iiinova — where your digital self keeps evolving

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Casey Dunn @caseywdunn.bsky.social · 25/08/2026

My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.

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Srinivas Ramachandran @4everbiochemist.bsky.social · 03/06/2026

New from the lab: cfDNA provides an unexpected window into telomere chromatin state and genome-wide chromatin changes that accompany telomere shortening, from a blood draw. We hope this opens a path toward monitoring telomere biology disorders with a blood test. www.biorxiv.org/content/10.6...

biorxiv.org

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Institute for Artificial Intelligence in Medicine @iaim-nu.bsky.social · 12/05/2026

@nucatsinstitute.bsky.social and @kristiholmes.bsky.social were pleased to host @compbiologist.bsky.social for a seminar discussing his lab's work developing #ComputationalMethods that organize poorly labeled data. The goal is to make millions of publicly available datasets discoverable.

Photo of Arjun Krishnan with Kristi Holmes in front of slides with the title "Everything Everwhere All At Once: Making Sense of Massive Public Data Collections."

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Ran Blekhman @blekhman.bsky.social · 29/04/2026

🧬 AI in Genomics Symposium next week! We're bringing together leading scientists from across academia and industry pushing the boundaries of AI in genomics research Join us May 8 at the University of Chicago - KCBD Auditorium, 9:30–5:00, reception to follow. No registration needed!

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Arjun Krishnan @compbiologist.bsky.social · 13/04/2026

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".

compbiologist.substack.com

What is the PhD actually for?

A response to Prachee’s “Free the PhD”, and a critique of my own work

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Arjun Krishnan @compbiologist.bsky.social · 07/04/2026

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

cu.taleo.net

Post-Doctoral Fellow

Click the link provided to see the complete job description.

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Arjun Krishnan @compbiologist.bsky.social · 06/04/2026

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.

doi.org

Build expertise first: why PhD training must sequence AI use after foundational skill development

Generative AI tools have arrived in PhD training environments faster than principled frameworks for their use. The debate has polarized between enthusiasts who argue trainees must adopt AI immediately...

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Ran Blekhman @blekhman.bsky.social · 05/04/2026

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

open.substack.com

You need to make AI guidelines for your lab

Here's why you should, and how to start

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Braasch Lab @ Michigan State University @fishevodevogeno.bsky.social · 03/04/2026

@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.

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Arjun Krishnan @compbiologist.bsky.social · 20/03/2026

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

Recognition Digest: February 27, 2026 - March 6, 2026

Summary:
0
Recognitions Received by Your Team

Recognitions
Looks like no one in this group has been recognized recently. Start the momentum and send a recognition!

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Arjun Krishnan @compbiologist.bsky.social · 09/03/2026

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.

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Stephen Turner @stephenturner.us · 09/03/2026

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/

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Arjun Krishnan @compbiologist.bsky.social · 18/02/2026

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 🧵

zenodo.org

Build expertise first: why PhD training must sequence AI use after foundational skill development

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Stephen Turner @stephenturner.us · 16/02/2026

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...

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Soragni:Lab @alice.soragnilab.com · 10/02/2026

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...

news.cuanschutz.edu

CU Anschutz Recruits National Leader to Launch Functional Personalized Medicine Initiative

CU Anschutz welcomes Alice Soragni to launch a Functional Personalized Medicine Initiative using rapid tumor organoid testing to guide treatment decisions.

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Braasch Lab @ Michigan State University @fishevodevogeno.bsky.social · 26/01/2026

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

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Arjun Krishnan @compbiologist.bsky.social · 08/01/2026

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

HMGP 7622
Rethinking Data Analysis — A researcher’s guide to avoiding missteps and misuse
Feb 3 – May 5, 2026 | Tue 2–3:30p

OVERVIEW
This is a short (1-credit) course designed to:
1) Discuss common misunderstandings & typical errors in the practice of statistical data analysis.
2) Provide a mental toolkit for critically thinking about statistical methods and results.

TOPICS
Estimating error, uncertainty • Underpowered statistics • Multiple testing • P-hacking • Pseudoreplication • Regression to the mean • Double dipping • Spurious associations • Visualization challenges • Reproducibility, replicability

PREREQUISITES
1) Introductory knowledge of statistics & probability
2) Introductory experience with data wrangling, analysis, & visualization using R/Python.

INSTRUCTOR
Arjun Krishnan
Associate Professor, Department of Biomedical Informatics
University of Colorado Anschutz Medical Campus
arjun.krishnan@cuanschutz.edu | @compbiologist | thekrishnanlab.org

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Arjun Krishnan @compbiologist.bsky.social · 06/01/2026

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...

