@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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Work with @adanpinto, @BenediktKessler & @TaoDong14 on enhancing cancer immunotherapy. #CancerResearch #Immunotherapy ndm.ox.ac.uk/study/dphil-the…
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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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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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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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I made a tool to compare Webb's new images to Hubble! johnedchristensen.github.io/… #JamesWebbSpaceTelescope
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"Aims 1 and 3 are well justified. However, experiments in Aim 2 lack sufficient justification, which reduces enthusiasm for this otherwise promising application".
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Really happy to have been able to present some of our work on molecular mechanisms of liver NMP at the #ITSmeeting in Berlin @NDSurgicalSci @OxTxResearch @kesslerlabox
Maria Kaisar@kaisar_maria17 May 2022
Congratulations to @letizia_lofaro for her presentation on molecular changes associated to NMP of the liver #ITSmeeting @NDSurgicalSci
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Phil Charles retweeted
QUOD Biobank@InQuod1 Apr 2022
Thank you to the British Heart Foundation for sharing the news of QUOD being named 'UK Biobank of the Year 2022' – check it out on their researcher noticeboard here: bhf.org.uk/for-professionals… @TheBHF @NDSurgicalSci @UniofOxford @NHSBT
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Come and work with us! The Lindgren @ceclindgren Lab at the Big Data Institute @bdi_oxford in Oxford is looking to hire a junior statistical geneticist/bioinformatician (finished or about to finish undergrad/masters): bit.ly/lindgren_bdi. Please share!
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Next-generation spatial MS: Deep topographic #proteomics of a human brain tumour @RomanFi13911774 @philcmsms DPF team @kesslerlabox @NDCNOxford @NDMOxford
Roman Fischer@RomanFi1391177422 Mar 2022
Have a look at our new preprint about spatial proteomics biorxiv.org/content/10.1101/…
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Have a look at our new preprint about spatial proteomics biorxiv.org/content/10.1101/…
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Please check out our ABPP-HT*—Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced DIA Mass Spectrometry Methods mdpi.com/1547676 #mdpiijms via @IJMS_MDPI. Congrats Hannah, Raphael and everyone involved! #ABPP #ubiquitin #deubiquitylases

ABPP-HT*—Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced...

Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has...

mdpi.com
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