Atul Butte
@atulbutte
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Chief Data Scientist @UofCAHealth・Director, Bakar Computational Health Sci Institute @UCSF_BCHSI・Distinguished Prof @UCSF・Entrepreneur・He/him・Opinions ⇨ my own
San Francisco, CA
Joined March 2011
All the data in the world will not make a difference, unless there are people ready to use it.
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Predicting eclipses is not the only thing science can do. If you loved today, you should see what we have in vaccines & climate change….
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Nice touch to boost participation! Blood donors in Sweden get a text message whenever their blood saves someone's life!
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@kristaraisa @Erika_Check @genomeresearch @Sanchitab @cdbustamante Aliens may indeed be real. But this isn't one of them.
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Thrilled! $10 million gift from Priscilla Chan & Mark Zuckerberg for @UCSF Inst for Computational Health Sciences!
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Wow, gorgeous! @UCSF releases latest designs for new Parnassus Heights hospital, working with design consultants @HerzogdeMeuron and architect @HDR_inc…
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Spent ~4 hrs volunteering as a runner today at @UCSF to help get our critical healthcare workers vaccinated. Learned a lot about the process. Opened vials good for 6 hrs. Doses have to be used rapidly after being made. We’re doing one per minute. Making progress….
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Awesome! A vaccination card (or proof of a negative #COVID19 test) will become a requirement at ~300 bars across San Francisco starting this week! via @SFBusinessTimes.
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I really believe that in 5 years, any academic medical center that ISN'T using their clinical data to improve the practice of medicine will be seen as irresponsible!.
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Wow! Companies headquartered in California can no longer have all-male boards, as per new California law signed today!
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@AuschwitzMuseum Wishing you peace. The Holocaust Memorial in Berlin was quite moving. Cannot be forgotten. Should not be forgotten.
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I think @zoom_us needs an audience button to send to the presenter "Yes, we can hear you and see your slides perfectly.".
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This is actually a big deal: the College of American @Pathologists (CAP) has secured the ability from @HHSGov & @CMSGov for pathologists to review slides remotely, blowing open digital telepathology! HT Greg Goldgof.
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Imagine for a moment, what if every time a drug failed a patient, we filed a bug report? What if we explored every treatment failure, clinically, biologically, and socioeconomically? So that it didn’t happen again in 2.0? #JPM20.
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Nearly 70% of San Francisco residents have had at least one shot of #SARSCoV2 vaccine!.
SF has given 5,538 new vaccines 💉. 1️⃣ 69% of residents (529,369) have received at least one shot. ✅ 45% of residents (342,613) are fully vaccinated. 🟩🟩🟩🟩🟦🟦⬜️⬜️⬜️⬜️.
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@DrJenGunter I say this loving phrase under my breath on occasions 😉.
Yes, well, that's the sort of blinkard, Philistine pig-ignorance I've come to expect from you non-creative garbage. #MontyPython.
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WOW, have to give credit to @Stanford on asking that their CARES act relief funds be rescinded, to leave more money for other colleges that need the money!.
Therefore, Monday morning we contacted the Department of Education to ask that our application for relief funds under the Higher Education Emergency Relief Fund section of the CARES act be rescinded.(5/6).
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Congrats to @MIT Bioengineering professor and entrepreneur @SNBhatia on being inducted into @theNAMedicine! If I’m not mistaken, that now makes you a triple threat, elected into @theNAMedicine @theNASciences and @theNAEng! BRAVO!
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BREAKING: New $50 million gift to @UCSF and @UCBerkeley to recruit 4 new 𝗷𝗼𝗶𝗻𝘁 faculty, to build a new 𝗷𝗼𝗶𝗻𝘁 PhD program in Computational Precision Health! Build real #machinelearning and #digitalhealth solutions w/ fairness & equity! Apply now!
I've always said that if we could fuse @UCSF & @UCBerkeley to tackle healthcare data science, its potential would be unparalleled. It's happened: a $50M gift will launch a joint program in Computational Precision Health, led by @Idasim & Maya Petersen. Wow.
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Electronic Health Record systems are costing billions of dollars… yet in general, we are barely using this data! Lets use this data in a safe respectful way to learn what's working in medicine, what's missing, & what might be excessive! #PSB19.
