So excited to be back in the office this week with renewed energy & lots to celebrate. Since last fall I've: 🤱 grown & nurtured a brand new human 🇨🇦 become a Canadian citizen 👩‍🏫 been granted a promotion with tenure ❤️ Collectively enabled by support from my family, community, colleagues & students

🔔 New paper alert! 🔔 I’m excited to share our new paper published in Genome Biology! 💡 We wanted to shed some light on a big question in human biology: what shapes a baby's biology? Inherited genetics, prenatal environmental exposures, or both? We took this question to the epigenetics field!

From @cp-patterns.bsky.social | #Bioconductor: Planning a third decade of comprehensive support for genomic data science | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓 ⬇️ www.cell.com/patterns/ful...

Congratulations to Ning Shen on her brilliant PhD defence earlier this week!! 💐👩🏻‍🎓 I'm extremely lucky to have worked with Ning over the past several years.

Microbiology and Immunology and the Michael Smith Labs are seeking candidates for an Assistant Professor of Teaching in STEM Public Engagement position. Learn more and apply at: www.msl.ubc.ca/careers/ #IndigenousinSTEM #BlackInNature #WomenInSTEM #MinoritiesInSTEM #DiversityInSTEM #STEMEducation

Happy 18th birthday ggplot2! #rstats

My Canadian university, Queen's, is offering TWENTY 4-year funded PhDs (40k CAD/yr) for a student of ANY citizenship who has been accepted at a top 100 US university but have had offer rescinded OR are reconsidering offer due to US policy. Details found here👇 www.queensu.ca/grad-postdoc...

Now out in Cell Reports - work led by Zheng Dong in collaboration with Kobor group - we characterize the advantages of using updated complete and pangenome references in short-read and array DNA methylation analyses. www.cell.com/cell-reports...

🧬 Another new preprint out of the lab: a statistical method and software for cell-type deconvolution of methylated sequencing reads, led by Ning Shen! 🧵👇 doi.org/10.1101/2025...

Exciting new work on GxE associations with the methylome in early life, led by @ericknavarro.bsky.social and collaboration with Kobor lab and others! 🧵 with highlights 👇👇

Not long after I started my lab, a prominent scientist told me it was “impossible” to be a successful PI and a mother Don’t ever let the naysayers tell you it can’t be done - of course it can! #HappyMothersDay this weekend to all the amazing scientist mamas raising their wonderful kids 🥰

Applications are open for select graduate studies programs at #SFU, including biomedical physiology, chemistry, molecular biology and @sfuphysics.bsky.social. Canadian and US students encouraged to apply by April 25. www.sfu.ca/gradstudies/...

UBC is hosting US Applicant Week from April 14-18, which allows US students to apply during an extended application period for graduate studies. Sixty graduate programs will be reopening applications for US applicants for September 2025 and January 2026 start dates - www.grad.ubc.ca/us-applicant...

Today UHN launches the Canada Leads 100 Challenge! 🇨🇦💯 We’re making an ambitious investment to recruit 100 world-leading scientists. Together, we'll drive the future of health research and position Canada as a leader in global innovation! Learn more: www.uhn.ca/corporate/Ab...

For anyone still using RSS feeds and noticed bioRxiv Collection feeds (www.biorxiv.org/rss) recently broke, here's a quick fix: in the URL for the "All Articles" feed, and replace `all` with the appropriate `coll_alias` from the broken link. e.g. Genomics feed: connect.biorxiv.org/biorxiv_xml....

Canada recently made non-Canadians eligible for federal graduate and postdoctoral fellowships. For high school students, it takes like 15 minutes to apply to a Canadian university because we don't demand that you produce a cringe-filled PR portfolio to "sell yourself."

Changes to MSc, PhD and postdoc funding programs from 🇨🇦 tri councils. Harmonization across councils, more awards, and new eligibility for international PhD and postdoc applicants!

Ahead of International Women's Day, and with attacks on critical #DEI programs in the US, I'm resharing this article ⏬ If this regressive shift spreads, we risk undoing many hard-won advances towards gender equality around the world We cannot let this happen 💪 #Diversity #Equity #Inclusion

Made some slides for scientists to talk about what's been happening & what we should do next. There are probably many people better qualified than me to talk about these issues. If that's you, please, please, please consider holding some virtual advocacy training sessions for researchers this week.

NIH plans to slash support for indirect research costs, sending shockwaves through science Capping these payments would ‘just grind our scientific complex to a halt,’ one researcher said @statnews.com www.statnews.com/2025/02/07/n...

Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com

Biologist, stop putting UMAP plots in papers! Blogpost here: simplystatistics.org/posts/2024-1...

