Arjun Krishnan @compbiologist
ML & data-driven discovery; Complex traits & diseases; Data reuse & open science. Associate Professor | Group leader @KrishnanLab | @compbiologist everywhere thekrishnanlab.org CU Anschutz Med Campus Joined May 2008-
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I am beyond humbled to take on the role of CSO at Cellular Intelligence while on leave from Penn! Thrilled to have the opportunity to work with an incredible team tackling hugely exciting and challenging problems!
We're excited to announce that Arjun Raj, Ph.D. @arjunrajlab has been appointed Chief Scientific Officer and named Scientific Co-Founder of Cellular Intelligence. Arjun joined us full time in 2025 while on leave from @Penn, where he is the Richard K. Lubin Professor of
ModGenePlexus: A module-based approach for post-omics, post-GWAS network-based gene classification academic.oup.com/bioinformatics…
Thanks for the link, interesting post by @blekhman, lots of good points! @compbiologist: "the best model is usually the one that is consistently number 2 in benchmarks across the literature." - Yes, it's Goodhart's curse, overoptimization for narrow targets will fail. (Though in more general GenAI domains, the problem is even harder because all the benchmarks are getting saturated as well!) On the importance of evaluations, the newer work on improving eval practices and reporting - @EvalConsensusAI / @evaluatingevals - seems likely to be relevant, though it needs to be adapted to bio models. Seems like a good place to continue exploring; both Noga Aharony and Reut Danino are separately interested in related issues; we should put something together on this! There are also a number of points in our RAND report that I think are touched upon, especially about prediction vs. validation, and about metadata (i.e. our discussion of the problem of multimodal data and integrating data;) rand.org/pubs/research_… And one last point - "a recurring theme... was that ignoring theory and history is a mistake" - that sounds like the bitter lesson isn't supposed to apply here; I remain skeptical. But as the Delphi explored, there may be fundamentally too little data in this domain to brute force answers; @alexijielu's approaches with self-supervision seem to be trying to address this. (And given that he's working to characterize limitations of current AI methods, I really wish we had gotten him into the Delphi Panel for our study!)
@curiouswavefn @lpachter Absolutely! Expanded thoughts are here: Build expertise first: why PhD training must sequence AI use after foundational skill development doi.org/10.5281/zenodo…
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: papers.ssrn.com/sol3/papers.cf… 🧵 1/
A Perspective reviews computational methods for cross-species knowledge transfer. nature.com/articles/s4159…
Excited to share this work. A huge effort from many team members, led by former @CUHMGGP PhD student and current @CrnicInstitute Post-doc, Dr. Lauren Dunn! Altered hepatic metabolism in Down syndrome: Cell Reports cell.com/cell-reports/f…
The call for poster abstracts for the 6th International Conference of the Trisomy 21 Research Society is now open! Conference registration for the conference, to be held June 17-20 2026 in Denver, CO, USA, is open as well. t21rs2026.com/call-for-poste…
Our perspective is now out in @naturemethods! Congratulations again to @yhbioinfo & the rest of the team! nature.com/articles/s4159…
Preprint 🚨 A review state-of-the-art computational strategies for cross-species knowledge transfer in biomedicine 💻👩🦰🐭🐟🪰🪱🧬🫁⚕️ Led by an excellent team at @KrishnanLab: @yhbioinfo, @ChrisAMancuso, & @kaylainbio in collab w/ @FishEvoDevoGeno 🧵 arxiv.org/abs/2408.08503
@baym I actively tell students in my class that we're never going to use those terms, just FP, FN, TP, TN, & their rates, and for good measure, show @drob's tweet: x.com/drob/status/78…
Remember, mixing up Type I and Type II errors is called a Type III error
As a fan of the super @nightsciencepod (highly recommend it!), I enjoyed listening to the latest episode of another favorite — Work Life — where @AdamMGrant talks to @nathanmyhrvold about invention & creativity! podcasts.apple.com/us/podcast/wor…
#ASHG24 Interested in comparing & transferring data & knowledge across species for translational biomedicine? This review is for you! We take a deep dive into methods & highlight gaps/challenges. Details on implementation, data, & benchmarks: github.com/krishnanlab/cr…
Preprint 🚨 A review state-of-the-art computational strategies for cross-species knowledge transfer in biomedicine 💻👩🦰🐭🐟🪰🪱🧬🫁⚕️ Led by an excellent team at @KrishnanLab: @yhbioinfo, @ChrisAMancuso, & @kaylainbio in collab w/ @FishEvoDevoGeno 🧵 arxiv.org/abs/2408.08503
#ASHG2024 #ASHG24 If you’re interested in effectively reusing public omics data and/or passionate about data discovery, data reuse, metadata, etc., do ping me!
