fungeLab @FungeLab
Functional genomics Lab, Dept. of Biochemical Engg. and Biotechnology, IIT Delhi, India. Joined June 2020-
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So, I am going to take this opportunity to shout out a big yay! to all my students and others in field ecology. You are generating data under conditions that many students from countries with impressive publications records will just never survive.
The road to death: Caspases, cleavage, and pores science.org/doi/10.1126/sc…
Our paper of the Drude2023 lipid force field is finally here! It would be a great tool to study membrane permeability and polarization effects involving biomembranes! With @alex_mackerell, Benoit Roux, Jeff Klauda and Rich Pastor. #charmm pubs.acs.org/doi/10.1021/ac…
Another snapshot of soft-money lab funding: the path to being able to fully cover my salary (green rows were funded).
Analysis of 272 oncogenic #GeneFusions in transcriptomics data from 5,190 #ChildhoodCancers reveals possible etiologies and therapeutic potential #CancerResearch @natrescancer nature.com/articles/s4146…
Incredibly proud to see our benchmark of single-cell preprocessing methods finally published 🥳🥳🎉 We show that despite its theoretical limitations, no other transformation consistently outperforms log(y/s+1). All details at nature.com/articles/s4159… and github.com/const-ae/trans…
An important new milestone in gene editing therapies
Today we report in @ScienceMagazine a one-time base editing treatment for Spinal Muscular Atrophy (SMA), the leading genetic cause of infant mortality worldwide, affecting ~1 in 10,000 births. science.org/doi/10.1126/sc… PDF: drive.google.com/file/d/1H1k8AA… 1/17
the latest release of the SG-NEx @nanopore long read RNA-Seq data resource! Includes 11 cell lines, direct RNA, PCR-cDNA, direct cDNA, short read RNA-Seq, m6ACE-Seq. Now with BLOW5 for all samples. Hosted on AWS for fast access and download speed
We are happy to announce the update release (v0.4.0) of the SG-NEx data on AWS (github.com/GoekeLab/sg-ne…). We now add raw signal data in blow5 format, with a usage tutorial, thanks to @hasindu2008 for helping with this release!
Review of 1,039 studies indicates that exercise can be more effective than counselling or medication for depression bjsm.bmj.com/content/early/… psypost.org/2023/03/review…
The world of Next-Generation Sequencing (NGS) post-#AGBT23: 1) Some will say that $ILMN Illumina is sleep-walking into a cliff: the company has been dominating the field with 80-90%+ of the market-share, but they are unable to retain their technological advantage to competitors:
1/10 Large eQTL resources enable identification of genes for which cis-eQTL effects colocalize with GWAS hits. We are happy to announce that our MetaBrain study and eQTL resource is now out at Nature Genetics (nature.com/articles/s4158…).
Interesting discussion below on the utility of small case GWAS. I used the FinnGen data to get a rough approximation of how many cases it takes to get a genome-wide significant association (as a crude proxy for "replication" I also required the trait to have a GWS locus in R8):
While I appreciate the sentiment, I am not a fan of such blind rules. Let me start with a 🧵 of some major human genetic discoveries (many translated to therapeutics) made with very few samples.
While I appreciate the sentiment, I am not a fan of such blind rules. Let me start with a 🧵 of some major human genetic discoveries (many translated to therapeutics) made with very few samples.
Grrr. It's 2023, and can we please stop funding/commissioning/publishing human genetic association studies with cases <1,000 (on case/control) or <1,000 overall (quantitative traits) in humans. It is just not going to work well. We know this.
50/50 I hope you've found this thread helpful and motivating. Follow me @theliverdoc for more educational real life stories on liver disease and health Please Like/Retweet the first tweet below to show you loved it <3
1/50 I met Pradeesh, in Oct 2022 He wanted to know if he could survive his liver failure on meds alone But I found something more sinister What followed was an intense battle, against not 1, but 2 terrifying foes Cancer & time & a unique love story that conquered both ❤️
New preprint from us! mRNAs act as chaperones for IDRs. mRNAs often bind to IDRs. This changes their conformational ensembles to drive protein complex assembly, and controls protein activity. Thank you @VickyLuo0223! biorxiv.org/content/10.110…
Fought cancer at 24. Fighting Crohns disease since 25. Moved to Bangladesh to better use my second chance at life at 29. But my hardest fight at 36 is "global health"- a field that systematically oppresses the oppressed. Not giving up. 2nd life anyways. But wish I were a cat.
GRAIL worked with 140 institutions on a benchmark atlas of cfDNA and isn't even bothering to deposit the raw data 😬
Online Now: Evaluation of cell-free DNA approaches for multi-cancer early detection dlvr.it/SdGLDC
Direct sequencing of proteins via nanopores? 🤯🤯🤯 nature.com/articles/s4158…
Has anyone used ChatGPT to review a paper or grant? 🤨
Dang… Dear ChatGPT: "Point out ambiguities in the following scientific protocol: [our smFISH protocol]" Have been asked many of these specific questions…
😷 #REPORT: What are the political conditions to avoid another #pandemic❓ Check out the policy recommendations on early warning and response from our fieldwork in #Botswana 🇧🇼 and #SouthAfrica 🇿🇦 ↓
Vineet @v1neetmittal
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Life Science Network @lifesciencenet
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Vishva Dixit @dixitvishva
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Constantin Ahlmann-El... @const_ae
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Timothy @TimReeves_
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IGNITE LIFE SCIENCE F... @ignitelsf
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antisense. @razoralign
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Mick W@tson ↙️ @BioMickWatson
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