All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.

Today the Trump admin abruptly and indefinitely terminated many of the activities of the National Institutes of Health, the $50B/year collection of agencies that power the US biotech and health ecosystems. Even if these orders were lifted tomorrow, the disruption would be enormous. Why care? 🧵

Hi, Vox reporter here: If you've had a study section, NIH travel, or other NIH-related meeting cancelled (or not), raise your hand! Reply or DM me, and repost for visibility if you're able. #academicsky @drugmonkey.bsky.social

I wrote about the ongoing debates over genomic data sharing and the use of such data for "abhorrent science", including some perspective papers that came out last month. A few key points: 🧵

We live in the ✨ world of tomorrow ✨

It's that time of year! (thought a little delayed for us in Canada due to the postal strike...)

Made a #short about my internal conflicts on academic publishing #AcademicSky #PhDlife "Stop asking me where I want to publish our paper. I don't care...I just want people to read it. And maybe learn from it. Even build on it. Ok?" Is this #hopecore or #hopelesscore youtube.com/shorts/GV7NJ...

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3) doi.org/10.1038/s415...

A new year, a new article in print! doi.org/10.1186/s130... Now out in Genome Biology, work led by Ning Shen: vmrseq is a statistical approach & R package for probabilistic modeling of single-cell methylation heterogeneity. It identifies and ranks regions of variable DNA methylation across cells.

Friends, We are hiring! My department (Computational Medicine) has an open rank faculty position search this year! I know we are late to the party, but please consider applying! Feel free to ask question here. recruit.apo.ucla.edu/JPF09935

Happy to share the publication for BayesDCA! We developed Bayesian approaches for Decision Curve Analysis (DCA) to assess clinical prediction models and tests. Grateful for all the mentorship and support from @keegankorthauer.bsky.social! Quick summary below ⬇️

Excited to see our work on Bayesian Decision Curve Analysis appear in Statistics in Medicine! doi.org/10.1002/sim.... Work led by @giulianonetto.bsky.social - check out the stellar thread (from the old platform) on our preprint here: x.com/giulianonett...

Korthauer lab members (and friends) recently tried our hands at the sport of curling! It was fun to all be beginners together.

(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n

Bioconductor 3.20 is released! 🎉🌟 Thanks to all developers and community members for contributing to the project! 🙌 👉 See the full release announcement: bioconductor.org/news/bioc_3_... #Bioconductor #DataScience #Bioinformatics #OpenSource

Happy to share two post-doc papers. We had amazing collaborators for both projects, even our supervisor @maxvcg.bsky.social joined in on the experimenting! pubmed.ncbi.nlm.nih.gov/39180406/ pubmed.ncbi.nlm.nih.gov/39448850/ where we explore unconventional roles of 5mC in mouse genome regulation

Scientific image libraries like the public domain Bioart (bioart.niaid.nih.gov) and open source Bioicons (bioicons.com) are looking very promising! Great to see useful alternatives to pricey subscription-based tools.

📣 Attention Stat/Biostat folks on the job market - UBC Statistics is hiring! 📣 www.stat.ubc.ca/assistant-pr...

Encouraged to see this response from Nature that a revision to the UMAP figure in the All of Us Paper is in progress: www.nature.com/articles/s41...

Why did Nature publish AlphaFold3 without its code? #AcademicSky 🧪💻🧬 www.nature.com/articles/d41...

A running start for day 2 of #STATGEN2024 with a lovely group jog through Schenley Park! Excited to lead a session on "Deciphering the genomic and epigenomic landscape of cell-free DNA" this afternoon!

NEW PAPER out today in the BMJ TRIPOD+AI: reporting recommendations for studies developing or validating prediction models for use in healthcare that use #machinelearning methods bmj.com/content/385/... #ArtificialIntelligence #AIstandards #OpenAccess

Great job in Canada for a bioinformatics education position with a great team. oicr.bamboohr.com/careers/331

Has the scientific literature been flooded with papers containing AI-generated text? I use rvest to scrape Google Scholar to quantify the number of publications containing obviously LLM-generated phrases over time (and compare to other phrases). Try it out for yourself! jef.works/blog/2024/03...

Excellent commentary - "All models are wrong and yours are useless: making clinical prediction models impactful for patients"

To group is natural, but there are no natural groupings. Just modeling decisions that society draws up and we feed to the algorithms to return results that we use as evidence to start the cycle all over again. Be aware of the system, question everything, and do better. /fin

Aside from obvious 'tortured phrases', are there any specific words that you've noticed seem to be used much more frequently in scientific writing over the past year or so? [I have an example in mind that I feel like I now see everywhere, but I might just have frequency illusion bias]