James Fraser (A$AP J)
@fraser_lab
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Professor and Chair @UCSF / @UCSF_BTS - dynamic structural biology and open science - (he/him)
Toronto/McGill/Berkeley/SF
Joined August 2013
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Pinned Tweet
Lab cleaning day... Check out this awesome lab timeline
@robbiediaz_
generated for the lab. 10 years and going strong!
@vanben11
@RahelWoldeyes
@DanielKeedy
@benjaminbarad
@thebieldeal
@mctucsf
@ernpossible
@InspiredPhotons
@tommy_lazarou
@irisdyoung
@sauloho
@GabbyEstevam
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Some great bravery on display here at 46 minutes:
See also:
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The
@QBI_UCSF
SARS-CoV-2 interactome paper is now out on
@biorxivpreprint
: - how does the virus, with its minimal genome hijack the cell? This systematic effort expressed 26 of the 29 viral proteins and identified 332 interactions with human proteins
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🚨🚨🚨 New Preprint Alert 🚨🚨🚨 - We have identified lead-like molecules against the SARS CoV 2 Macrodomain using a combination of fragment merging and docking
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I'm still in shock from receiving the news of my dear friend and mentor Dan Tawfik's death yesterday. Danny was so gracious to take me into his lab as a visiting PhD student in 2010. I cold emailed him asking to visit, only meeting him after landing in Israel! (pic from 2010)
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Fuck you.
The Senate and the nation mourn the passing of Justice Ruth Bader Ginsburg and the conclusion of her extraordinary American life.
My full statement:
50K
6K
23K
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Congratulations to my friend and lab neighbor
@yifan_ucsf
for his election to
@theNASciences
- wish we could take one of our pictures of us not practicing social distancing right now!
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I am riveted by what seems (at least to this non-developmental biologist) as a potentially messy priority fight about GROWING MOUSE EMBRYOS FROM SCRATCH OUTSIDE AN ANIMAL 🤯 - draws my attention in part because of the use of
@biorxivpreprint
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🚨 SARS-CoV-2 data release! Today the
@QBI_UCSF
Coronavirus Structural Biology Consortium and our friends at
@DiamondLightSou
/
@IvanAhelLab
are releasing the results of a massive X-ray fragment screen on the Macrodomain, a relatively understudied, but important, SARS enzyme 1/10
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Our new dean, Kathy Giacomini,
@UCSF
@ucsfpharmacy
has appointed a bunch of faculty to her leadership group. I'm joining this group of amazing colleagues as Vice Dean of Research.
What does that mean (and why would I agree to do this)? 🧵
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Interesting (in a positive way!) seeing the Baker Lab/
@UWproteindesign
and
@generate_biomed
diffusion model preprints drop via PDF on their individual websites, not on
@biorxivpreprint
- expect this might become more normal for really fast-moving ML fields. (links in 🧵)
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Stop what you are doing and read this preprint from Dan Tawfik's lab: - it's got it all, primordial genes, phase separation, ORNITHINE! I repeat ORNITHINE! Profound implications for origin of life research. Congrats to Liam and coworkers
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Cool! Also I am incapable of not cringing reading my interview...
👏👏The inaugural
@IUCr
W. H. and W. L. Bragg Prize for outstanding early-career crystallographers has been awarded to James Fraser
@fraser_lab
(UCSF, USA) and Jean-Philippe Julien
@jphilippejulien
(SickKids/UToronto, Canada). Read inspiring interviews at
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🚨🚨🚨 New preprint alert! We teamed up with
@thisismadani
and
@nikhil_ai
of
@SFResearch
. Yes, a collaboration with
@Salesforce
(the giant SaaS company)!
TLDR: AI language models generate active proteins and we even determined the X-ray structure of one!
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Dan Salah Tawfik (1955‐2021)—A giant of protein evolution | EMBO reports
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NEW POLICY: I'm no longer reviewing papers that aren't posted as preprints/only reviewing papers that are posted as preprints
#ASAPbio
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🔔🔔🔔Calling all structural biologists (professors, trainees, industry, academia)!