Annotating Publicly-Available Samples and Studies Using Interpretable Modeling of Unstructured Metadata 1. This study introduces txt2onto 2.0, an improved NLP and ML-based tool that automates the annotation of unstructured biomedical metadata, linking samples and studies to
Congratulations!!
Annotating Publicly-Available Samples and Studies Using Interpretable Modeling of Unstructured Metadata 1. This study introduces txt2onto 2.0, an improved NLP and ML-based tool that automates the annotation of unstructured biomedical metadata, linking samples and studies to
Our preprint 'Chemical Language Model Linker: blending text and molecules with modular adapters' is now out on arXiv, led by @Dengyifan1012. ChemLML is a method for text-based conditional molecule generation that uses pretrained text models like SciBERT, Galactica, or T5. 1/
Have you ever wondered what it takes to complete a postdoc? @compbiologist, PhD, from the @KrishnanLab kicked off our Bytes to Bedside Seminar Series with a workshop exploring how to have an effective postdoc. Discover more about his insights ▶️ bit.ly/3Yf5zik
Join us to learn more about the Human Medical Genetics and Genomics PhD Program on October 21!
Interested in learning more about the Human Medical Genetics and Genomics Program at CU Anschutz? Join us at 1PM Mountain on Monday, October 21, for the 2024 BIOMED PHD EXPO!
Today, @compbiologist, PhD, joined us for Bytes to Bedside. To celebrate #NPAW2024, he led a workshop offering valuable tips for planning a successful postdoc that emphasized the importance of not putting your life on hold, learning new skills, and following through on projects.
🙏Thank you, SfN (@SfNtweets). I am humbled and honored to receive this award, which has recognized many excellent scientists in recent years. Special thanks to my postdoc mentor, Erin (@erin_schuman), for the nomination.@MPFNeuro @maxplanckpress
SfN is proud to announce the recipients of the 2024 Promotion of Women in Neuroscience awards, who will be honored at #SfN24. Through mentorship, professional development and outstanding careers, these seven researchers have made significant contributions to the advancement and
🌟Celebrating #WomeninMedicineMonth with @JRegensteiner, a trailblazer in women's health research! As Director of the Ludeman Family Center, her groundbreaking work and BIRCWH award highlight her commitment to advancing women's health. Thank you for inspiring the next generation!
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Mehdi Sharifi Tabar @M_sharifitabar
189 Followers 590 Following Postdoc -Gene regulation/Epigenetic/Immunity. Honorary Lecturer, Usyd. Representative of AEpiA & Sydney Protein Group
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2K Followers 5K Following Alum:Fergusson,SPPU,IITB. Prof@IITD Interests: cognition-affect, decisions, mind-brain, PFC, sex dif.+sharing treepics. PI, mom, WoSResearcherID:H-5212-2019
