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Reposted by Keegan Korthauer 🇨🇦

BF Francis Ouellette @bffo.bsky.social · Sep 11

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...

Bioconductor: Planning a third decade of comprehensive support for genomic data science

This opinion piece discusses the Bioconductor project for open-source bioinformatics and the engineering concepts underlying its effectiveness to date. Since the inception of Bioconductor in 2002 with...

www.cell.com

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · Sep 5

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.

A person who just earned her PhD is standing next to her supervisor and holding a bouquet of flowers; the title slide of her oral defence presentation is in the background showing her thesis topic: "Probabilistic modeling of high-throughput sequencing data for enhanced understanding of DNA methylation heterogeneity."

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Reposted by Keegan Korthauer 🇨🇦

UBC Microbiology and Immunology @ubcmicroimmuno.bsky.social · Jul 22

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

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Reposted by Keegan Korthauer 🇨🇦

Hadley Wickham @hadley.nz · Jun 10

Happy 18th birthday ggplot2! #rstats

Balloon wall art inspired by the ggplot2 hex sticker. The display features a hexagonal frame made of black balloons, filled with white balloons inside and surrounded by a background of light and dark blue balloons. A line graph with black balloon segments and round coloured nodes runs across the centre, and the word “ggplot2” is spelled out in black balloon letters below the chart.

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Reposted by Keegan Korthauer 🇨🇦

Tom Hollenstein @tomhollenstein.bsky.social · Jun 5

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...

Queen’s Special U.S. Doctoral Recruitment Initiative | School of Graduate Studies and Postdoctoral AffairsDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown arrowDown...

Queen’s University is a globally engaged, research-intensive institution dedicated to attracting and supporting exceptional PhD students who will significantly advance our research mission.

www.queensu.ca

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 29

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...

Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data

Dong et al. characterized the significant advantages of reference genome updates, specifically the T2T-CHM13 and the human pangenome, in DNA-methylation analyses. Compared to the previous GRCh38 assem...

www.cell.com

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 15

decemedip is available on GitHub and we welcome feedback! github.com/nshen7/decem...

GitHub - nshen7/decemedip: An R package for deconvoluting cell types in bulk-tissue/cell-free MeDIP-seq data leveraging a Bayesian hierarchical model. Depends on RStan.

An R package for deconvoluting cell types in bulk-tissue/cell-free MeDIP-seq data leveraging a Bayesian hierarchical model. Depends on RStan. - nshen7/decemedip

github.com

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 15

We show that decemedip can identify tissue-of-origin in many bulk tumour samples as well as in cell-free DNA from cancer patients, and these latter estimates are correlated with parallel measurements of circulating tumour DNA content.

3 panel figure depicting: (1) violin plots of decemedip-estimated non-blood cell type proportions across healthy and several cancer types, showing increased proportion of non-blood cell type proportions across most cancer types, (2) the moderate correlation between estimated proportion of tissue-of-origin for these cancer types and a parallel measurement of circulating tumour DNA content, and (3) same as (2) but for estimated non-blood cell type proportion.

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 15

In addition to estimating cell type proportions and their uncertainty intervals, decemedip translates cross-platform measurements between MeDIP-seq counts and fractional methylation levels.

$Diagram depicting output for decemedip: (1) deconvoluted cell type proportions and their uncertainty intervals, and (2) translation with uncertainty between MeDIP-seq counts and fractional methylation.$

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 15

We present decemedip, a reference-based model to estimate cell type composition of immunoprecipitation-based DNA methylomes (MeDIP-seq). While tools exist for deconvoluting absolute methylation levels (BS-seq), this is the first approach applicable to efficient affinity-enrichment protocols.

Plate diagram for decemedip model depicting number and relationship between input and estimated parameters, which are represented by letters/symbols.

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 15

🧬 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...

decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylomes

MeDIP-seq is an enrichment-based DNA methylation profiling technique that measures the abundance of methylated DNA. While this technique offers efficiency advantages over direct methylation profiling,...

doi.org

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · May 15

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 👇👇

Erick Navarro-Delgado @ericknavarro.bsky.social · May 14

🤔 Have you ever wondered how much does genetics and the environment contribute to shaping the DNA methylome? If the answer is yes, check out some of my latest research!

www.biorxiv.org/content/10.1...

