Jeremy Baskin

@[email protected]
293 Followers
250 Following
48 Posts
Click chemist, cell biologist, #chembio & #lipidtime enthusiast, & occasional classical pianist (he/him). Also @basktastic on Twitter.
Show threadJeremy BaskinApr 15, 2023

further democratize long-read sequencing for routine plasmid analysis & guide future efficiencies as tech improves.

Give it a spin at Google Colab (https://colab.research.google.com/github/MasaakiU/MultiplexNanopore/blob/master/colab/MultiplexNanopore.ipynb) or @GitHub (https://github.com/MasaakiU/MultiplexNanopore).

Congrats to HFSP postdoctoral fellow Masaaki Uematsu, who did it all (except write these toots)! /end

Google Colaboratory

Jeremy BaskinApr 15, 2023

Do you (want to) use whole-plasmid sequencing (e.g. @plasmidsaurus) but are put off by $15/sample? Use SAVEMONEY—our (postdoc Masaaki Uematsu’s) algorithm that lets you mix 6 or more plasmids/sample & computationally de-mixes reads!

https://colab.research.google.com/github/MasaakiU/MultiplexNanopore/blob/master/colab/MultiplexNanopore.ipynb

https://www.biorxiv.org/content/10.1101/2023.04.12.536413v1

How it works: 1/n

Google Colaboratory

Show threadJeremy BaskinApr 15, 2023
Incredibly, you can reliably mix together plasmids differing by as few as 2 bases & up to 6 (or even more) plasmids in a single sample, which lowers the effective cost of whole-plasmid sequencing to less than that of a single Sanger run! We hope that SAVEMONEY will... 5/n
Show threadJeremy BaskinApr 15, 2023
SAVEMONEY has two basic parts: (1) pre-survey & (2) post-analysis. Pre-survey examines your plasmid maps and tells you which groups of plasmids to mix together. Post-analysis classifies, aligns, and generates consensus sequences for each plasmid in the mixture. 4/n
Show threadJeremy BaskinApr 15, 2023
Multiplexing exists for long-read sequencing but typically involves extra barcoding or is geared toward those with their own sequencers. SAVEMONEY (Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You) is for users of 3rd party services. 2/n
Show threadJeremy BaskinApr 15, 2023
Nanopore sequencing typically provides 100s of reads/sample to generate a consensus sequence. But Masaaki realized that w/prior information of expected sequence & Bayesian analysis, you can get sequences w/~30 reads/plasmid—in other words, money is being left on the table. 3/n
Jeremy BaskinFeb 14, 2023

Glycans are sweet,
Nucleic acids—they’re fine.
Proteins are interesting,
But nothing beats #lipidtime!

#ValentinesDay #badpoetry

Jeremy BaskinFeb 3, 2023
🚨New manuscript: interorganelle lipid transport is rapid, & it is hard to quantify discrete steps in this network, mediated by lipid transfer proteins working at membrane contact sites between different organelles. We (Dongjun Liang & Lin Luan) harness chemoenzymatic tagging & super-fast #bioorthogonal chemistry to make fluorescent lipids that report on PM-to-ER phospholipid flux mediated by a family of lipid transfer proteins at these contact sites! https://doi.org/10.1101/2023.02.01.526230 #lipidtime #chembio
Jeremy BaskinJan 21, 2023
WeedenKimJan 20, 2023

A phishing message from an account pretending to be me is going around my department.

I'm deeply offended by the typos and grammatical errors.

If the phisher uses "utilize," I swear I'll hunt them down and force them to copy lines from Strunk and White.

Jeremy BaskinJan 21, 2023
Stuart CantrillNov 19, 2022

If you want to reconnect with those from #ChemTwitter who have created accounts here in the #Fediverse, here is a Google Sheet that >400 people have added themselves to.

https://docs.google.com/spreadsheets/d/1qdJvHHvu-BC4N6nk1jNMhTwoBrIaqHLUCZRf9pCQwDs/edit?usp=sharing

If you want to add your details, you need to either fill in this Google Form: https://forms.gle/gF9MLUGMWs23EFix6 or just ask me to add your details if you'd rather not use a Google product (note: the form does not capture e-mail addresses).

#ChemiVerse #Chemistry #ChemToots

ChemCommunity on Mastodon (Responses)

ChemCommunity on Mastodon Sheet maintained by @[email protected] (DIRECT FEDIVERSE LINKS IN COLUMN G) TO ADD YOURSELF TO THIS SHEET, PLEASE COMPLETE THIS FORM: <a href="https://forms.gle/gF9MLUGMWs23EFix6">https://forms.gle/gF9MLUGMWs23EFix6</a> IF YOU WANT TO BE ADDED BUT DON'T WIS...

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