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Nicholas Tatonetti, PhD

@tatonetti.bsky.social
719 followers 53 following 54 posts

Making drugs safer one billion data points at a time. @CedarsSinai Prof, @Stanford BMI, @Columbia DBMI, EiC of BioData Mining, he/they enby 🏳️‍🌈

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Reposted by Nicholas Tatonetti, PhD
Communications Biology @commsbio.nature.com · 13h
Somatic Y chromosome loss is mapped at single-gene resolution across cancers and is shown to follow region-specific patterns associated with transcriptional dysregulation and poorer clinical outcomes. @tatonetti.bsky.social @cedarssinaicancer.bsky.social www.nature.com/articles/s42003-026-10875-9
nature.com
Recurrent deletions and regulatory disruption of the Y chromosome in cancer - Communications Biology
Using high-coverage whole-genome sequencing and transcriptomics of male cancer cell lines, the authors map the landscape of somatic Y chromosome loss at single-gene resolution. Y chromosome erosion is...
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Reposted by Nicholas Tatonetti, PhD
samuel mehr @mehr.nz · 21/07/2026
the most realistic scene in Jurassic Park is when two scientists make a questionable decision — traveling to an undisclosed location with a strange man — on the promise of three years of modest funding
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Reposted by Nicholas Tatonetti, PhD
Aubrey Hirsch @aubreyhirsch.bsky.social · 20/07/2026
I wrote about the history, politics, and persistence of giving babies their fathers' last names. And in doing this research, I've concluded that all last names are bad actually!
aubreyhirsch.substack.com
Why Is Dad's Name Still the Default?
the history, politics, and law of patrilineal naming
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 18/05/2026
It's time again for the AMIA Translational Bioinformatics Year-in-Review! This year: 2k papers triaged, 600+ reviewed. The final set is wild. Foundation models, multimodal bio, spatial everything, generative proteins, and some pure brain candy. Can't wait to present! #Amplify2026
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 23/04/2026
OnSIDES v3.1.1 is out! 🎉 Updated with drug labels through April 2026 from all four sources (US, UK, EU, Japan): - 41K+ product labels - 6.9M drug–adverse event pairs - 4,097 ingredients Also fixes some bugs — if you're using that., please upgrade. github.com/tatonetti-la...
github.com
Release OnSIDES v3.1.1 · tatonetti-lab/onsides
Updated April 2026 with the latest drug labels from all four regulatory sources. Summary Type v3.1.0 v3.1.1 Products 42,268 41,119 Adverse effects 5,472,613* 6,928,666 Ingredients 1,955 ...
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 06/03/2026
GI fellow Jamil Samaan noticed something odd when using AI ambient scribes and speech transcription tools Clinicians with non-native English accents appeared to confuse the model He and Yassi Fatapour decided to investigate, now out in npj Digital Medicine www.nature.com/articles/s41...
nature.com
Accent related errors in clinical speech transcription and a LLM-based remedy - npj Digital Medicine
npj Digital Medicine - Accent related errors in clinical speech transcription and a LLM-based remedy
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 05/02/2026
New editorial in BioData Mining: A crisis of overconfidence in clinical AI led by @cedarssinaihsu.bsky.social PhD student, Jacob Berkowitz. Why sounding confident can be more dangerous than being inaccurate, and why calibration needs to be central in clinical AI. link.springer.com/article/10.1...
link.springer.com
A crisis of overconfidence: Why confidence, not accuracy, is the real risk in clinical AI - BioData Mining
BioData Mining - Language models today are trained to convey confidence in their outputs, regardless of whether those outputs are correct. The alignment methods we use to make them helpful also...
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Reposted by Nicholas Tatonetti, PhD
Geoffrey A. Fowler @geoffreyfowler.bsky.social · 26/01/2026
You can now connect ChatGPT to an Apple Watch. So I imported 29 mil steps & 6 mil heartbeats into the new ChatGPT Health. It graded my heart health an F. ⁉️ Cardiologist @erictopol.bsky.social called it “baseless.” Any bot claiming to give health insights shouldn’t be this clueless. Even in beta. 🧵
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Reposted by Nicholas Tatonetti, PhD
Nick Andert @nickandert.bsky.social · 23/01/2026
I suspect Holly Mitchell is going to find in the coming years that she shares Henry Waxman's legacy as someone who blocked a whole part of the LA region from getting rail for decades due to needless, pointless capitulation to fearmongering. Her time on the Metro Board will not be remembered kindly.
