@biochemistries

Bio,chem,code∈combiℕatorics. ML & systems biology. Sci paper feed @naivelocus, tech alt. @permutans, & maths papers @appendens.

 London, England
spin.systems
Joined December 2013
  • Tweets16.5K
  • Following4.2K
  • Followers1.5K
1.6KMedia
Replying to @naivelocus
#FirstPaper ! 🍾😀💫 Molec. principles of gene fusion-rewired PPI nets in cancer cell.com/molecular-cell/full… @MRC_LMB @MolecularCell HT @naivelocus
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nature
@Nature30 Apr 2023
Tasmanian devils’ contagious facial cancers sequenced for first time go.nature.com/3n9nU0J
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Potential differences in ion density can occur not just across PL membranes but on microdroplets of water and air, including it turns out biological condensates, driving redox doi.org/10.1016/j.chempr.202…
Phys.org
@physorg_com28 Apr 2023
Newly discovered electrical activity within cells could change the way researchers think about #biologicalchemistry doi.org/gr6sk6 phys.org/news/2023-04-newly-…
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Phys.org
@physorg_com28 Apr 2023
Researchers decipher the structure of protein methyltransferase from the mpox virus @IOCBPrague @NatureComms doi.org/gr54kv phys.org/news/2023-04-deciph…

Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors...

Nature Communications - Monkeypox virus is a pathogen with pandemic potential, encoding for its own RNA capping machinery. Here, the authors present crystal structures of its 2′-O-RNA...

nature.com
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NimwegenLab@NimwegenLab20 Apr 2023
Hey, weren't you a co-author on that? nature.com/articles/s41586-0… Yes, I was, but the Nature editors neutered the letter to the point that I felt I could no longer in good conscience put my name on it. The most egregious (and final straw for me) was the insistence to change 1/n

Insufficient evidence for non-neutrality of synonymous mutations

Nature - Insufficient evidence for non-neutrality of synonymous mutations

nature.com
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Aaron@aaron_mckenna15 Apr 2023
Pretty awesome survey of what ChatGPT can do: arxiv.org/abs/2303.13528. We've changed our graduate bioinformatics class to allow/encourage LLMs, it's nice to be able to focus on the bigger picture in homework questions (+ edge cases).

Many bioinformatics programming tasks can be automated with ChatGPT

Computer programming is a fundamental tool for life scientists, allowing them to carry out many essential research tasks. However, despite a variety of educational efforts, learning to write code...

arxiv.org
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Comparison of 1,800 de novo vs. 1,800 randomly computer generated proteins found they are moderately more soluble, despite similar structural potential/protease resistance after controlling for AA freq/length phys.org/news/2023-04-de-nov… 📄 Heames et al. (2023) dx.doi.org/10.1038/s41559-02…

Study compares de novo proteins with randomly produced proteins

Proteins are components of every cell. How they have changed in the course of evolution for the purpose of taking on new functions in the body, has long been a subject of research. The fact that...

phys.org
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✍️ The seahorse has two tendons that allows it to lift its head and suck in prey at high speed phys.org/news/2023-04-seahor… 📄 A power amplification dyad in seahorses (2023) dx.doi.org/10.1098/rspb.2023…
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Phys.org
@physorg_com13 Apr 2023
Naming system for #transferRNA fragments to increase research productivity, standardization @naturemethods doi.org/gr4xf4 phys.org/news/2023-04-rna-fr…
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“[Smart Immune]’s experimental cancer trial, hop[es] its novel technology will one day allow HIV patients to rebuild their immune system” — Gates Fdn. usually funds ID but is funding early stage trial in leukaemia patients after chemotherapy, could also improve CAR-T
FT for Schools@ft4s16 Apr 2023
Gates Foundation makes unusual investment in experimental cancer trial on.ft.com/3L560FF

Gates Foundation makes unusual investment in experimental cancer trial

Smart Immune is developing technology it hopes will help patients rebuild their immune systems

ft.com
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expert reaction to reports that £1.6 Billion of R&D funding has been returned to the Treasury sciencemediacentre.org/exper…
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NEW: CRISPR pioneer Feng Zhang is building a secretive new startup to solve gene-editing's biggest problem — getting into more parts of the body Meet Aera Therapeutics, which has raised $200 million to advance Zhang's work: businessinsider.com/exclusiv…

CRISPR pioneer Feng Zhang is building a secretive new startup trying to solve gene editing's...

Backed by GV and Arch Venture Partners, the stealth startup Aera Therapeutics is trying to solve gene editing's big delivery problem.

businessinsider.com
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Booking for boosters 50-64s officially opens tomorrow. If you’re in that age-range, it might just be worth ignoring the front page text and trying the link now. nhs.uk/conditions/coronaviru…
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David Dohan
@dmdohan13 Oct 2022
ProtNLM (Protein Natural Language Model) annotates previously "uncharacterised proteins" in @uniprot in English Instead of a restricted tag set, it predicts function as language: [amino acids] -> "CRISPR-associated endonuclease Cas9" Collaboration between @GoogleAI and @emblebi
EMBL-EBI@emblebi13 Oct 2022
Ever got a result back saying uncharacterised protein? 😩 @uniprot and @GoogleAI have teamed up to create a natural language processing model that has generated over 40 million protein annotations to address this challenge. ebi.ac.uk/about/news/technol…
Protein structure

ALT Protein structure

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.@CDCgov releases very preliminary analysis that suggests the #monkeypox vaccine is offering protection after a single dose. But outside experts urge the finding should be interpreted with a lot of caution. statnews.com/2022/09/28/earl…

Early analysis suggests monkeypox vaccine is reducing risk of infection in U.S.

A very preliminary analysis of data from 32 states appears to suggest that the monkeypox vaccine being used in the United States is reducing the risk of infection among vaccinated people.

statnews.com
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Eric Topol
@EricTopol19 Sep 2022
"We discovered a simple peptide that inhibits infection by all major variants of #SARSCoV2 with nanomolar efficacies." pnas.org/doi/10.1073/pnas.22… @PNASNews @emkailu @StanfordMed @HHMINEWS
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Why do birds have different eye colors? The short answer is we don't know. The long answer is in our new review article, up now as a preprint! We look at the pigments, genes, and evolutionary forces that give birds eyes their colors. ecoevorxiv.org/5h4pk/
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Mateo Prochazka@teozka15 Aug 2022
It's sobering that, globally, we are not able to produce enough supply of smallpox vaccine at pace to meet the demand for monkeypox control. Many countries with hundreds (or thousands!) of cases have not even started vaccinating yet, let alone launched a vaccination strategy.
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1. There's a new #monkeypox technical brief out from @UKHSA. Always an interesting read. A 🧵 HSA's modeling suggests the outbreak isn't expanding, though they acknowledge cases are certainly being missed and that makes it hard to accurately gauge things.
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Sebastian Raschka
@rasbt6 Aug 2022
Want to tinker with the 200M+ protein structures from AlphaFold in your favorite DataFrame format (pandas!)⁉️ Thanks to a kind contribution by @arian_jamasb, this is now possible in the latest BioPandas dev version as of this morning! github.com/rasbt/biopandas
Demis Hassabis
@demishassabis28 Jul 2022
A year ago we open-sourced #AlphaFold Today we're freely sharing the predicted structures of all 200M+ proteins known to science - almost the entire protein universe! It's our gift to humanity, and a demonstration of the benefits AI can bring to society dpmd.ai/AF-22-LI
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