Figure depicting the four classes of important questions that frequently arise when using research organisms to study biomedical questions and translating findings to humans. a, How to predict disease–gene or function–gene relationships across species? Diagram depicts genes in each species associating with specific functions, diseases and phenotypes. b, How to identify functionally equivalent molecular components across species? Diagram depicts finding the most equivalent gene, pathway or expression module or phenotype between species. c, How to infer perturbed molecular profiles across species? Diagram depicts gene expression in each species as a result of taking a particular perturbation like a drug. d, How to map equivalent cell types and cell states across species? Diagram depicts alignment of cell types across species. This Perspective comprehensively lays out the landscape of recent and state-of-the-art data-driven strategies, including those that leverage artificial intelligence and machine learning (ML), for answering these questions.

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Srinivas Ramachandran @4everbiochemist.bsky.social · 16/12/2025

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...

biorxiv.org

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Kelly Sullivan @kellydsullivan.bsky.social · 14/02/2025

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.

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Arjun Krishnan @compbiologist.bsky.social · 22/01/2025

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.

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Arjun Krishnan @compbiologist.bsky.social · 20/12/2024

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...

pmc.ncbi.nlm.nih.gov

“When a Measure Becomes a Target, It Ceases to be a Good Measure”

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Titus Brown @titus.idyll.org · 16/12/2024

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.)

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Denis Wirtz @deniswirtz.bsky.social · 14/12/2024

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-...

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Evan Brenner @evanbrenner.bsky.social · 10/12/2024

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

A morning landscape shot from the rooftop of a building in Aurora, CO. The scene faces west towards the Front Range mountains, with the city skyline of Denver in the center of the shot. The view, rows of scattered buildings, evergreens, and brown branches of leafless deciduous trees, rising up into the mountains, is blanketed in a crisp white layer of snow. The sky is a sharp blue to white gradient with clouds enveloping the highest mountain peaks including Mt. Blue Sky in the distance. Some goofy Canadian geese are in mid-flight at around the level of the horizon, and while you can't hear them in a photo, I certainly could at the time.

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Arjun Krishnan @compbiologist.bsky.social · 09/12/2024

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…

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Harmit Singh Malik @harmitmalik.bsky.social · 09/12/2024

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/

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Tim Triche, Jr.🔰 @timtriche.bsky.social · 03/12/2024

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

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Tim Triche, Jr.🔰 @timtriche.bsky.social · 03/12/2024

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

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Samuel Gamboa @samueldgamboa.bsky.social · 28/11/2024

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

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Arjun Krishnan @compbiologist.bsky.social · 27/11/2024

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...

podcasts.apple.com

The art of invention with Nathan Myhrvold

Podcast Episode · WorkLife with Adam Grant · 11/26/2024 · 27m

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Pedro Beltrao @pedrobeltrao.bsky.social · 26/11/2024

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...

Meeting topics and invited list of speakers

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Saez-Rodriguez Group @saezlab.bsky.social · 26/11/2024

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

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Jacquelyn Gill @jacquelyngill.bsky.social · 23/11/2024

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.

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Jeremy Berg @jeremymberg.bsky.social · 24/11/2024

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

media.tenor.com

homer simpson from the simpsons is holding a cup in front of a picture

ALT: homer simpson from the simpsons is holding a cup in front of a picture

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Braasch Lab @ Michigan State University @fishevodevogeno.bsky.social · 22/11/2024

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!

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Denis Wirtz @deniswirtz.bsky.social · 19/11/2024

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-...

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The Black Women in Computational Biology Network @blkwomencompbio.bsky.social · 04/03/2024

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

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Arjun Krishnan @compbiologist.bsky.social · 08/12/2023

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

compbiologist.substack.com

Computing for life

A new space for reflections at the interface of data, ML/AI, and biomedical research

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Arjun Krishnan @compbiologist.bsky.social · 29/11/2023

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/...

github.com

GitHub - krishnanlab/obnb: A Python toolkit for setting up benchmarking dataset using biomedical net...

A Python toolkit for setting up benchmarking dataset using biomedical networks - GitHub - krishnanlab/obnb: A Python toolkit for setting up benchmarking dataset using biomedical networks

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Anthony Mathelier @amathelier.bsky.social · 14/11/2023

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-...

academic.oup.com

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

Abstract. JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profil

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 14/11/2023

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...

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Anthony Mathelier @amathelier.bsky.social · 10/11/2023

🧬 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...

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Arjun Krishnan @compbiologist.bsky.social · 11/10/2023

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

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Arjun Krishnan @compbiologist.bsky.social · 10/10/2023

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!

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Ben Langmead @benlangmead.bsky.social · 03/10/2023

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...

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Anne Carpenter @drannecarpenter.bsky.social · 03/10/2023

“…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

statnews.com

The Karikó problem: Lessons for funding basic research

"Fund people not projects" is easier said than done. A better way to fund science is to bend over backward to fund a truly diverse range of people and ideas, even including those perceived as unpopula...

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