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 13/01/2026
Excited to announce our new project with ARPA-H which advances methods to artificially accelerate the aging of organoids to study drug toxicities over time!! A current huge gap in our understanding and our models. www.cedars-sinai.org/newsroom/ced...
cedars-sinai.org
Cedars-Sinai Will Pioneer AI in Drug Safety With New Funding
Cedars-Sinai receives an up to $5,054,235.00 award to develop KronosRx, a platform using AI and 'patient avatars' to predict adverse drug reactions, improve cli
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 16/11/2025
Is "Agent Engineering" the next big thing? Getting so-called "AI Agents" to work together effectively isn't trivial. @moorejh.bsky.social and I discuss the need for rigorous development in our latest editorial in BioData Mining biodatamining.biomedcentral.com/articles/10....
biodatamining.biomedcentral.com
From prompt engineering to agent engineering: expanding the AI toolbox with autonomous agentic AI collaborators for biomedical discovery - BioData Mining
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Reposted by Nicholas Tatonetti, PhD
Jason Moore @moorejh.bsky.social · 07/11/2025
Deskilling? cacm.acm.org/news/the-ai-... #deskilling #ai
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 08/11/2025
👀 Health AI PhD Information Session hosted by Cedars-Sinai! This event is an opportunity for interested students to learn more. November 21 @ 8 AM PT Register: forms.office.com/r/vMreBMZQak
forms.office.com
Microsoft Forms
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Reposted by Nicholas Tatonetti, PhD
Jason Moore @moorejh.bsky.social · 27/09/2025
Application period for the Cedars-Sinai PhD Program in Health AI is now OPEN! Come study cutting-edge AI in a top hospital with clinical rotations, clinical collaborators, & easy access to clinical data - please RP! www.cedars-sinai.edu/education/gr... #artificialintelligence #bioinformatics #phd
cedars-sinai.edu
PhD in Health Artificial Intelligence
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Reposted by Nicholas Tatonetti, PhD
Jason Moore @moorejh.bsky.social · 25/09/2025
Nice piece in the NYT about the risks of "magical thinking" with AI that allow big tech to hype their products www.nytimes.com/2025/09/25/o... #artificialintelligence #magic #hype #llms
nytimes.com
Opinion | There’s Nothing Magical in the Machine
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 14/09/2025
Loving my state rn. California’s $23 Billion Plan to Restore Federal Cuts to Scientific Research www.nytimes.com/2025/09/13/u...
nytimes.com
California’s $23 Billion Plan to Restore Federal Cuts to Scientific Research
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 09/09/2025
AI methods are great tools for advancing drug safety surveillance. We show that LLMs can accurately identify and extract essential concepts from messy product drug labels. Just published in _Drug Safety_! Great work led by @undinagislad! link.springer.com/article/10.1...
link.springer.com
Leveraging Large Language Models in Extracting Drug Safety Information from Prescription Drug Labels - Drug Safety
Introduction Adverse drug reactions (ADRs), including those resulting from drug interactions, remain a leading cause of morbidity and mortality. Structured product labels (SPLs) serve as a primary sou...
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 28/08/2025
We used AI to audit 21,000+ RCTs. The result? -- only 15% of trials fully comply with CONSORT guidelines. Transparency in clinical trials has a long way to go. Amazing work by Apoorva in my group! jamanetwork.com/journals/jam...
jamanetwork.com
An LLM Analysis of Reporting Quality of Randomized Clinical Trial Articles
This study uses a zero-shot large-language model to automatically assess compliance with the Consolidated Standards of Reporting Trials guideline for English-language randomized clinical trials publis...
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Reposted by Nicholas Tatonetti, PhD
Andrew D Thaler @drandrewthaler.bsky.social · 27/08/2025
The top three science funders are the US, China, and Japan. The three fund more science than every other country, combined. In 2024, the US funded more scientific research than China and Japan, combined. The US also funds more science than every other country except for Japan and China, combined.
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Reposted by Nicholas Tatonetti, PhD
Annual Reviews @annualreviews.bsky.social · 20/08/2025
The 2025 volume of the Annual Review of Biomedical Data Science is now online. Take a look at the most read article from this new volume, "Spatial Transcriptomics Brings New Challenges and Opportunities for Trajectory Inference" arevie.ws/45D2NWD @marylynritchie.bsky.social @tatonetti.bsky.social
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Reposted by Nicholas Tatonetti, PhD
Jeffrey Barrett @jeffbarrett.eu · 07/08/2025
This creates a fun game that rewards superfluous, outlandish (dare I say outre?) verbiage.