#Crystallography
#NMR
#CryoEM
#IntegrativeModeling
- Now that we are publishing preprints - let's take our data release policies into the 21st century and release the data
#ASAPpdb
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Thanks! Huge honour to follow in the footsteps of previous winners like
@FujimoriLabUCSF
@HanaScientist
Congratulations
@fraser_lab
Jaime who just won the 2019 Byers Award in Basic Science for his exceptional creativity, innovation, & boldness in his science, and who contributes generously & significantly to the USCF science community
#UCSFProud
@UCSF
@ucsfpharmacy
@UCSFMedicine
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I was going to make a worm joke, but I was too busy fucking myself...
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🚨NEW PREPRINT ALERT🚨 SARS CoV 2 encodes a "macrodomain" that removes ADPribosylations, an important post-translational modification that our cells use in immune signaling. The trouble - we lack good assays and molecules as starting point for structure-based design of inhibitors
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Black Lives Matter - Here is our lab's reflection on what we are doing and what we will do better going forward:
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Our lab is recruiting for a scientist who will engage in research projects (50%) and will manage daily wet lab operations (50%). Initial science focus will be protein purification and crystallography. Please RT (and see thread below)
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Here's an action that I think
@HHMINEWS
can take to help under-represented (incl. Black) scientists. Get reviewers to provide constructive feedback to ALL applicants to its fellowships to increase the diversity among scientists. 1/3
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Returning to Montreal! Flew to SFO 12 yrs ago to start grad school at Cal, returning 12 years later as a grizzled prof
#PS31
@ProteinSociety
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Regarding AF3 and the inability to validate the claims in the paper,
@Nature
says it wants to be "in conversation" with our community around ensuring openness of the research ecosystem. 🧵
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Fraser lab juggle challenge
#2
🍔🍔🍔 - challenge by
@GabbyEstevam
, cinematography by
@jeffgraySF
- burgers by
@GottsRoadside
and
@ImpossibleFoods
!
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Just asked to review a paper - but we've already written a first draft of the review already (because we were writing a comment on the preprint "pro bono")! The editor will be happy with the 1 day turnaround - stymies my efforts to review a
@biorxivpreprint
unprompted each month!
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This is a big one! Congrats to
@TheVillaLab
for figuring out how LRRK2 decorates microtubules -
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Motivated by serving as a panelist for a "Faculty Application" lunch event
@ProteinSociety
meeting and recent tweets, I decided to write down my process for evaluating faculty applications.
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How it started…… How it’s going! Mask off day
@ucsf
research buildings! Vaccines are awesome!!!
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Come be my friend! We are searching for a new faculty member in our (awkwardly named, more on that in 🧵) Department of Bioengineering and Therapeutic Sciences (BTS).
This is a great opportunity to join the discovery/basic science community of
@UCSF
1/
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Come start your lab in our department
@UCSF
, which is one of the most scientifically diverse here!
We are particularly interested in candidates working at interfaces between exisiting strengths in the dept. and the wider discovery community at UCSF.
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Come join
@UCSF
! We are looking for new faculty colleagues, continuing our multiyear initiative fostering equity and inclusion in biomedical research. This search is joint across all discovery/basic science depts. I'm on the committee, happy to answer q's!
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@mbeisen
The only thing worse is the way that SAME WEBSITE puts the figure legend text OVER THE IMAGE - WHY??????
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New preprint from my sabbatical work in Nogales lab - Effects of α-tubulin acetylation on microtubule structure and stability - huge congratulations to first author (my mentor!) Lisa Eshun-Wilson (us pictured below in our Acetylated/dAcetylated shirts)
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First time back in the lab since April- second time since March 3rd!!!
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This is a new one!
@JCIM_JCTC
- very interested in what the "ethics policy" is for public preprint review here.
