What is the PhD actually for, especially now that AI can do increasingly more of what we train scientists to do? compbiologist.substack.com/p/what-is-th... A response to @pracheeac.bsky.social's thought-provoking essay "Free the PhD".

Sean Davis & I are hiring a postdoc to work on turning massive public biological data collections into reusable engines for discovery. #ML / #AI + large-scale omics + open software Details + apply: cu.taleo.net/careersectio... seandavi.github.io | thekrishnanlab.org @cubiomedinfo.bsky.social

A lab using my recent articles on AI use during PhD training doi.org/10.5281/zeno... & doi.org/10.5281/zeno... to kickstart a discussion and draft guidelines for their group is exactly the kind of use I hoped these articles would inspire! Highly recommend reading Ran's post.

I wrote about why every lab should have AI use guidelines, and how to do it. open.substack.com/pub/blekhman...

@compbiologist.bsky.social and @fishevodevogeno.bsky.social present newly minted Dr. Hao Yuan @yhbioinfo.bsky.social! @michiganstateu.bsky.social Amazing work @ the intersection of computational, biomedical, and evolutionary biology! Hao starts a postdoc in the @edwardmarcotte.bsky.social Lab soon.

We have a new platform for employees to give and receive kudos, and it's weekly digests are brutal!

Enjoyed working w/ Stephen & Agnes on this! Gave me a chance to think systematically about where AI 🤖 can backstop human 🧑🏼‍🔬 fallibilities in peer review (fatigue, ordering effects, bias) vs. where human judgment remains essential (novelty, feasibility, creative leaps) while grappling w/ the risks.

Peer review reliability is shockingly low. Meta-analyses show reviewer agreement barely above chance, and grant outcomes often depend more on who reviews than what's proposed. Our new preprint with Agnes Urban and Arjun Krishnan @compbiologist.bsky.social : papers.ssrn.com/sol3/papers.... 🧵 1/

PhD programs worldwide face an urgent question: How should trainees use ChatGPT, Claude & similar tools? Now online: two resources on thoughtfully integrating generative AI into research training. 📄 Conceptual framework: zenodo.org/records/18649847 📋 Practical guide: zenodo.org/records/18452319 🧵

From Arjun Krishnan @compbiologist.bsky.social Expertise before augmentation: a practical guide to using generative AI during research training: zenodo.org/records/1845... Build expertise first: why PhD training must sequence AI use after foundational skill development: zenodo.org/records/1864...

Happy to share this new, very intentional chapter. I have left UCLA after 14 years to join the University of Colorado Anschutz as Professor of Biomedical Informatics and Neurosurgery and the inaugural Marsico Chair in Excellence in Functional Precision Medicine/n news.cuanschutz.edu/dbmi/cu-ansc...

Our Fish EvoDevoGeno Lab @michiganstateu.bsky.social has its 10th anniversary today! 🐠🐟🧪🧬🔬 Thanks to all lab members - present & past, pictured or not - for making the last decade a success! & thanks to our partners in crime of the @brainyfishguts.bsky.social Lab, too! #EndlessFishMostBeautiful

I'm looking forward to re-teaching: Rethinking Data Analysis — A researcher’s guide to avoiding missteps and misuse This is an advanced short course on developing a mental toolkit for rigorous practice & critical consumption of statistical data analyses. 🧵 1/4

A Perspective reviews computational methods for cross-species knowledge transfer. www.nature.com/articles/s41...

Our Perspective article on Computational Strategies for Cross-Species Knowledge Transfer is now published in @natmethods.nature.com! This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵 www.nature.com/articles/s41...

Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones) But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ : www.biorxiv.org/content/10.6...

This preprint is now out after peer review! Check it out: www.cell.com/cell-genomic.... Huge congrats (and thanks!) to the whole team that contributed!

Very proud to be a member of this team. A huge group effort to improve the lives of those with Down syndrome. Thank you to everyone that has helped us along the way.

Congratulations! Kudos to @richabdill.com & @samanthagraham.bsky.social for leading this huge project! Thanks for bring us onboard! Mansooreh Ahmadian & Parker Hicks lead the part of the work on inferring study annotations from unstructured metadata and text from the linked publications.

A favorite! Interestingly, Goodhart stated (in 1975): “Any observed statistical regularity will tend to collapse once pressure is placed upon it for control purposes.” Marilyn Strathern generalized it in 1997 to its famous version👇🏽 pmc.ncbi.nlm.nih.gov/articles/PMC...

Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH." (I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)

Last update of our databases for the year. Download them here: 493 early-career funding opportunities: research.jhu.edu/rdt/funding-... 313 postdoc fellowships: research.jhu.edu/rdt/funding-... 189 PhD fellowships: research.jhu.edu/rdt/funding-...

The views from the office are another real perk of working here at @cubiomedinfo.bsky.social.

