By the way, our lab is recruiting across experimental and computational roles (scientists, postdocs, RAs) so if you're excited by the bridge RNA discovery and the potential for genome design, please contact me!
Just shared at
@KeystoneSymp
a new
@ArcInstitute
discovery of the bridge RNA recombinase mechanism: a new class of natural RNA-guided systems that retains the key property of programmability from RNAi and CRISPR while enabling large-scale genome design beyond RNA and DNA cuts
I was homeschooled until college. To show I was academically prepared in my apps, I took 8 AP exams—the max I could schedule and register for. Went to the bookstore and bought 2 prep books per exam, read all 16 cover to cover over 2 months.
That was my American high school
Assistant Professor Daniel Craig after another week of grant deadlines, re-learning the chi^2 test, and reading 40 abstracts but 0 papers. He loves his job, students, and cold brew coffee.
Is DNA all you need?
In new work, we report Evo, a genomic foundation model that learns across the fundamental languages of biology: DNA, RNA, and proteins. Evo is capable of both prediction tasks and generative design, from molecular to whole genome scale.
Just got my green card and used Global Entry for the first time. 2 sec interaction after the kiosk: “Mr. Hsu, anything to declare? No? Welcome home!”
I didn’t realize how much this could mean to me. And what it still feels like to be an immigrant even after so many years here
Delighted to announce the Arc Institute
@arcinstitute
, a new, independent scientific institution dedicated to the study of complex human disease. Working with our partners
@UCBerkeley
@Stanford
@UCSF
, our mission is to accelerate progress in biomedical research and therapeutics.
Just shared at
@KeystoneSymp
a new
@ArcInstitute
discovery of the bridge RNA recombinase mechanism: a new class of natural RNA-guided systems that retains the key property of programmability from RNAi and CRISPR while enabling large-scale genome design beyond RNA and DNA cuts
TikTok is hiring a computational chemist to "speed up classical molecular dynamics and quantum chemistry algorithms with artificial intelligence and high-throughput computational methods"🤯
The ability of molecular biologists to control DNA has relied on enzymes derived from the phage-microbe arms race. In this new work, we systematically mined thousands of new serine integrases (LSRs) and developed them for human genome editing. 🧬
Delighted to try out the world’s first CRISPR-edited salad from Conscious Foods and
@PairwisePL
. Mustard greens were edited with Cpf1/Cas12a to reduce their spiciness while retaining their nutritional content (which is 2X better than romaine lettuce). 🙏
@zhangf
for the invite
At
@ArcInstitute
, we're launching the Arc Science Fellows program for early-career scientists to start their own lab right after grad school with $250K/year research budget + salary.
I'm running an info session next Fri (Dec 16 at 1pm PT)! Sign up here:
In an era of RNA delivery and therapeutics, we sought to “write” RNA molecules directly into messenger RNA to replace disease-causing exons or engineer synthetic proteins
Our new work on RESPLICE enables fully programmable and highly efficient (45-90%) transcriptome engineering
Hot take - biology is the only one with truly difficult ideas. That’s why everyone is trying to apply math, physics, ML, etc to understand biological principles and behavior
Does biology have truly difficult ideas? Studying math, comp sci, physics, etc., one quickly encounters material that is hard to truly grasp (and many of us get to a point where we mentally just can't go further, while some others can). Does this exist in biology? If not, why?
I don't normally do this but can't resist sharing this email I recently got: "“Respected Sir, I am writing to express my keen interest in your lab, where I can utilize my experience in cut-throat scientific research.”
Excited to announce that my lab is moving this fall to
@BerkeleyBioE
. We develop new biotechnologies (and not just CRISPR-Cas!) to control brain and immune cell function for improving human health. Hiring at all levels (postdocs, grad students, RAs) -
The best coronavirus/SARS-CoV-2 biology lecture I have seen so far, by Britt Glaunsinger
@UCBerkeley
@berkeleyMCB
@HHMINEWS
@igisci
. Covers where it comes from, how it gets into the cell, replicates in the host, and exploits the immune system against you.
It takes too long to start your own lab—the average R01 recipient is 42 y/o 😵. Want to start your independent research group out of grad school?