Chi-Jing Leow @chijingleow
8 Followers 50 Following PhD student in the Braasch Lab at Michigan State University.
Anar Rzayev @AnarSnowball
460 Followers 2K Following Cooking proteins with ML @ ISTA 🇦🇹 Ex-Research student @ KAIST 🇰🇷 | Prev CS & MATH @ EPFL 🇨🇭 | Bronze medals @ IMO 2017, 2019 🇧🇷 🇬🇧
Sierra Niemiec @SierraSkyN
16 Followers 74 Following Passionate about Biostatistics, Dogs, and Mountains
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brody graham @brodygraham11
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Tsung-Che Wu @TsungCheWu
333 Followers 1K Following Medical oncologist @ NTUH in Taiwan, phase 1, GI cancer, HCC, BTC, ESCC, CRC, lung cancer Tsung-Che (Nathan) Wu
Karl Petri @Karl_Petri
695 Followers 1K Following Emmy Noether group leader @Uniklinikum_Wue & @Uni_WUE. CRISPR, CAR-T, Hemato-Oncology, previously @JoungLab, views my own
Lambert Moyon @lambosaur
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Rui Yang @RuiYang53922541
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392 Followers 826 Following Scientist; Bioinformatics|Genomics|Data Science & Engineering|R|Nextflow|Human-AI collaborative intelligence (CINTEL) 🇵🇱🇦🇺
Michael Bronstein @mmbronstein
59K Followers 8K Following #DeepMind Professor of #AI @UniofOxford / Director #AITHYRA / Chief Scientist @proximabio / https://t.co/kZpGpDzYeV (opinions are mine) 🤖🧪🧬🎶🐎
alex rubinsteyn @iskander
7K Followers 5K Following Genomics + immunology + ML = personalized cancer immunotherapy | https://t.co/nReVwtVHPq | https://t.co/8DWibdfDWa
Max Beining @MaxBei2
6 Followers 115 Following PhD candidate for computational based Protein and Peptide Design at University Leipzig
Marco Matthies @MarcoMatthies
393 Followers 8K Following Interested in natural philosophy and machine learning
Anshul Kundaje @anshulkundaje
33K Followers 3K Following Federally funded academic research is the innovation engine of the US economy. Reform is welcome. Destruction will have long term consequences.
Michael Hoffman @mich... @michaelhoffman
23K Followers 6K Following Chair, Comp Bio & Medicine Program, Princess Margaret Cancer Centre, @UHN. Assoc Prof, Medical Biophysics, University of Toronto. COI https://t.co/CvupKNIjZr
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64K Followers 2K Following Just another LLM. Tweets do not necessarily reflect the views of people in my lab or even my own views last week. https://t.co/fZAnUCqd12
Lior Pachter @lpachter
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Itai Yanai @ItaiYanai
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CU Department of Biom... @CUBiomedInfo
829 Followers 828 Following Education | Research | Clinical Impact DBMI connects basic science and medicine with clinical and translational scientists at the @CUAnschutz Medical Campus
Harmit S. Malik @HarmitMalik
43K Followers 7K Following Study genetic conflicts professionally. Try to avoid conflicts in personal life (with mixed results). @HutchBasicSci @fredhutch @HHMINEWS He/him
Anne Carpenter, PhD @DrAnneCarpenter
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Jian Ma @jmuiuc
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Casey Greene @GreeneScientist
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140 Followers 26 Following Our mission is to improve access to diagnosis, research, and care for all individuals with undiagnosed and ultra-rare conditions.
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ARPA-H @ARPA_H
9K Followers 240 Following Official Twitter account of the Advanced Research Projects Agency for Health (ARPA-H). Privacy Policy: https://t.co/Z855rcfwXT Engagement ≠ endorsement
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Daniela Witten @daniela_witten
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John Quackenbush @johnquackenbush
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Dr. Fan Zhang ⛵️ @FanZhang_Jessie
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Erin LeDell - ledell.... @ledell
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AsiaR Community @AsiaR_comm
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Su-In Lee @suinleelab
3K Followers 273 Following Boeing Endowed Professor in the Allen School of Computer Science at the University of Washington; @uwcse https://t.co/TSBy7bHgCS
M. Madan Babu @m_madan_babu
2K Followers 2K Following Dept. of Structural Biology, St. Jude Children's Research Hospital Chair in Biological Data Science Director, Center for Data Driven Discovery @StJudeStructBio
seemay chou @seemaychou
11K Followers 1K Following scientist. @arcadiascience @asterainstitute @navigationfund. texan in CA.
Edward Marcotte @edward_marcotte
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71K Followers 493 Following Data & Society is a nonprofit research institute that studies the social implications of data-centric technologies, automation, and AI.
Data Science JEDI Out... @DataSciJedi
957 Followers 482 Following Justice, Equity, Diversity, & Inclusion (JEDI) Outreach Group of the American Statistical Association @AmstatNews. Become a member at https://t.co/Byh7Cajtdi
Gary Bader @garybader1
2K Followers 68 Following Professor, University of Toronto https://t.co/oJeDcaLoGD https://t.co/lcSStJrc0M
Javier Santoyo @jsantoyo
6K Followers 898 Following Genomics & Bioinformatics Scientist #Omics #NGS #LongReads | Also @ https://t.co/TCJKash6C1 | Opinions my own. He/HimTrends for United States
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