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Here's the slide I showed today at @UCSFChildrens Pediatrics Grand Rounds. What do the bullets mean? Here's a thread
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Congratulations to @UCSF for the Regental approval for our 30 year vision and plan: The Future of Parnassus Heights!
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Stunned and thrilled to be one of the 505 scientists, engineers and innovators from around the world and across all disciplines elected into the 2022 class of @AAAS Fellows! Thank you to all my lab members and collaborators, past and present!
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To me, the Republican Party is now forever branded as the party that prevented a peaceful transition of power & denied the people's vote, w/ terrorists attacking the capitol police in a coup attempt. This video should be shown against all future candidates. This is that party.
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Some of the lessons I've learned in the past 20 years working with #machinelearning in biomedicine @Stanford #cs522 #cme500
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THRILLED to finally announce today our new Program in Computational Precision Health joint between @UCSF and @UCBerkeley! New $50 million gift to recruit 4 _joint_ faculty to build a new PhD program across our two schools, led by Drs. @IdaSim and Maya Pederson!.
We're thrilled to announce that @idasim (Ida Sim, MD, PhD) @UCSF_BCHSI physician, informatics researcher, and entrepreneur will be faculty lead for a groundbreaking joint program between @UCSF @UCBerkeley computational precision health. #UCSF.
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Ok ok, I think we're reaching peak California now… we're labeling water as vegan and gluten-free?! 😜
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Finally, I can announce what a real honor it is for me to be inducted into the American Institute for Medical and Biological Engineering @AIMBE today! #AIMBE2019
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Would you get into a self-driving car trained only in Mountain View? Probably not. Then we better not tolerate medical #AI algorithms trained w/ small populations or only certain race/ethnicities!
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Out today in @NatureMedicine: our call for the building of a #DeepLearning Healthcare System! Great work by @BeauNorgeot and @BenGlicksberg! #JPM2019 #JPM19 #PSB19
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YES! Sunnyvale-based @CepheidNews receives Emergency Use Authorization from @US_FDA for 45-minute #SARSCoV2 point of care testing, can operate on Cepheid's 23,000+ automated GeneXpert® Systems worldwide!
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Wow! Six departments at @UCSF have voted to remove beef and pork from departmental events, for climate sustainability! Sustainability
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Some of the lessons I've learned in the past 20 years working with #machinelearning in biomedicine #DANS2019
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The successful future for #AI isn't going to be about evaluation of ROC curves and precision and recall. It HAS to be about evaluating how good, how fair, and how representative the training data were.
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Congratulations to @UCSF colleague and friend @Bob_Wachter for induction into @theNAMedicine for his major contributions in patient safety and quality and digital health (and certainly all your public outreach during #COVID19 kept many of us going too)! #NAMmtg
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Will say it again: I really believe that in 5 years, any academic medical center that ISN'T using their clinical data to improve the practice of medicine will be seen as irresponsible! #PSB19.
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Whoa! In @NEJM_AI: .A Multimodal Biomedical Foundation Model Trained from 15 Million Image–Text Pairs… fully open-access foundation model! .
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20 yrs ago today, I started my research career by joining @zakkohane's lab, who on my 1st day, introduced me to something new called a "microarray." I'm truly thankful for all the friends, colleagues, trainees, mentors & of course family who guided me these past 20 yrs!.
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@JakeYeston Exactly… they weren’t even close.
Back to old reliable @PaloAltoMedical Foundation; @Theranos couldn't find a vein for the venous draw. :-( What's their valuation again?.
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Thrilled to be joining the editorial board of @JAMA_current, helping @KBibbinsDomingo keep this world-renowned journal up-to-date with the latest advances in biomedical #informatics, #artificialintelligence, data analytics, and #realworldevidence .
We congratulate @atulbutte on his appointment to the @JAMA_current editorial board. Dr. Butte brings decades of experience in biomedical #informatics, #artificialintelligence, and data analytics to our board. Welcome, Dr. Butte!.
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Thanks @EricTopol for highlighting our #deeplearning paper! As you know, I'm a big fan of #AI in medicine, and I think this new field as just begun! Let's use EHR data in _safe_and_respectful_ ways to help patients and improve the practice of medicine!.