Come to my
@ArcInstitute
Fellows Program info session next Wed (Nov 15, 12pm PT). You'll get a $250K/year research budget + salary.
At Arc, we give early career scientists a springboard for launching their independent careers through our Science Fellow program.
Learn more at our virtual information session next Wednesday, Nov. 15, from 12-1pm PST, hosted by Arc co-founder & Core Investigator
@pdhsu
. 👇
Arc should create a OpenAI residency type program where they take in software engineers and let them rotate between labs.
SWEs get to work on problems in biology + lab productivity almost certainly increases. Eventually creates an incredible hacker culture in the institute!
Paul Nurse, who won a Nobel for his work on the cell cycle, calls for more daring theory in biology and criticizes current trends in large scale data generation. We probably need to reimagine the Discussion section of papers!
Tour de force engineering
@Nature
by
@jgooten
@omarabudayyeh
discovering Cas7-11 as a collateral-free RNA targeting tool. Also a beautiful story of CRISPR evolutionary biology blurring the lines of multi-subunit and single effector defense systems
There is no shortcut to the struggle. More senior researchers went through the exact same journey. The most valuable class I ever took was an epigenetics class where we had to deep-read the primary literature. I had a special highlighter for words or methods I didn’t understand
I was thinking about Karpathy's "only compare yourself to younger you" and how I found reading AI research papers intimidating in 2022 because I didn't understand the terminology + math symbols. It really just takes practice reading 100s and then suddenly it's no big deal.
Happy to share our huge collaborative effort
@UCBerkeley
@UCSF
to systematically evaluate coronavirus antibody tests. We'll be updating with new data at - 10 lateral flow assays and 2 ELISAs so far. Read more
@nytimes
:
Great to have our study out in
@NatureBiotech
today!
>50% knock-in of multi-kilobase DNA payloads into the human genome for functional genomics, synthetic biology, and future therapeutics
He turned DNA sequencers into a biological time machine. Growing up, I eagerly read Svante’s work in Popular Science and first met him in 2016 shortly after starting my lab. His zest for life and humorous curiosity really stood out. Neanderthal Man is a highly recommended read!
BREAKING NEWS:
The 2022
#NobelPrize
in Physiology or Medicine has been awarded to Svante Pääbo “for his discoveries concerning the genomes of extinct hominins and human evolution.”
It’s an exciting time to work at the intersection of biology and AI across the spectrum from pure atoms to pure bits
Historic opportunities in our lifetime for synthetic biology, body/brain-computer interfaces, and robotics
In this new work with
@SKonermann
's lab, we developed a Cas13 platform for high-throughput phenotypic screening and, using deep learning, elucidated the design principles underpinning its RNA targeting efficiency across ~130,000 guide RNAs tiling 55 essential gene targets.
also underappreciated: reading actual textbooks long after you’ve left formal school
I have a whole spiel about the chasm that is adult learning. Remarkably few people continue to digest structured or didactic content when they don’t “have” to
The most impactful near-term thing we can do in science publishing to improve research culture is to prominently credit and display co-first authors.
It should be immediately clear. Right now, readers have to click on author contributions or decode weird superscript symbols 👇
🚨 We are hiring 2-3 more faculty
@arcinstitute
to join our current team of 4 Arc Core Investigators, who also hold faculty appointments at our partner universities
@Stanford
@UCBerkeley
@UCSF
. Your lab at Arc HQ will be fully funded for up to 20 people
It was an honor to host PG and other friends of Arc today for a sneak peek of some of our latest, unpublished discoveries
It's a crazy time to work at the interface of biology and AI. Come join us!
I went to visit Arc Institute and it was one of the most impressive things I've ever seen. They only just started and they've already made multiple big discoveries. I can't imagine a more impactful organization you could donate to.
It’s early days
@arcinstitute
but we will do our best! We’ve grown to over 150 people and have many roles that we’re continually opening on a rolling basis
Current goals are to model a virtual cell, create a new life form, and develop rational ways to target Alzheimer’s disease
Today on
@biorxivpreprint
, we combine genome-scale CRISPR activation and knockout screening to elucidate the functional landscape of SARS-CoV-2 host factors in human lung epithelial cells and systematically define their proviral and antiviral roles.