You can't rescind my review - it's out there on BioRxiv. I don't do it to help the journal, I do it to help the authors. They can choose whether to use it or not!
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Congratulations to future Dr.
@stephanie_mul
- with my electronic signature attached, the only thing standing between her and a PhD is
@yifan_ucsf
conquering his
@DocuSign
login instructions
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Postdocs: if you want to review for experience, you can review preprints and post the comments directly on
@biorxivpreprint
. No need to wait for a journal to prompt you!
What mechanism is there to get a post doc on a list to review manuscripts? I have an eager post doc that wants to gain experience?
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Didn't get a chance to watch in real time - but damned if this isn't up there with the best American content ever produced! Stunning and moving words and performance. So optimistic about what is ahead of us!
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Watched the first 15 min of Dune! The way it was meant to be seen: At 545AM… on my phone… with the Octonauts blaring in the background on my kids iPad. Really looking forward to the next 15 minutes!
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I've never read a self-own as bad as this David Sabatini lawsuit... what a fucking asshole.
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With a fair bit of turnover in the lab recently, we've been taking a bit of time each lab meeting to go over one section of the "Lab Compact, Philosophy, and Resources" document that Jen and I drafted pre-pandemic
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LOVE MY LAB (past and present)! ❤️❤️❤️
Happy 10 year lab-iversary
@fraser_lab
! Thank you for being an amazing mentor. I can’t wait to have beer AND tacos very soon.
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Or not... it's been quite an up and down few days. Very on point for 2020! I've decided to cancel my appointment. I hope someone who is less housebound than me gets a vaccine sooner because of it. Thread below for what has happened in the last few days.
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We had a great lab "mini-retreat" yesterday, outside of our lab building, Genentech Hall. The lab is 1/3 pre-COVID, 1/3 mid-pandemic joiners, and 1/3 arrived since Labour Day! It was the first time some had even met in person, so the time was right to reconnect on our science! 1/
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Check out what my twitterless friend and colleague Ron Vale has been up to in his final months around
@UCSF
before he departs to
@HHMIJanelia
- creating a 21st century biology textbook:
@ExploreBiology
focusing on the stories behind the discoveries
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I'm so happy today! I remember 4 years ago - as a vocal Canadian, everyone asked "are you moving back?" And I remember waking up after Trump won and thinking "No, this is my home now" - While I miss living in Canada in a lot of ways, I feel even more American now.
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Great profile of an
@ImpossibleFoods
scientist I know in the kids section of today's NYTimes...
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Jennifer Li was kind enough to update the lab cartoon! A lot of turnover recently means fun new captions
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We are recruiting
@UCSF
Faculty Fellows - this is a straight from the PhD to independent lab position with generous research support (and the potential to apply for additional funds, such as the NIH DP5). Details here: - nominations due 1/13/23
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Really enjoyed reading this paper: which suggests that our qFit-ligand analysis () and work by Ajay Jain () are perhaps too conservative in point out multiple conformations of ligands in X-ray structures! 55%!
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The question of the day at our older son's daycare (4 and 5 year olds)... I wish I could say he was responsible for the "soldier cells" answer, but there is another parent doing better immunological teaching to their kids, it is the
@UCSF
daycare after all
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So moved by the words of
@francesarnold
and
@KamalaHarris
in announcing the science team! watch it!
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Leaving beautiful Copenhagen! Thank you to
@LindorffLarsen
for hosting me here and showing me around. Wonderful to reconnect with
@HenrietteAutzen
and see her thriving in🇩🇰after her postdoc next door with
@yifan_ucsf
.
