"Absurd ad hoc analysis pipelines are justified solely by their results, not by their logic. And once they are published, open code just makes things worse, because other researchers use the code to publish more rubbish."

Yes, we should give you guidance up front. Also, as I frequently say, if you ever have a question about what your editor wants to see in a revision, ask us to review/approve a revision plan. I never want my authors losing sleep over my expectations. Truly.

Sometimes authors summarize their responses to 3-6 major points raised by the reviewers in their resub cover letters or at the top of their rebuttal letters. This is so super helpful to editors, because it brings us right up to speed after not having read the paper/reviews for months. THANKS!!

If we are really serious about deepening our understanding, we need more than high-quality data generation.

We need high-quality refutable scientific hypotheses, high-quality interpretable computational methods, and high-quality training to set up future scientific work force!

Inspiring read to understand where the genomics study of complex psychiatric disorder stands now.

Very excited how spatial transcriptomics contributes enlightening mediating effect of genetic risk variants.

Some cool work is brewing!

www.nature.com/articles/s41...

my work with @stephaniehicks.bsky.social and @boyiguo.bsky.social has been published in Biostatistics! tldr: the mean-variance bias exists in SRT data & impacts SVG detection. we propose #spoon, available on @bioconductor.bsky.social, to address this! pmc.ncbi.nlm.nih.gov/articles/PMC... 🤩

#SpotSweeper is now published!

Check our journal club session summary of the pre-print version by @lahuuki.bsky.social

The new features @boyiguo.bsky.social + @mictott.bsky.social added in this revised manuscript enhance the use cases for #SpotSweeper: 👀 #VisiumHD data!

youtu.be/f72XcXmtkfw?...

Thanks, Keri! Greatly appreciate the privileged experience working together, and your mentorship!

Great collaboration motivates methodological and biological innovation!

Grateful for the opportunity to work together with @martinowk.bsky.social and @lieberinstitute.bsky.social, investigating the molecular pathology of neuropsychiatric disorder, coming soon! 😉

Important methods development for spatial transcriptomics (ST) data from @mictott.bsky.social @boyiguo.bsky.social @stephaniehicks.bsky.social - congrats!

Applying this method to our QC workflow has substantially improved many new ST datasets generated across diverse regions/tissues in the human 🧠

Excited to announce that I'll start as a tenure-track assistant professor @uofuphs.bsky.social this fall. #BiostatsElevated

The #GUOmics lab will focus on developing biologically informed machine learning methods to decode spatial and population-scale omics data. Look forward to exciting colabs!

🤔Could quality control create more harm than good? We explore this question in the context of #SRT.

SpotSweeper is developed to combat implicit selection bias.

Led by fellow rising star @mictott.bsky.social and collab with amazing mentor @stephaniehicks.bsky.social

👉: bsky.app/profile/mict...

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

"An open letter to graduate students and other procrastinators: it’s time to write"
www.nature.com/articles/s41...

Enjoyed reading the article, and reflect on my own writing workflow.

Plan to include in my lab handbook as resources for trainees.
#PDL#writing#comp-lab

Spatial-aware metrics are indeed timely needed!

Excited to share a new algorithm that we have been working on over the last year.

💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄

Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪

thank you @stephaniehicks.bsky.social and @boyiguo.bsky.social for your amazing mentorship on this project! so excited that this is finally out

💪, hope you've set up all! It's better to have them figured out early than right on the spot!

Not trying to pick a fight. Instead, it is something I, as a postdoc, recently being thinking about, what skills that faculty jobs take and are being interviewed/evaluated for, at least at "junior" level.

I see your point. But I would also argue that industry jobs have better classifications, or at least more explicit naming of duties, e.g. project managers. Ppl are explicitly interviewed for their managing skills. I image faculty just three classifications without explicit evaluation such skills?

May be "writing grants" is just a surrogate for the discrepancy between junior scholars' imaged responsibility of a faculty job, "doing science" vs what the job really takes to do science, where scientific investigation is a small part.

Not grants, but my dissertation in R markdown. Overall, not much problem for me and as I used Rmarkdown as a wrapper of latex for most of the part, even formatting, given the final output is a pdf.