Jacob H

Officially a 'Data Scientist' but really a cancer bioinformatician

[Eszter Lakatos @EszterLakatos42]

New paper: delighted to share our work presenting the in-depth landscape colorectal cancers from the 100,000 Genomes Project!
Thanks to this unprecedented dataset, we could identify new drivers, subgroups and anatomical/molecular correlates in CRC. https://t.co/55Qze9l7PY

[The ICR @ICR_London]

📰BREAKING: Genetic causes of #ColorectalCancer revealed 🧬

Led by researchers at the ICR, @UniofOxford, and @OfficialUoM, a new study published in @Nature offers insight into colorectal cancer's development and response to treatment.

Read more ⤵️
https://t.co/d42BqCZ6pl

[Giulio Caravagna @gcaravagna]

Super excited to see CNAqc out in @GenomeBiology, our tool to validate clonal and subclonal copy numbers from bulk sequencing. 2nd paper from the lab in 2024 after TINC in @NatureComms [https://t.co/CXP23vNO8x]

Paper: https://t.co/t2cWrbvbdC
Tool: https://t.co/sbBY4fNnH3

1/n

[Freddie Whiting @WhitingFreddie]

When should we call non-genetic changes in a phenotype 'plasticity' in cancer? In our opinion article we translate definitions from evolutionary biology to describe non-genetic phenomena in cancer and discuss ways to identify them.

https://t.co/Dn7sO2SSdy

[JRNLclub @JRNLclub]

.@jhouseham discusses how genetic variation and transcriptional plasticity contribute to intra-tumoral heterogeneity in colorectal cancer. @Nature @trevoragraham @AndreaSottoriva @CEC_ICR @ICR_London @humantechnopole #colorectalcancer #JRNLclub https://t.co/EUp93O9nsJ

[The ICR @ICR_London]

🧬Dr Jacob Househam, a #postdoc in @trevoragraham's team in the ICR's @CEC_ICR, talks through their recent @nature paper on #CancerEvolution in #BowelCancer for @JRNLclub.

Watch the talk: https://t.co/6GBeUO3az0

Read the paper: https://t.co/DKOh8M4jjc

[Trevor Graham @trevoragraham]

Delighted this is now up on @biorxivpreprint, it's been a long haul & huge team effort. Especially thanks to @HoulstonLab_ICR & @group_tomlinson for the final push to tie it all together. @GenomicsEngland is a tremendous research resource, hope others can build on our start here.

[Trevor Graham @trevoragraham]

How do the #genome, #epigenome and #transcriptome co-evolve in colorectal #cancer? In the second of two papers in @nature, we find gene expr is not strongly heritable & evaluate "driverness" of muts directly in patient tumours https://t.co/11goJRjWgT @AndreaSottoriva #EPICC2 1/7

[Jacob H @jhouseham]

Very excited to share our research just published in @nature. In two joint papers we use multi-region multi-omic data to study how colorectal cancers evolve. This was a huge group effort including @trevoragraham, @AndreaSottoriva, Timon Heide and many others! #EPICC1 #EPICC2

[Trevor Graham @trevoragraham]

How do the #genome, #epigenome and #transcriptome co-evolve in colorectal #cancer? In the second of two papers in @nature, we find gene expr is not strongly heritable & evaluate "driverness" of muts directly in patient tumours https://t.co/11goJRjWgT @AndreaSottoriva #EPICC2 1/7

[Andrea Sottoriva @AndreaSottoriva]

How do the #genome, #epigenome & #transcriptome co-evolve in colorectal #cancer? In the 1st of 2 studies in @Nature we measure the contribution of #chromatin accessibility in #cancer #evolution. #genetics and #epigenetics interplay! #EPICC1 @trevoragraham
https://t.co/SqjatBp4Yn

[Vinaya Gunasri @vinaya_sn]

Screening can prevent or spot cancer early, but language barriers prevent ethnic minority groups from benefiting fully from screening.

We've translated @CR_UK screening videos into Sylheti (Bengali) & Urdu ⤵️

#CloseTheCareGap | #WorldCancerDay
https://t.co/2yrJxEu5Qp [1/6]

[Andrea Sottoriva @AndreaSottoriva]

#EPICC (Evolutionary Predictions in Colorectal Cancer) project pre-print 3/3: (epi)genetic control vs plasticity in intra-tumour transcriptional heterogeneity, chasing the phylogenetic signal of cancer cell’s RNA. Thanks @wellcometrust @The_MRC @CR_UK: https://t.co/lVBS5IndQX

[Trevor Graham @trevoragraham]

Towards the genotype-phenotype map in CRC. Using matched DNA&RNAseq data we ask if gene expr patterns are heritable (answer: not often), & if somatic mutations have gene expr consequence (answer: not often). Suggests cellular #plasticity is common in CRC. @AndreaSottoriva #EPICC

[Trevor Graham @trevoragraham]

Here we measure "driverness" of putative #driver mutations in #colorectal #cancer. Clonal selection detected with evolutionary #genomics & #mathonco. Fit phenotypes defined with matched #RNAseq & #ATACseq. Most putative CRC drivers are effectively-neutral! @AndreaSottoriva #EPICC

[Andrea Sottoriva @AndreaSottoriva]

#EPICC (Evolutionary Predictions in Colorectal Cancer) project pre-print 2/3: neutrality vs selection with spatial single-gland WGS & inference. What drives real subclonal expansions and effects on chromatin and RNA. Thanks @wellcometrust @The_MRC @CR_UK. https://t.co/K6tP5gra4u

[Trevor Graham @trevoragraham]

First of our #EPICC papers looks at chromatin structure evolution in colon #cancer. We show heritable somatic changes in #chromatin, including at known driver genes, & transcription factor binding site accessibility changes that induce stemness & #immune evasion. @AndreaSottoriva

[Andrea Sottoriva @AndreaSottoriva]

#EPICC (Evolutionary Predictions in Colorectal Cancer) project pre-print 1/3: concomitant multiomic spatial profiling of genome, chromatin and RNA on single glands. Non-genetic drivers and global #epigenetic rewiring. Tnx @wellcometrust @The_MRC @CR_UK https://t.co/KVNyZFW8Sl

[Giulio Caravagna @gcaravagna]

We have posted another manuscript in #bioRxiv (🤯 @jhouseham @wchcross ), which is about performing "quality control" from bulk WGS assays of tumour. We integrate somatic mutation and CNA segments to determine a score for consistency of the somatic calls.

https://t.co/WNCntq9xCM

[Jacob H @jhouseham]

A big thanks to @trevoragraham and all of his lab for their support over the last few years! And thanks to my examiners! #PhD

[Trevor Graham @trevoragraham]

Delighted for Dr @jhouseham who passed his #PhD viva this afternoon with minor corrections. A hard earned doctorate, really well done Jacob. I look forward to the time we can celebrate together in person!

[Eszter Lakatos @EszterLakatos42]

Our paper on neoantigen evolution is out! https://t.co/mD4JESJYtB
A great collaboration with @trevoragraham @marcjwills_ @jhouseham @wchcross @LuisglsZ @ara_anderson @research_junkie @cgatenbee @AndreaSottoriva @cssb_lab @BenjaminWerner_
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