Phil East
@philipeast
Followers
147
Following
268
Media
12
Statuses
262
Bioinformatician @ The Francis Crick Institute, computational biologist, data consumer. Londoner, cyclist, Francophile, plant eater. Comments are my own.
Joined July 2009
Our work with @philipeast and @JulianDownward on #KRAS oncogenic signalling and resistance to therapy in lung adenocarcinoma (#LUAD) is out in @NatureComms! Tweetorial 🧵 Please share 🙂 https://t.co/oZAIAcOukO
5
54
186
We are hiring! We have a fantastic opportunity for a motivated bioinformatician to work at @TheCrick on a large multi-omic single-cell project in immuno-oncology. please RT 🙂 @BABSBioinformat #multiomics #singlecell #immunoOncology
0
8
7
Art exhibition on biomarker research in breast cancer at @ICO_cancer. Results are displayed in the form of digital art, and each artwork is accompanied by an scientific explanatory note. #BreastCancerResearch #Biomarkers #MSCAFellow #Horizon2020 #MSCA #DataVisualization
0
1
6
The UK government is dumping our plastic waste on other countries while claiming to be a world leader in tackling plastic pollution. The government is fuelling health and nature emergencies - it must take responsibility. #Wasteminster https://t.co/i19wH6lYRF
0
1
1
Interested in mechanisms of immune evasion in KRAS-mutant NSCLC? Check out my poster at #AACR2021 where we investigated this using an in vivo CRISPR screen in a novel model of immunogenic KRAS-mutant lung cancer. #Downwardlab
https://t.co/Cf16uIukNn
1
7
22
Oncogenic RAS transcriptional activity predicts outcome and response to chemotherapy in lung adenocarcinoma is the latest from a collaboration with the #downwardlab and our own @philipeast and @gavinpaulkelly with a nice thread from @sdecarne #KRAS #lungcancer #bioinformatics
Excited to share our preprint on #KRAS in #lungcancer. With @phileast, we show that oncogenic RAS transcriptional activity predicts outcome and response to chemotherapy in lung adenocarcinoma whereas KRAS mutational status does not! Please share 🙂 https://t.co/JpMMzZMf2p
0
3
5
Checkout our latest work showing oncogenic #RAS activity measured by transcriptional signature activity #RAS84 predicts response to chemotherapy in #lungcancer with a nice thread by @sdecarne Thanks to #downwardlab @BABSBioinformat @SwantonLab @TheCrick
https://t.co/Pm9IJ5osWS
biorxiv.org
Activating mutations in the driver oncogene KRAS occur in 32% of lung adenocarcinomas, leading to more aggressive disease and resistance to therapy in preclinical studies. However, the association...
Excited to share our preprint on #KRAS in #lungcancer. With @phileast, we show that oncogenic RAS transcriptional activity predicts outcome and response to chemotherapy in lung adenocarcinoma whereas KRAS mutational status does not! Please share 🙂 https://t.co/JpMMzZMf2p
0
1
8
Look #KRAS goes mainstream. There is even a quote from our very own Obi-Wan Kenobi @TheCrick The epic battle with cancer's 'Death Star'
theguardian.com
Forty years after the mutant genes that cause the deadliest cancers were discovered, drugs that target them could be approved
0
14
35
Scientists agree that eukaryotic cells, which humans are made from, evolved from bacteria over two billion years ago…doesn’t get much more prehistoric than that! In other words...BIMINI BON BACTERIA 🦠
0
0
3
And here's a nice commentary on the Apobec preprint from one of the first authors, @sdecarne
Very happy to have this preprint out 😊 With @jboumelha we expressed the cytidine deaminase APOBEC3B in several models of #NSCLC to generate mutations, and try to make these models immunogenic.
0
0
2
And I would also like to thank @anacondainc @condaforge #bioconda and everyone else who submits software packages, for making my and @BABSBioinformat lives much easier than they use to be.
0
1
6
Additional analysis was carried out using R/bioconductor/tidyverse @RobertGentleman @hadleywickham @Bioconductor with special thanks to the #VariantAnnotation, #deepSNV, #signeR, #GenomicRanges, #Rsamtools and #BSGenomes packages.
1
0
1
For the characterisation of clonal/subclonal variants and the CNV correction of the VAFs we used the 'Subclonal deconstruction of mutations' approach published by @SamraTurajlic et al. in
1
0
1
For the relative and absolute copy number analysis we used #cnvkit. Their docs were really useful, particularly for the absolute calls. https://t.co/uWen8dm9Jd
1
0
1
For the alignments, BWA/samtools/Picard @lh3lh3 @htslib #picardtools
https://t.co/3Trnpa8myC
https://t.co/djDQj3AKcl
https://t.co/kaQl0uCpng
github.com
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) - lh3/bwa
1
0
1
On the bioinformatics side there are a few additional shout outs to the community for software and methods that made the analysis possible. For the somatic SNV calls we used Mutect 1&2 from @gatk_dev @TheBroad
https://t.co/9151Ss0PDZ
gatk.broadinstitute.org
include '../../../../common/include/common.php'; include_once '../../../config.php'; $module = modules::GATK; $name = docSN::toolDocs; printHeader($module, $name, topSN::guide); ...
1
0
2
Really interesting work here on Apobec and the development of Kras-driven immunogenic lung cancer models by @sdecarne, @jboumelha & @JulianDownward. Very happy to have been able to help out by providing the #bioinformatics. Congratulations to all involved, great work.
Great work here describing an immunogenic Kras-driven lung cancer model by @sdecarne, @jboumelha & @JulianDownward #downwardlab @thecrick with #bioinformatics by our own @philipeast from BABS #cancerresearch #lungcancer #kras #immunoOncology #apobec
1
1
3
Another great collaboration with @BoultonLab and @APoetsch 🥳 2 papers in the space of a week! Something positive to end the year with...
Our latest📰: Loss of the helicase RTEL1, as well as stabilization of G4s, cause R-loop-dependent transcription-replication conflicts and overlapping transcriptional changes. Led by the postdoc Panagiotis Kotsantis, with great help from @APoetsch ➡️ https://t.co/u51dlKHODh 1/
0
2
11