Bob Langer wasn't always one of the most famous scientists. His first 9 grant apps were rejected. No chemical engineering department in the country would hire him as faculty, so he started out in the Nutrition dept at MIT.
An energizing interview:
🧵 of insanely overlooked places to eat in SF:
yongzi ji for amazingly authentic HK-style wonton noodle soup. less than 10 things on the menu so you know it’s good. a hole in the wall run by an impossibly sweet older couple
pro-tip: add ~3:1 vinegar:soy sauce to taste
RNA targeting has vexed the field of programmable biology for 20 years since the Nobel-winning discoveries of RNA interference and CRISPR
In this new work with
@SKonermann
, we attack the problem with AI and data scale, enabled by massive screens and mechanistic interpretability
🧬New paper + tool out of
@pdhsu
@skonermann
Labs, led by
@StanfordBioE
Ph.D. student
@JingyiWei4
: a new RNA targeting CRISPR enzyme paired with a convolutional neural network (CNN) model predicting highly efficient guide RNA sequences for transcriptome engineering.
Basic science is not at odds with industry science and I don’t understand why they are perceived as competing verticals. Going to industry after my PhD made me a better scientist. We just need to make sure the flow of talent is bidirectional
You can't simultaneously say there are so many talented people so we need to add more positions and up paylines, and at the same time say academia will be decimated because some percentage of people are leaving. 4/6
Reading progress reports from
@arcinstitute
is inspiring. They get so much done so fast. They're like a startup of research. It must be very exciting to work there.
So fun to learn from
@BarackObama
about leading a 3M person organization, 51/49 decisions, and the things people don’t realize about the Situation Room. Thanks so much
@fdesouza
, for the invite!
Zoom interview tips for faculty job market:
1. Clearly link your past research to future vision - spell out your trajectory
2. Understand the dept and goals of the search. Research fit is key
3. How would you amplify your colleagues?
4. You are the expert. Own your work :)
New
@arcinstitute
building wouldn’t be complete without a new sequencer, and luckily our
@illumina
Novaseq X Plus just arrived.
Thanks
@fdesouza
for inviting us to be launch partners! We’re now ready to sequence everything
@arcinstitute
"Science saves lives" - sure, but what are the numbers?
This analysis of randomized phase III trials estimates that the (ongoing) war on cancer has generated 14.2 million life-years for cancer patients on a federal investment of $326 per life-year!
Herb Boyer was 37 years old in 1973 when he reported, along with Stanley Cohen, the construction of recombinant DNA plasmids for the first time
That work was done right here in the Bay, in a UCSF-Stanford collaboration. How do we reactivate our history of great technical depth?
"I wonder for people in their 20s if they shouldn't go to San Francisco.
The entrepreneurs are held in excessively high regard in my view.
I think that San Francisco doesn't really encourage the pursuit of really deep technical depth."
-
@patrickc
Full episode out tomorrow
German study on viral load kinetics and seroconversion timescale, out in
@nature
. Highlights huge time sensitivity of swab testing, viral loads in upper respiratory tract tank after ~5 days of symptoms (swabs are yellow line, orange is sputum).
More ML advances from
@arcinstitute
🔥
@genophoria
's lab reports in
@CellGenomics
a machine learning model that predicts RNA secretion. This will enable cool applications in noninvasive diagnostics and synthetic biology!
Are you interested in designing DNA and visualizing the generated protein?
Our team member
@ai_with_brains
just put Evo, our DNA foundation model, into a simple colab notebook so you can interact with evolution in a browser :)
Is DNA all you need?
In new work, we report Evo, a genomic foundation model that learns across the fundamental languages of biology: DNA, RNA, and proteins. Evo is capable of both prediction tasks and generative design, from molecular to whole genome scale.
Prediction: anti-aging drug development is going to hard-pivot into obesity/metabolism drugs. Semaglutide is just the first beachhead to make a big dent in healthspan for the overweight.
