Chris Cole @_chriscole_
Statistical Genetics @DeepGenomics. DPhil from @UniofOxford. 🧘☕️🏕 chrisbcole.me Toronto Joined March 2013-
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We (@deepgenomics) are hiring a statistical geneticist to develop and apply methods at the intersection of systems biology, genomic AI, and traditional genetic target discovery. CAN/US remote or hybrid, DM me with any questions! jobs.lever.co/deepgenomics/2…
I usually find myself writing about genetics for work but decided to try something different; here's a small #BookReview / reflection after reading @EdCaesar's captivating "The Moth and the Mountain". I had a lot of fun writing this! chriscole.substack.com/p/trauma-at-th…
It's out! Really excited to share our recent work creating a foundation model for RNA biology and applying it to VEP and oligonucleotide therapeutic design. Huge team effort across both computational and experimental groups; it's an exciting time for AI in genomics 😀
It's out! Really excited to share our recent work creating a foundation model for RNA biology and applying it to VEP and oligonucleotide therapeutic design. Huge team effort across both computational and experimental groups; it's an exciting time for AI in genomics 😀
Our work ‘A curated census of pathogenic and likely pathogenic UTR variants and evaluation of deep learning models for variant effect prediction’ is now published in Frontiers in Molecular Biosciences: 🧵 frontiersin.org/articles/10.33…
Hot off the press, LanceOTron is a really elegant solution to peak calling using deep learning -- I had the opportunity to help out on this project and was really impressed with how clean the peaks were compared to conventional approaches like MACS2. academic.oup.com/bioinformatics…
Welcome to Deep Dive, our new interview series on the potential of applying AI to RNA therapeutics. Our first interview is with our CEO and founder, Brendan Frey, PhD, FRSC, and Tal Zaks, MD, PhD, and member of our Strategic Advisory Board. #AI #deeplearning #futureofmedicine
After an incredibly fun and interesting discussion of my thesis with amazing examiners @stschiff and @bioinfbloke, very happy to say that I am #PhDone. I had an amazing time working in Oxford with @gertonlunter, @milnetom68, @FoldingGenome and others, thank you to everyone.
Our 2022-23 CCSF scholarship competition is now open for applications!! 😃 We have 14 scholarships, worth £5000 each, for exceptional Canadian postgrads studying in the UK. The deadline is midnight Friday 11 March. More info and eligibility criteria here: canadianscholarshipfund.co.uk/information-fo…
On first glance, Github CoPilot seems to handle simple bioinformatics tasks quite well. Looks like a great way to reduce boilerplate in any case.... Some care is needed on the part of the user as in the last case (hg19 to grch38), not sure what it's got going on there.
In case it's useful, I wrote a small #python tool to figure out the build of bed/bigwig files by comparing the max length of chromosomes to known assemblies. You can add whatever builds you want, try it out from pypi! github.com/Chris1221/wgba
I wrote a tiny #RStats package that remembers the script you used to create a PDF plot with ggplot2, check it out if your memory is as bad as mine! github.com/Chris1221/ggso…
📣Job Alert📣Senior Postdoctoral Research Fellow position open in my group @bdi_oxford, working on tree-based imputation methods for Biobank scale data in collaboration with Janssen. Less experienced (i.e., just finishing PhD) can also apply. my.corehr.com/pls/uoxrecruit…
For some reason, unzipping a compressed file and streaming it to data.table::fread is ~2.5 times faster than allowing the package to handle the decompression. Is there a satisfying reason why this should be the case? #RStats
💀🎲 Getting ready for #ISBA9? Looking to have some tounge-in-cheek fun during the (notoriously)...numerous human population genetics sessions? Lets play some bingo! ancientpopgen-bingo.firebaseapp.com/?game=ancientp… (If I'm missing anything feel free to send more card suggestions!😜)
For my much more knowledgable #popgen friends, is anyone aware of methods for Ne or migration inference that are reasonable sensitive in the < 5kya time period?
Getting ready for the first #stdpopsim hackathon today - let's see how many new species we can get into the catalog!
Published today in @NatureBiotech, check out the new bayesian, haplotype-based, variant caller Octopus developed by my lab-mate Dan Cooke. Watching this go from presentations in lab meetings to a mature piece of software has been really exciting. nature.com/articles/s4158…
Incredibly happy to say that after an immense amount of work from lots of people including @gertonlunter, @shajoezhu, and Donna, our method (SMC2) for demographic inference from whole genomes using a particle filter is published! 🥳journals.plos.org/plosone/articl…
Its not too late, but almost, to apply for a DPhil in an amazing✨⭐️🌿 program in Genomic Medicine and Statistics @NDMOxford @OxfordMedSci ox.ac.uk/admissions/gra…
Take a look at the life and people of @UofTanesthesia through @instagram instagram.com/torontoanesthe… #CaRMSMatch #CaRMS2021 #UofTAnesthesia
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