Nathan Smits
@natenstuff1
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Joined March 2019
Excited to share CpGPT, a new foundation model for DNA methylation, crafted to understand the 'language' of epigenetics! 🧬🤖 What’s CpGPT? CpGPT is a transformer model pre-trained on CpGCorpus, a huge dataset of public DNA methylation info. By integrating sequence, positional,
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If you use a "Random number generator" aka Nanodrop to spec your DNA/RNA, some advice: 🧬Measuring DNA/RNA in H20 = highly inaccurate/variable values. 🧬Purity ratios of samples below 20ng/ul are not reliable. NEB dived deep into when it becomes limiting: https://t.co/s2OGGrMGov
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so glad that our endless discussions about the nitty gritty of CRISPR screens resulted in this awesome paper - congrats @gilan_omer and everyone in @TheDawsonLab
https://t.co/RyiqLUCTEh
nature.com
Nature Structural & Molecular Biology - Here the authors develop CRISPR–ChIP to enable the identification of factors required for chromatin regulation. Using this new method, they unveil...
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Ohio cryptic lineage update. We’ve made no progress identifying the individual, but we have learned a few things. 1/
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Very nice to show you around 😀 And unexpectedly (and sadly) tricky to talk science in my native tongue !
Thank you @natenstuff1 Nathan Smits and Andrew Ewing for chatting about #nanopore sequencing research @TRI_info in different species and health&disease models #transposable elements #Brisbane
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Imprinting in placenta via nanopore. Worth a read if you're into that sort of thing! Gratitude to all involved, foremost the co-lead authors Michalea Kindlova and Hannah Byrne (no twitter afaik). Many thanks to @QLDFamilyCohort for making this possible.
biorxiv.org
The placenta is a temporary organ present during pregnancy that is responsible for coordinating all aspects of pregnancy between the mother and fetus. It has a distinct epigenetic, transcriptomic,...
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🚨I am recruiting for a fully-funded PhD position to work at the interface of #mRNA and cell therapies. You will join a passionate team at the @AIBNatUQ and @BaseDna mRNA facility. If you are interested send me an email or DM. Please retweet! https://t.co/fcgdLd376N
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So proud that my first PhD student @robinleetroskie just passed her thesis defence with flying colours! Robin-Lee was an amazing student who made huge progress in understanding human pseudogene functions. You can read part of her work here: https://t.co/F9d7BQlnlz Congrats Dr!
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Congratulations to Alex Carleton @Carleton_Alex on a stellar Honours thesis defence! Alex did an incredible amount of work in 10 months in my lab, establishing the basis for an exciting PhD project. #ProudPI #imnotcryingyourecrying @MaterResearch @UQ_SCMB @Faulkner_Lab
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Great to contribute to this paper describing @_adamewing's tool Methylartist. Methylartist enables easy visualisation of modified bases from @nanopore reads. It can generate a variety of visualisations including ridge, violin, locus and chromosome plots.
Working with @nanopore modified base call data? Consider methylartist: https://t.co/cESNEO6yGQ. Appilcations Note online now at https://t.co/F55C7yxIPC. Many thanks to @SethCheetham and Michaela Kindlova.
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Working with @nanopore modified base call data? Consider methylartist: https://t.co/cESNEO6yGQ. Appilcations Note online now at https://t.co/F55C7yxIPC. Many thanks to @SethCheetham and Michaela Kindlova.
academic.oup.com
AbstractSummary. Methylartist is a consolidated suite of tools for processing, visualizing and analysing nanopore-derived modified base calls. All detectab
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Is L1 retrotransposon activity in the brain specific to only some neuronal lineages? Check out our new preprint👇where we find L1 is activated by the SOX6 transcriptional program of parvalbumin (PV) GABAergic interneuron development. 1/n https://t.co/7wsPKVaUK6
biorxiv.org
Transposable elements (TEs) are a reservoir of new transcription factor binding sites for protein-coding genes[1][1]–[3][2]. Developmental programs that activate TE-derived regulatory elements could,...
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Had a wonderful conversation with @MadeleineMHKing about various things, including: the importance of relations between Researchers and Policy makers, how to tackle imposter syndrome, and the importance of diversity. Thank you @ScienceAU for such a wonderful opportunity #SmP2022
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Thank you so much for this wonderful opportunity!
So excited for @YohaannJafrani of @GeneticsAus on winning an LGBTQI+ Scholarship sponsored by @ARC_EQUS! Yohaann is a PhD Candidate @MaterResearch working on complex next-generation gene research. Have a great time at #SmP2022 Yohaann!
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Had a blast at the Lorne @GenomeConf Saw heaps of amazing presentations and had some great chats! Also very excited about this😀
Congratulations to all our presenters for making #lorneGenome such a wonderful meeting. Special congratulations to our talk and poster prize winners 👏👏👏
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I'm looking to hire a full-time Research Assistant for my team at Mater. A broad molecular biology skill set is a must. Happy to answer questions about the role on DM or email. Please RT. https://t.co/1S6FpHBRAo
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SquiggleNet, from @baobaoyaobaobao, @LabWelch & co, a method for classifying Nanopore reads direct from their electrical signal. This is faster than basecalling + alignment, so allows realtime analysis on a laptop. It needs no reference database. https://t.co/XZVCBqL9Zu
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