Deep learning #AI using the electronic health record input to predict the complex course of patients with rheumatoid arthritis #RA @JAMANetworkOpen by @BeauNorgeot @AtulButte @UCSF_BCHSI @UCSF @UCSFMedicine
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Humbled & honored to serve as a new member (ad hoc for now) of Advisory Committee to @NIHDirector! Amazing for me to be here, considering my 1st exposure to @NIH was as an @HHMINEWS med student researcher back in 1993! My 1st ACD; Francis Collins's last 😢
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"When we… look at the 10s of 1000s of lives in California that will have been spared… most important was that leaders of all types﹘whether they were in govt or in businesses﹘took it seriously… and did the right thing early"﹘@Bob_Wachter @UCSF on @CNN
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From @NBCNews: Virtually all hospitalized Covid patients have one thing in common: They're unvaccinated
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Whoa! @Google launches the BioMed Explorer, uses Natural Language Processing on top of @NLM_NIH PubMed to find papers and answer questions!.
Introducing BioMed Explorer, a new state-of-the-art NLP tool that expands the corpus of the COVID-19 Research Explorer ( from CORD-19 to all of PubMed. Use BioMed Explorer to find relevant papers for complex biomedical questions at
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Can you believe our _entire_ @UCSFMedicine leadership is learning today about #bigdata, #ai, models and their biases, and digital health, at our retreat today? Maybe all academic med centers should be heading this way? 😊 #JPM20 #UCSFPROUD
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Hilariously adversarial! Slowly move a wagon full of smartphones running @GoogleMaps and it appears as a traffic jam to others getting directions!.
Performance artist generates virtual traffic jams in Google Maps by pulling a wagon full of smartphones .
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Hey docs, especially those of you in Northern California: with the air quality this bad, I think we need to put #climatechange in our lane too….
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Way before CRISPR, we were excited about ribozymes, for which Thomas Cech won the @NobelPrize in 1989. One of my ideas in 1994-5 was to design software that could customize target selection, given what was known about the cutting "rules" and the known genome. My C code helped me
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300+ air in Silicon Valley right now. 200s with LRAPA correction. I can see the smoke pass by outside the house. It’s that thick. Parts of California in the 500s. Parts of Oregon in the 700s. Even an optimist like me is having trouble today. 😢 #ClimateChange
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Whoa! @Medtronic is publicly posting the design specifications for their Puritan Bennett™ 560 ventilator for innovators and engineers! HT @CatchTheBaby.
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Amazing generosity: Chuck Feeney donated $8+ billion to charities, universities, and foundations anonymously or through Atlantic Philanthropies; gave away 375,000% more money than his current net worth! 🙏🏽 from @StevenBertoni.
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@XaMoto19 @gaygaud @kristaraisa @Erika_Check @genomeresearch @Sanchitab @cdbustamante Our estimate is that this child was born only ~40 years ago. With all the abnormalities, it would be hard to live after birth without a lot of problems….
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Whoa! "The 50,000 journal articles produced annually by [ @UofCalifornia ] researchers on its 10 campuses represent 10% of U.S. output."
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@jonathanenlared @Austen Triple tap. Take more than you need. Three fingers simultaneously to paste. Trim when you paste. Took me years to learn about triple tapping.
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Wow! Israel to Sequence 100K People, Create Genomic Database to Support 'Digital Health' #PrecisionMedicine
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Thrilled @US_FDA approved drug for @Progeria! Patients organized early 2000s → @NIH R21 RFA 2002→ gene identified 2003→ mechanism in late 2000s→ candidate drugs→ first trial 2012→ yesterday’s success. Remembering the early days, friends and struggles. And remembering Sam.
FDA approves first drug for rare disease that causes premature aging in children
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I worry our medical system doesn’t yet understands the coming impact of this…
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@CaponeOFFICIAL @Erika_Check @genomeresearch @Sanchitab @cdbustamante Yeah, it's in there, very unusual mutations in a handful of genes that we know are involved in bone growth. This child just happened to get a bunch of hits across the DNA at the same time. (I'm one of the scientists involved 🙂).
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Wishing @ASlavitt all the best on his new adventure @USofCare, ensuring all Americans get quality affordable health care!