Monday motivation from the wonderful @pracheeac.bsky.social: “[I hate the term] incentive structure… if you ask people to do a thing that they perceive to be against those processes and principles, well, you can't ask that — that it's somehow unacceptable…

I participated in a faculty panel a few weeks ago in which senior (ahem) faculty gave advice on careers in academia by pretending luck had very little to do with our success. One piece of advice riled me up, in which it was argued that a reason for their success was their ability to say no. 1/

Same reason that nanopore work with direct clinical application gets published in Annals of Obscurities while the tumor poopome and AlphaFold3 (which wasn’t even competitive in CASP16!) get published in Nature over the objections of highly qualified reviewers

Because it makes for a better $$$ barrier to entry. Broke: we fit a linear model and predicted results of a CRISPR screen Woke: we burned down the Amazon to train a 96-head transformer on 500 million cells and did ALMOST AS WELL as the linear model that runs on my phone

Sharing a Shiny app I've been working on at @leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org. shiny.sph.cuny.edu/BugSigDBEnri... #rstats #microbiome #microbiomeresearch

As a fan of the super @nightsciencepod.bsky.social (highly recommend it!), I enjoyed listening to the latest episode of another favorite — Work Life — where @adamgrant.bsky.social talks to Nathan Myhrvold about invention and creativity! podcasts.apple.com/us/podcast/w...

Abstract submissions are still open for the CSHL Network Biology meeting in March 11 - 15 2025 (abstract deadline: Jan 10). A large fraction of talks will be selected from the abstracts. On behalf of the organizers, we look forward to welcoming you there. meetings.cshl.edu/meetings.asp...

We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵 Paper: doi.org/10.1101/2024... Docs: networkcommons.readthedocs.io

I feel this in my bones. In early career, I had access to more support and flexible funding. As I transitioned to mid-career, not only did a lot of those buffers go away, I was taking on more institutional responsibility, including to fix systemic issues and protect more people.

A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.

Only five days left to apply for our Functional Genomics in animal model systems faculty position at Michigan State University! 🦋🐍🐸🐟🐢🐞🐓🦀🐙🐛🦎🐜🦇🐀🦗🦜🦞🐊🪱🪸🪰🕷️🐚🐖🐝🦄 We love research connecting genomes to biodiversity and are highly supportive of developing non-traditional model systems. Come join us in MI!

Check out our updated database of 189 PhD fellowships and funding opportunities. For each fellowship, we provide a description, $ amount, deadline, link to funder and eligibility criteria (such as citizenship). Good luck! Download freely here: research.jhu.edu/rdt/funding-...

Thank you to everyone who joined our Town Hall on Opportunities for Allyship in Computational Biology last week, our largest event yet! We are grateful to have partnered with Chrissie Bonner of Illustrating Progress, who provided a live graphic recording of our event. 1/2

The world doesn’t need one more blog, and yet I started one and plan to write semi-regularly! compbiologist.substack.com/p/computing-...

Very much looking forward to #MLCB2023, meeting folks & learning a lot! Do checkout our PMLR poster, led by Renming Liu: Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks Preprint: doi.org/10.1101/2023... Code: github.com/krishnanlab/...

Excited to announce the 10th release & 20th-anniversary update of JASPAR, a leading resource in computational regulatory genomics! Important to note that JASPAR has a new URL: jaspar.elixir.no The manuscript can be found at academic.oup.com/nar/advance-...

As jobs are coming out and folks are applying, here's your regular reminder of lots of examples of successful job apps (mostly research academia but also industry, PUI, gov). And if you've gotten a job recently, please consider contributing! github.com/RILAB/statem...

🧬 Opening for a postdoc in our vibrant team at NCMM, University of Oslo, to generate deep learning models to enhance JASPAR & UniBind, boosting gene regulation research. The project is in collab with @anshulkundaje.bsky.social and @wywywa.bsky.social. Plz share. www.jobbnorge.no/en/available...

My new book on clinical AI is out! Kudos to my co-authors! link.springer.com/book/10.1007... #bioinformatics #artificialintelligence #machinelearning #healthcare #healthAI

Everything you said + Google Scholar citation & author alerts + Semantic Scholar email digests.

I strongly recommend getting a paid account on Interfolio, asking your letter writers to upload their letter there ONCE, and you sharing the letters directly from there for all your applications, even those that request referee emails!

This is an all-area tenure-track faculty search in JHU Computer Science -- "substantial growth across all research areas" -- definitely including Comp Biology & Genomics. Please apply & spread the word, friends. cra.org/job/johns-ho...

“…and who started in a non-tenure track position only to get demoted from there. Let’s give her a few million dollars in unrestricted funding over the next 10 years.”” www.statnews.com/2022/02/01/k... H/T Lucy O’Brien

[1st post!] Checkout this comprehensive review & perspective on the "Current and future directions in network biology" arxiv.org/abs/2309.08478. A bunch of us got to lead the section on "Machine learning on networks". Kudos to the whole community and to Dr. Tijana Milenković for the leadership!