@philcmsms

Bioinformatician, @ceclindgren group and formerly @kesslerlabox. Maybe a bit too fond of javascript.

 Bicester, UK
Joined September 2020
  • Tweets53
  • Following41
  • Followers38
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Age-Modulated Immuno-Metabolic Proteome Profiles of Deceased Donor Kidneys Predict 12-Month Posttransplant Outcome @philcmsms @bdi_oxford @InQuod @kesslerlabox @NDSurgicalSci @NHSBT_RD that medrxiv.org/content/10.1101/… @beck_vaughan @Sarahfawwaz

Age-Modulated Immuno-Metabolic Proteome Profiles of Deceased Donor Kidneys Predict 12-Month...

Organ availability limits kidney transplantation, the best treatment for end-stage kidney disease. Deceased donor acceptance criteria have been relaxed to include older donors with higher risk of...

medrxiv.org
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Goodbye to weeks-long quantification! directLFQ for label-free quantification (LFQ) allows arbitrarily large #proteomics sample cohorts (>100,000) at improved accuracy. It shifts ion traces on top of each other, scaling linearly in DDA or DIA. biorxiv.org/content/10.1101/…

Accurate label-free quantification by directLFQ to compare unlimited numbers of proteomes

Recent advances in mass spectrometry (MS)-based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks in the bioinformatics...

biorxiv.org
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(1/n) How accurate and precise are DIA (dia-PASEF here) peptide quantities? nature.com/articles/s41467-0…. This is affected not just by quantification algorithms but also the FDR of MBR.
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I’m excited to share our paper ‘A New Graph Node Classification Benchmark: Learning Structure from Histology Cell Graphs’ which was selected for oral presentation at the New Frontiers in Graph Learning workshop at NeurIPS 2022! @glfrontiers🧵 arxiv.org/abs/2211.06292
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when you're only allowed 4 figures in the main text
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I am so very proud to have been awarded the 2023 Mary Lyon Medal by the @GenSocUK ✨
The Genetics Society@GenSocUK18 Nov 2022
Congratulations to Prof Cecilia Lindgren @ceclindgren, director of @bdi_oxford, the winner of our Mary Lyon Medal for her research dissecting the genetic landscape of common complex diseases. #awards #genetics genetics.org.uk/medals-and-p…
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Clear and efficient summary of Oxford whole organ perfusion studies by @JPHunterTxSurg (with lots of high res pictures to follow lunch 🙂) plus of course shout out to Mito Queen @letizia_lofaro at @InQuod.
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.@InQuod symposium 2022 about to begin in Newcastle. Ready for a day of cool transplant science!
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Work with @adanpinto, @BenediktKessler & @TaoDong14 on enhancing cancer immunotherapy. #CancerResearch #Immunotherapy ndm.ox.ac.uk/study/dphil-the…
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First two lines are spot on, but I can under-predict a Gantt without any outside help
ErrantScience@ErrantScience6 Nov 2022
Gantt charts are one of the few charts that are entirely made from wishful thinking
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Phil Charles retweeted
Fengchao Yu@fcyucn6 Nov 2022
#proteomics #SoftwareDeveloper Please vote. Which one is better? Closed source project with good methods description and tutorials. Or open source project with bad/vague methods description and (almost) no tutorial.
59%Closed source, good doc
41%Open source, bad doc
129 votes • Final results
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Full marks for paper title
Molecular Neurodegeneration@MolNeuro4 Oct 2022
'Liver-ing in your head rent free: peripheral ApoE4 drives CNS pathology' Lesley Golden & Lance Johnson @LJohnsonLab @UKSBCoA @UKYMedicine #apoe #AlzheimersDisease molecularneurodegeneration.b…
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🚨Postdoc Position🚨 @ceclindgren lab at @bdi_oxford are looking for a #proteomics and #IntegrativeOmics bioinformatician to look at transplant outcomes w/ @kaisar_maria & ADMIRE. Come join a lovely lab working with a huge range of bioinf techniques! 👉tinyurl.com/3ywy39bw
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Closes in 2 weeks!
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Dr Maria Kaiser discussing the Admire Study, which assesses donor kidneys and monitors transplant recipients with the aim of ensuring that more non-suitable kidneys are excluded before they are transplanted. – at Camden Town, London
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HT-MS maps the sepsis plasma proteome and clinical subgroups in 2622 patients @proteomOX @KnightGenetics @RomanFi13911774 @philcmsms @CmdOxford @NDM medrxiv.org/content/10.1101/…

High-throughput mass spectrometry maps the sepsis plasma proteome and differences in response

Sepsis, the dysregulated host response to infection causing life-threatening organ dysfunction, is an unmet global health challenge. Here we apply high-throughput tandem mass spectrometry to deline...

medrxiv.org
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Closes on Tuesday!
Phil Charles@philcmsms29 Jun 2022
🚨Postdoc Position🚨 Come work at the awesome, lovely, welcoming @ceclindgren lab at @bdi_oxford, in collaboration with @kaisar_maria & the ADMIRE project. We're modelling kidney transplant outcomes, integrating omic, imaging & clinical data. Closes 26/7. tinyurl.com/3v5737b7
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Phil Charles retweeted
nature
@Nature13 Jul 2022
Ex-Google chief’s venture aims to save neglected science software go.nature.com/3o4r2HO
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Do you want to investigate whether a peptide not detected by the search engine is really present in the raw data using the deep learning prediction? Explore AlphaViz that allows you to do this and much more in our preprint out now on bioRxiv! biorxiv.org/content/10.1101/…
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