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 06/08/2025
With the correct rhetorical device you can make complete jibberish sound like poetry. Just ask Shakespeare (or better read Forsyth's The Elements of Eloquence)
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 06/08/2025
Just came across this fail. Literally everything that's wrong with AI/tech in healthcare. Not only is the patient and doctor buried in their devices, but they're facing AWAY from each other 🤦‍♂️!! Technology should facilitate and center the humanity of healthcare. Not do whatever this is.
From left to right. Patient facing left and looking at their phone. Doctor facing right looking at a tablet.
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Reposted by Nicholas Tatonetti, PhD
Kieron Gillen @kierongillen.bsky.social · 08/07/2025
I’m petrified about today’s science news. Genetically modifying crabs to have cheetah genes? This could go sideways fast.
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Reposted by Nicholas Tatonetti, PhD
Jason Moore @moorejh.bsky.social · 02/07/2025
What is Vibe Coding and how can it be used to advance biomedical research? @tatonetti.bsky.social & I explain in this editorial biodatamining.biomedcentral.com/articles/10.... #bioinformatics #datascience #coding #vibecoding
biodatamining.biomedcentral.com
Vibe coding: a new paradigm for biomedical software development - BioData Mining
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 02/07/2025
Vibe coding is coming for biomedical software development, my first editorial as Co-Editor-in-Chief of @BioDataMining with @moorejh.bsky.social biodatamining.biomedcentral.com/articles/10....
biodatamining.biomedcentral.com
Vibe coding: a new paradigm for biomedical software development - BioData Mining
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 02/07/2025
If anyone is wondering, yes we will be monitoring the safety and side effects of drugs from the moment they hit the market
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 02/07/2025
So the market for our drug safety monitoring algorithms just opened up 👀
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 22/05/2025
Excited that our paper on GenAI-based text normalization is out at Journal of Biomedical Informatics! If you ever had a bunch of messy text and need to map it to a controlled terminology, then this is the method for you. www.sciencedirect.com/science/arti... Special 👏 to Jacob Berkowitz!!
sciencedirect.com
Biomedical text normalization through generative modeling
A large proportion of electronic health record (EHR) data consists of unstructured medical language text. The formatting of this text is often flexibl…
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 21/05/2025
Learn observational data from the best. @ColumbiaDBMI and @OHDSI are offering summer school to learn all the real-world-data analysis tips and tricks. columbiauniversity1.regfox.com/ohdsi-summer...
columbiauniversity1.regfox.com
TBD3
Online registration for Columbia OHDSI Summer School starts on April 9th 2025. Online registration ends July 11th 2025.
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Reposted by Nicholas Tatonetti, PhD
Streets For All @streetsforall.org · 23/04/2025
✅ PASSED SENATE TRANSPORTATION COMMITTEE: SB 445 by @scottwiener.bsky.social that streamlines permit approval process for transit projects to tackle cities that cause costly delay against transit.
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 10/04/2025
What a fabulous discussion and meeting! Off to a fun start.
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Reposted by Nicholas Tatonetti, PhD
Mark Hoffman @markhoffmankc.bsky.social · 09/04/2025
Looking forward to starting the Nexus Informatics conference tomorrow morning. First up - @tatonetti.bsky.social Nicholas Tatonetti delivering our opening keynote! Can't wait! I will be giving the Friday morning keynote, "Welcome to the Jungle – Real World Data Surrounded by Data Gardens" !
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 03/04/2025
Our OnSIDES db -- the worlds most up-to-date resource of drug side effects is published at @MedCellPress For all your drug safety analysis and prediction needs. OnSIDES is the first resource to combine US, UK, EU, and Japanese data all in one place. www.cell.com/med/abstract...
cell.com
OnSIDES database: Extracting adverse drug events from drug labels using natural language processing models
Tanaka et al. present OnSIDES (on-label side effects resource), a database of drug adverse events extracted from drug labels using a fine-tuned PubMedBERT model, including pediatric-specific adverse e...