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So unbelievably proud of Lillian Kenner for her amazing Clement's Award Lecture for best thesis in
@UCSFBiophysics
for her PhD work with Adam Frost. Lillian was my first hire as a technician when I started my lab at UCSF and is now a postdoc at
@genentech
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one of the biggest distortions of the public's understanding of science is the idea that peer-review is equal to an unequivocal endorsement of the validity of the work. Journalists should take the responsibility to vet claims in preprints or papers equally - great ones already do
this is such bullshit - the biggest threat to the proper public understanding of science is not preprints - it's the lie we tell the public (and ourselves) that journal peer review works to separate valid and invalid science
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A benefit of open reviewing is emailing editors a link to a comment when they ask you to review something you already reviewed. How much time is lost by not having open/transferrable reviews move with the preprint/manuscript?Seems more important than universal submission format
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I'll add the exclamation point for this one!
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UCSF people! Check out - a new aggregator of all of our basic science seminar series, supergroups, special guest talks, and thesis talks. There is a cool weekly email feature too! Let me or
@_jonzhang_
know if we are missing something.
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Paper of the year! Seriously... read this! So much $ and time wasted through an artifactual signal in drug repurposing.
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One of the most shocking things about moving to the US from 🇨🇦. Here
@UCSF
, employees are not eligible for parental leave until they have worked here for 1 year! THIS IS HORRIBLE, holding people hostage. Embarrassing for our institution and our country
In our lab every person who needs maternity/paternity leave gets up to 12 months fully paid leave. The US system that fails to offer paid leave is inhuman. Having the opportunity to take care of a newborn or a newly adopted child is not a luxury it’s a human right.
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Still blows my mind that this conformational change happens in the crystal! 🤯💎- lots of exciting biophysics to do with this. May also be super important for understanding catalytic mechanism/substrate specificity of macrodomains
We also found some unexpected protein dynamics within the catalytic site of Mac1 in the crystal structures for a handful of compounds. Perhaps offering novel pockets for small molecules design? (Video by
@fraser_lab
)
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With
@Nature
toothless response to the lack of ability to validate the claims of AF3 paper, we will close our open letter for new signatures on Tuesday.
If you haven't signed - please do and make a statement about appropriate methods/code in publications
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Enjoy my prerecorded lecture while I attend to childcare this AM! A huge honour - thank you to my lab members past and present, mentors, collaborators, and family&friends!
Tune in at 15:45 CEST to hear
@IUCr
W. H. and W. L. Bragg Prize Lectures from joint winners James Fraser
@fraser_lab
(left) and Jean-Philippe Julien
@jphilippejulien
(flanked by nominators Lynne Howell and Emil Pai). Thanks to Selection Comm and all involved
#IUCr2021
@ECA_social
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A couple of weeks ago, a journal asked me to guest edit an article. I noticed it has a great preprint and said I would do it under 1 condition: I would like to post the reviews! The journal declined. So I went ahead and got 4 qualified reviewers (🧵)...
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Fellow Bay Area jews - if darkness is the 9th plague, what should we be doing with our first born right now??? Anyone got any lambsblood to paint on my doorway?
@mbeisen
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I was on the radio this morning - since Radio is an old technology, using this very old photo of me seems appropriate...
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Well it appears
@blsabatini
has deleted his account and his vile thread defending his brother…
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Congrats
@robbiediaz_ucsf
on passing your qual!
@ReddingLab
and I are proud of you!!!
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2 more review requests today where I use my gmail template (cc'ing the corresponding author, covered here...) and wait to see if I will review...
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Thank you to
@HHMINEWS
for your support of
@robbiediaz_ucsf
! For me, mentorship means supporting people in figuring out how to grow at this current stage to prepare them for the next stage of their career (whether that is in industry, policy, culinary arts, or even academia)
Congratulations to all the 2019
#GilliamFellows
and their advisers! We’re asking them: What does mentorship mean to you?
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My favourite website admin task: updating the cartoon (drawn by ex
@SEP_UCSF
student Jennifer Li). Bye:
@InspiredPhotons
,
@mctucsf
/
@MThompsonLab
,
@leahtangroe
,
@HectorChaires6
. Hi: Jen (overdue),
@joseluisolmosjr
,
@EricRGreene1
,
@willowcoyote
, Daniel and longer hair for
@ernpossible
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New (final? haha never!) collaboration with former grad student
@benjaminbarad
: Clone this website! a guide for how to start a new lab website based on the permissively licensed template Ben started 6 years ago and we keep refining
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One of the happiest days of the year - PhD hooding ceremony. Congrats to new PhDs
@stephanie_mul
and
@robbiediaz_
- here's a peek into the backstage fun with
@IanSeiple
and the view from the mainstage at the end of the ceremony!