RAMEN: Dissecting individual, additive and interactive gene-environment contributions to DNA methylome variability in cord blood

DNA methylation (DNAme) is the most commonly studied epigenetic mark in human populations. DNAme has gained attention in the Developmental Origins of Health and Disease field due to its gene expressio...

www.biorxiv.org

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Reposted by Keegan Korthauer 🇨🇦

Johanna Joyce @johannajoyce.bsky.social · May 9

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 🥰

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Reposted by Keegan Korthauer 🇨🇦

SFU Faculty of Science @sfuscience.bsky.social · Apr 16

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/...

Lead the Way: Graduate Studies at SFU in Canada for Fall 2025 & Spring 2026

Select SFU graduate programs are opening their applications particularly for Canadian students choosing to remain and study in Canada as well as US students looking to study outside the US. Applicatio...

www.sfu.ca

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Reposted by Keegan Korthauer 🇨🇦

Matthias Görges @mgoerges.de · Apr 7

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...

From April 14-18, select UBC graduate programs at UBC Vancouver will re-open their applications for US citizens to be considered for September 2025 or January 2026 entry - they are ready to provide quick admissions decisions for these applicants. If you are a prospective graduate student from the United States considering Canada for graduate school – now is the time.

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Reposted by Keegan Korthauer 🇨🇦

University Health Network @uhn.ca · Apr 7

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...

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · Apr 4

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....

RSS | bioRxiv

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

Reposted by Keegan Korthauer 🇨🇦

Michael Hendricks 🇨🇦 @michaelhendricks.bsky.social · Mar 27

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."

Drug Monkey @drugmonkey.bsky.social · Mar 26

elifesciences.org/articles/106...

Science Under Threat in the United States: The impact on undergraduate students

Anti-science policies, funding cuts, scientific censorship and the US withdrawing from international commitments are worrying members of the ReForm Lab at the College of William & Mary.

elifesciences.org

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Reposted by Keegan Korthauer 🇨🇦

Frank Beier @beierlab.bsky.social · Mar 14

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!

NSERC - Latest News - Launch of the new Harmonized Tri-agency Scholarship and Fellowship programs

As announced in Budget 2024, the scholarship and fellowship programs administered by the three federal research funding agencies – the Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council (NSERC), and the Social Sciences and Humanities Research Council (SSHRC) – have been streamlined into a new harmonized talent program called the Canada Research Training Awards Suite (CRTAS) that will open for applications in summer 2025.

www.nserc-crsng.gc.ca

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Reposted by Keegan Korthauer 🇨🇦

Johanna Joyce @johannajoyce.bsky.social · Mar 7

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

Johanna Joyce @johannajoyce.bsky.social · Nov 25

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️

So how can we ever achieve #gender #equality?

We discuss various strategies in this #Cell Commentary

#WomeninSTEM

www.cell.com/cell/fulltex...
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Reposted by Keegan Korthauer 🇨🇦

Laura White @laurakwhite.bsky.social · Feb 10

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.

The War on Science (Feb 2025 teach-in draft)

The War on Science What’s happening? What can we do about it? An interactive teach-in for biomedical researchers Please share, modify, and repurpose this template presentation (with credit). Good luck...

docs.google.com

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Reposted by Keegan Korthauer 🇨🇦

Elisabeth Bik - Perpetrator 5, a fraudulent microbiologist @elisabethbik.bsky.social · Feb 8

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...

NIH plans to slash support for indirect research costs, sending shockwaves through science

The NIH said Friday night that it would slash support for indirect costs on all existing and future grants to 15%

www.statnews.com

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Reposted by Keegan Korthauer 🇨🇦

Carl T. Bergstrom @carlbergstrom.com · Feb 4

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

INTRODUCTION

thebullshitmachines.com

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Keegan Korthauer 🇨🇦 @keegankorthauer.bsky.social · Jan 30

I'd be a bit offended by the LLM's claim to have taken my lecture and made it 'coherent' 😝

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