SynBio afterwork talks and networking event on Thursday 24th of April
events.humanitix.com
April 16, 2025 at 11:32 AM
Reposted by Deepak Shilkar
ayakimovich.bsky.social
The lack of high-quality annotated #datasets is hampering applications of #AI in Optical #Microscopy. Let's change this together! I'm honored to be serving as the collection's Guest Editor. More in: go.nature.com/4hyDnNK 🧪 @natureportfolio.nature.com
@casusscience.bsky.social

@hzdr.bsky.social
Annotated Optical Microscopy Datasets
This Scientific Data Collection of articles focuses on datasets of annotated microscopy images from a variety of cell types and tissues.
go.nature.com
April 10, 2025 at 11:47 AM
Reposted by Deepak Shilkar
ritastrack.bsky.social
Yeah the word and Excel online feel very obviously retrofitted to purpose rather than designed for web browsers. Cluuuunky.
April 11, 2025 at 2:13 AM