#ucsfgrads
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congrats to Andrej Sali
@UCSF
on his election to the National Academy of Sciences! - one of heroes and most generous mentors!
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On a day when
@MichaelNADbio
gave a fantastic
@QBI_UCSF
seminar all about ADPribosylation, our preprint using Neutron Crystallography of the SARS CoV 2 Macrodomain is posted (🧵 below)
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Fuck it. I've decided to solicit some reviews for the article on my own, which I will edit and post on
@biorxivpreprint
- have 2 excellent reviewers lined up already and 1 request pending. Stay tuned....
Today
@PNASNews
asked me to guest edit an article (recruit reviewers, help guide the authors in response, etc). Since it had a
@biorxivpreprint
, I said sure ... IF ... I could post the reviews (under my name, but protecting anonymity of others) after the paper was published.
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I've been declining reviews for manuscripts that aren't posted as preprints for the last couple of months (I get about 1-2 requests to review per week). I've been emailing the authors for every paper I decline to suggest posting.
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Lab cartoon updated!!! Thanks to former
@SEP_UCSF
high school intern Jen (now Associate Scientist at RemeGen Biosciences) who answers the call every year 🙏 I am missing doing science with this amazing group of people right now and am inspired by their actions!
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We need this but for masks at meetings. Covid doesn’t spread as much by touch! Red = come near to talk to me only if you are masked indoors and outside. Yellow = comfortable talking masked indoors and unmasked outdoors. Green = I’m trying to get BA.5.
My partner went to a conference in Europe last week - they gave out wrist bands, what an ingenious idea! Red = social distancing wanted; yellow = fist pumps only; green = handshakes and hugs.
Anyone else seen this sort of thing?
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Reaction of
@robertodequincy
/
@lab_stroud
to me telling him about a X-ray structure of an AI-generated artificial lysozyme AND him in the audience (circled) as DC Phillips unveils the structure of the first natural enzyme Hen Egg White Lysozyme. Read more:
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When collecting data
@advlightsource
two things never get old: excitement from seeing diffraction from new crystals and this view!
@mctucsf
@LBNLBioSci
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Science needs ideas, people, and $. 2 years ago, I nearly ran over
@IanSeiple
biking to my sabbatical with
@NogalesLab
/
@lisaeshunwilson
. Jenna and
@D_John_Lee
joined the project. And support from
@rsanghvi
and
@adityaag
allowed us to make a big bet on antibiotics and CryoEM.
Sometime ago, we made a pledge to support one scientist annually to take bold bets with no strings attached. I'm excited to share James Fraser and his collaborators' research on tackling antibiotic resistance that was recently published Sept 23 in Nature.
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Today
@PNASNews
asked me to guest edit an article (recruit reviewers, help guide the authors in response, etc). Since it had a
@biorxivpreprint
, I said sure ... IF ... I could post the reviews (under my name, but protecting anonymity of others) after the paper was published.
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Weird flex!
Charles Chiu, an infectious disease doctor at UCSF, sequenced the first omicron variant ID’d in the U.S.
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But it can still only be called an Impossible burger if it comes from the Impossible region of France
Smart folks win, as does the planet.
@ImpossibleFoods
EU rejects plan to rename veggie burgers ‘veggie discs’ | The Independent
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Our lab is having a great "virtual" retreat this week. About a year ago we were up in Tahoe for science, skiing, and socializing. Our activities include (thread):
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A safe-for-public-consumption version of our lab's guide for COVID-19 (started on Sunday - updated continuously since then): - encouraged to share it wider by some I shared it with privately over the last few days
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