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So great to get this gift from @dvir_a as he was leaving @UCSF. Directly reminds me of an important lesson I learned from @ZakKohane, which I now pass on to those in my lab.
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Thrilled to announce our new @NEJM_AI article (!.Lead author @madhumitasushil worked with @TravisZack2 @vekennedy @divneetM @bmeow19 all in @UCSF_BCHSI @UCSFCancer. To computationally understand where patients are in their care journey, we have to.
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CONGRATS to our daughter @ButteKimi on her 1st first-authored peer-reviewed publication, this week in #JAMIAOpen! The two of us have used #wearables for many years. She analyzed 5 yrs of our step & sleep measurements & made some amazing discoveries! 🧵👇🏽.
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THRILLED to announce Philter, our new tool to deidentify clinical text. Now more than ever, safe & responsible sharing of #EHR data is needed to fight pandemics & disease, but text is hardest to share. @BeauNorgeot built a new tool w/ a great team!
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Thanks so much to my nominators Drs. Adam Wright @adamatw, Julia Adler-Milstein @j_r_a_m, William Hersh @williamhersh, Isaac Kohane @zakkohane, Christopher A. Longhurst @CALonghurst, Lucila Ohno-Machado, and Philip Payne @prpayne5! #amia2023.
Congratulations to my good friend and colleague @atulbutte for receiving the @AMIAinformatics William Stead Award for Thought Leadership in Informatics at #amia2023!
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Astounding! PubMed Central reaches milestone of 1 billion full-text #openaccess articles downloaded! Congrats!
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Remember: #Charlottesville "largest hate-gathering" only 6000. We had 100K+ #MarchforScience, 4M+ #WomensMarch. THAT'S who we really are.
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Went to an ethnic grocery today in Santa Clara. Had to get my temperature scanned to get inside.
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Wow! 26 million people have already taken an ancestry/DNA test at home? Closing in on 100 million in ~2 years?! Whether you believe in these or not, one thing is clear: with only few exceptions, the medical establishment is not part of this world.
We crunched the numbers and found more than 26 million people have taken an at-home ancestry test.
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San Francisco launching new mobile vaccination team called Vax to You, will come to you if you have a group of 5 people or more needing #COVID19 vaccines!
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BREAKING: Suresh Gunasekaran is our new CEO of @UCSF Health @UCSFHospitals, from Univ Iowa Health @UIHealthcare! 20+ yrs experience in health care admin, information tech, w/ focus on quality, safety, patient service, collaboration, operational excellence!
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Please be extra careful out there this weekend! Our #COVID19 admissions across @UofCAHealth are at record highs, with no slow down or end in sight right now. Please wash hands, wear a mask, and keep distanced.
1/7 Daily #COVID19 update from our 5 academic med centers: 1,177 #SARSCoV2 positive patients have needed admission to date in any of our 12 hospitals; 689 patients have been discharged home. @UofCAHealth hospitals cared for 211 #SARSCoV2 positive inpatients yesterday.
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Let's change "normal"! Using EHR data from a million patients to create ethnic-specific "normal" ranges… #AMIA2017
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WOW, way to go @UCLAHealth and @UCIrvineHealth! New database of more than 83,000 deidentified surgical outcomes aimed at advancing research and training artificial intelligence algorithms now online! #ai #ehr #opendata.
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6 years at @UCSF and @UofCAHealth and still love working with such great friends and colleagues!.
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Time for the cap and gown today! Graduating my first @UCSF PhD student @BeauNorgeot (and 11th for my career)!
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My slide presentation on Thinking about Twitter for Academics (presented earlier today at @UCSF) is #openaccess here and the thread below has some thoughts on each slide.
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Today I learned at the @NIAID_news #AI symposium… PubMed Central has 9.9 million full text articles (. and here's how to access each article via API in BioC XML format … even the tables are parsed out!
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Just drop the mic now, @ashishkjha!.
One for the history books!.@ashishkjha chats about #vaccines with @elmo's dad, Louie!.@RasuShrestha @AcademyHealth @EricTopol @Bob_Wachter @KBDeSalvo
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Wish you knew how Next Generation Sequencing worked, but were too afraid to ask? Check out this great tutorial from @Illumina…
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