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 24/03/2025
In 2018 I wrote about how medical science could benefit from how humans approach cooking -- all of us continuously testing and experimenting new ideas constantly. Feels even more true in 2025. www.annualreviews.org/content/jour...
annualreviews.org
Science as a Culinary Art: How Data Science and Informatics Will Change Knowledge Discovery for Everyone | Annual Reviews
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 17/03/2025
We just opened a new collection at BioData Mining for submissions! Our ability to collect data has outpaced our ability to make sense of it. In this collection we want to see papers that are addressing this growing gap. www.biomedcentral.com/collections/...
biomedcentral.com
Advances in Data Mining for Biomedical Informatics and Healthcare
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 11/03/2025
Thank you @amiainformatics.bsky.social for an having me for another fun Translational Bioinformatics Year in Review! #YIR25 #IS25 Here are the slides of the top papers of the year: tatonettilab-resources.s3.amazonaws.com/TBI-Year-in-...
tatonettilab-resources.s3.amazonaws.com
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 11/03/2025
Putting the final touches on tomorrow's Translational Bioinformatics Year-in-Review *Playlist* @AMIAinformatics #IS25 #YIR25 open.spotify.com/playlist/5YE...
open.spotify.com
TBI Year-in-Review 2025 Pittsburgh
Playlist · Nicholas Tatonetti · 15 items
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 09/03/2025
reviewing papers for my annual Translational Bioinformatics Year-in-Review at the AMIA 2025 Summits in Pittsburgh and came across this gem -- needless to say I feel attacked.
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Reposted by Nicholas Tatonetti, PhD
MwahahahahahadScientist @mads100tist.bsky.social · 01/03/2025
If you're in the US, considering Europe for your PhD, and you identify as a minority, I will chat with you and review any application documents you need 🧪
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Reposted by Nicholas Tatonetti, PhD
Jace D. Flatt, PhD, MPH (They/He) @jaceflatt.bsky.social · 01/03/2025
Just received notice that our grant was terminated. 5R24AG066599-03 TheRiseRegistry.org
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Reposted by Nicholas Tatonetti, PhD
Jeremy Berg @jeremymberg.bsky.social · 08/02/2025
A Primer on Indirect Cost Rates
media.tenor.com
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
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Reposted by Nicholas Tatonetti, PhD
Carl T. Bergstrom @carlbergstrom.com · 08/02/2025
1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 29/01/2025
Saw this great suggestion from @roxanadaneshjou.bsky.social, so I’ll go. NIH funded helped my lab discovery that using ceftriaxone (generic antibiotic) and lansoprazole (Prevacid) together will cause dangerous arrhythmias.
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 16/01/2025
Huge drug effects news!! Major breakthrough in figuring out what in grapefruit interferes with drug metabolism. Can’t wait to dive into the solution to this decades long mystery. 🤓 www.nytimes.com/2025/01/10/s... via @NYTimes
nytimes.com
On Meds? You May Be Able to Eat Grapefruit Again Someday.
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Reposted by Nicholas Tatonetti, PhD
Jason Moore @moorejh.bsky.social · 07/01/2025
Branding large language models as artificial intelligence primes customers to believe they have capabilities they lack cacm.acm.org/opinion/arti... #artificialintelligence #llms
cacm.acm.org
Artificial Intelligence Then and Now – Communications of the ACM
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Reposted by Nicholas Tatonetti, PhD
Eric Topol @erictopol.bsky.social · 06/01/2025
"We estimate that the sources of drinking water for up to 23 million Americans could be contaminated above regulatory thresholds by wastewater-derived PFAS [forever chemicals] alone." @pnas.org www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Nicholas Tatonetti, PhD @tatonetti.bsky.social · 28/12/2024
Chaz Dean is the Dr Zizmor of LA. #iykyk
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Reposted by Nicholas Tatonetti, PhD
Atul Butte @atulbutte.bsky.social · 23/12/2024
Whoa! In @NEJM_AI: A Multimodal Biomedical Foundation Model Trained from 15 Million Image–Text Pairs… fully open-access foundation model! ai.nejm.org/doi/full/10....
ai.nejm.org
A Multimodal Biomedical Foundation Model Trained from Fifteen Million Image–Text Pairs
Biomedical data are inherently multimodal, comprising physical measurements and natural-language narratives. A generalist biomedical artificial intelligence (AI) model needs to simultaneously proce...
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Reposted by Nicholas Tatonetti, PhD
Science Magazine @science.org · 23/12/2024
Women leave academia at higher rates than men at every career stage, and attrition is especially high among three groups: tenured faculty, women in non-STEM fields, and women employed at less prestigious institutions, a #ScienceAdvances analysis finds.
scim.ag
Gender and retention patterns among U.S. faculty
Women faculty are more likely to leave their jobs than men, most often due to workplace climate, rather than work-life balance.
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