The importance of practicing having fun is extremely underrated. Have fun at work too! Science is hard enough and it’s way too easy to forget how cool it is that we get to build the future
Awesome to see a new Science paper from Stanley Qi at Stanford using our Cas13d system for RNA live FISH! Hundreds of labs have our plasmids, you can get them on
@Addgene
:)
Exciting! 1. No humoral responses to Cas9 detected, 2. Chromosomal translocations with triple KO detected but decreases over time (no apparent growth adv), 3. Long term engraftment - avg half life of T cells is 84 days vs 1 wk with previous engineered NYESO T cells
Following the first U.S. test of
#CRISPR
gene editing in patients with advanced cancer, researchers report findings in Science that represent an important step toward the ultimate goal of using gene editing to help a patient’s immune system attack cancer.
Congratulations to incoming Arc Science Fellow
@zhou_jingtian
for leading a landmark study in
@Nature
illuminating the epigenomic landscape of brain-wide projection neurons! We are excited to have Jingtian join us next month
@arcinstitute
!
One of the key problems in discovery science is the lack of attractive, long-term career options for staff scientists. In tech, "staff software engineer" is a highly respected position that recognizes exceptional individual contributors. I have several ideas to solve this.
I'm really inspired by our efforts
@UCBerkeley
@UCSF
@igisci
to fight COVID-19. So many incredible scientists putting our heads together. Here's how we are trying to help:
My lab is hiring for this - if you're interested in helping out, DM or email me
RNAs have been historically very challenging to drug.
@arcinstitute
and
@ucsf
investigator Hani Goodarzi
@genophoria
reports an AI framework for targeting microRNAs with small molecules (with implications for breast cancer and RNA drivers of other diseases)
Arc loves AI and RNA!
It’s Monday
@arcinstitute
! The new Arc HQ will open in Spring 2023 and house
@Stanford
@UCBerkeley
@UCSF
faculty and graduate students, as well as institute scientists, postdocs, and operational staff
Arc is building at the intersection of biology and AI.
This requires high throughput systems for model output validation and interpretation, not just more data for model training
Most importantly, we need all of these experimental and computational capabilities under one roof
Seems like tech is in love... 🧬💘
"Where do I think the next amazing revolution is going to come? And this is going to be flat-out one of the biggest ones ever. There's no question that digital biology is going to be it." — Jensen Huang, CEO of Nvidia
"Biology is the next big
☀️It’s a great week at Arc as we welcome our new Core Investigator
@genophoria
and his lab, and our first Science Fellow
@zhou_jingtian
! We’re proud to add these talented minds to our ranks, bringing with them a multidisciplinary approach to human disease research. Welcome, all!
Basic science has never been more important. To advance biology beyond a largely descriptive discipline to an engineering field, we are going to require several biotechnological revolutions. This arc will take us beyond single genes and cells to characterize systems behavior
It’s basically standard for tech company startups to have cofounders that complement and lift each other, yet actively discouraged in academic lab startups
It gets worse: in many departments, co-senior authored papers don’t even count for tenure
This should change
Had a potentially life-changing experience yesterday listening to a talk by
@BobFarese
and
@TobiWalther
and realizing the benefits of having the kind a scientific partnership that comes with having a joint lab. I’m thinking now that I would really love to do that!
my current read. what an amazing scientist. she literally just spent years vibing with corn and studying their patterns to discover the most fundamental mechanism of genetic diversity
enjoyed spending a few days exploring the latest in AI with friends and experts in LLMs, material science, chips, compute, biology, national security, and policy
thanks
@natfriedman
and
@alexandr_wang
Principles of biological computing
@Nature
- thin RecA filaments stretch throughout the cell, allow fast search for sequence homology in bacterial genomes by reducing dimensionality. Conceptually similar to hash tables
After receiving her CRISPR therapy for her genetic form of degenerative blindness, one patient dyed her hair green - her favorite color, because "I can see them a lot more brilliantly now. It's just amazing"
Congratulations to everyone
@editasmed
.
Renato Dulbecco of DMEM fame spent most of his career
@salkinstitute
. When my lab was there, we would purify CRISPR proteins in the cold room using his lab's rusty old column chromatography stands (they were all labeled with his name). I almost took one home...