Sanjay Srivatsan
@SRsrivatsan
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Assistant Professor at @fredhutch . Previously, @UWproteindesign , @uwgenome , and @NIAIDNews . Building sequencing tools to explore biology.
Seattle, WA
Joined December 2013
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Thrilled to announce the opening of the Srivatsan Lab () at the
@fredhutch
. The lab will be building new sequencing technologies to understand how our cells and bodies form over the course of development.
The newest
@FredHutch
Basic Sciences lab opens its doors! The
@SRsrivatsan
Lab is developing new sequencing technologies to interrogate structure-function relationships during vertebrate development. The lab is growing and hiring at all levels:
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I'm virtually defending my thesis next Wednesday from 3:30 to 4:30 PM PST 🥳🥳🥳 I'm going to be talking about two single cell technologies I've developed, one for chemical genomics and another for spatial transcriptomics. DM me if you're interested and I can forward a link.
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I've been working at the
@seattleflustudy
with
@lea_starita
for the past month and we've been trying to work out (along with others) how to circumvent RNA extraction. In this brief paper we put forth a very simple protocol -results are *preliminary* (1/n)
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Elated to have our paper () out this week
@sciencemagazine
, I can't thank
@joselmcfaline
,
@vram142
,
@JShendure
and
@coletrapnell
enough. I've learned so much over the course of this project -- beyond the science the people we work with is most important
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Check out our paper —>
Our paper on sci-Space, a spatially resolved version of sci-RNA-seq, is out today!
Led by
@srsrivatsan
and
@mregier13
, Joint work with
@JShendure
and
@kellystevenslab
. (Art by
@nigelsussman
)
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Check out our latest, where we use scaled single cell sequencing as a phenotyping tool. One of the key conceptual advances is the ability to estimate variation in organismal phenotype by resolving cells to individual organisms with at least n=8 replicates per condition.
Our preprint on deep phenotyping of genetic perturbations of zebrafish embryos with single-cell RNA sequencing is now online. Led by
@LSaund11
and
@SRsrivatsan
, with David Kimelman,
@CeciliaMoens
,
@RaibleLab
and
@JShendure
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Pour out a virtual 🍺 for projects that didn't pan out. I just cleared out 10 freezer boxes full of constructs and primers. I can still remember the excitement I felt when I cloned each gene or made each plasmid
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I'm so sad, shocked, and heartbroken that Debbie is no longer with us at
@uwgenome
. Her mentorship style had the effect of making you feel singularly unique. I know we're going to feel her absence at research reports and miss hearing the crazy stories she often regaled us with .
NHGRI greatly valued Debbie’s wise input. Here she is at a June 2018 town hall
@UW
, an early event in the Genomics2020 Strategic Planning Process that yielded the 2020 NHGRI Strategic Vision. The other photos are from the Finale Meeting for the 2011 NHGRI Strategic Vision!
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Congratulations
@JShendure
!! So proud to be in the Shendure Lab where doing science is always fun
Congratulations Jay Shendure of
@UW
, newly inducted
#NASmember
!
#NAS160
#genetics
#molecularbiology
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Finally, none of this is possible without the incredible infrastructure and set up
@seattleflustudy
by
@mjonasrieder
,
@HelenChuMD
,
@LockwoodDNA
,
@debnick60
,
@lea_starita
,
@JShendure
and many others. They have been tireless and single-minded in getting ahead of this pandemic.
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It was a blast to see y'all!! I feel like this is very on-brand for a MSTP student
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I’m very thankful to get this work out there. Last March I had my doubts as to whether COVID testing could be this simple, so it was heartening to see many other groups converge on the same solution
Terrific backstory on SwabExpress and
@UW
's Husky Coronavirus Testing Program.
@SRsrivatsan
@bethkarenmartin
@lea_starita
@LockwoodDNA
@HelenChuMD
and many other
@BrotmanBaty
@seattleflustudy
students and staff
SwabExpress:
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One thing I've learned from this pandemic is that the science community is amazingly open and willing to work together.
@srikosuri
is a great example -- he's put an incredible amount of energy behind coordinating , connecting and communicating between groups. (7/n)
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I was personally a little freaked out when a protocol this simple was giving us such good results. Luckily
@bjorn_hogberg
notified me of this excellent paper where they present very similar results. (6/n)
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Thank you
@OMIBS_MBL
! The course put together by
@bewersdorflab
,
@AlisonJNorth
, Jacqueline Leung, Andrew McCall,
@angiedidomenico
,
@LessardMark
and
@ImagingBridg
was amazing and comprehensive.
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😬😬😬😬😬
I'm virtually defending my thesis next Wednesday from 3:30 to 4:30 PM PST 🥳🥳🥳 I'm going to be talking about two single cell technologies I've developed, one for chemical genomics and another for spatial transcriptomics. DM me if you're interested and I can forward a link.
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I'm so happy for Jennifer Doudna and Emmanuelle Charpentier. Somehow, I had Jennifer Doudna as my Bio1A professor at
@UCBerkeley
. I had no idea at the time (2009) *WHO* it was that was teaching us about the central dogma and basic molecular/cellular biology
BREAKING NEWS:
The 2020
#NobelPrize
in Chemistry has been awarded to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing.”
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I’ve had a fun and fantastic science week. Spent last Friday with
@arjunrajlab
and this week I was hosted by
@satijalab
first at
#nyunextgen19
and then just hanging out at
@nygenome
. If you’re ever in Seattle and want to come to
@uwgenome
let me know!! I’d love to pay it forward
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Using either heat inactivated virus and COVID-19 positive swabs collected from study participants, we find that simply vortexing a swab in a simple buffer followed by RT-qPCR is comparable to conventional RNA extraction methods. (2/n)
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maybe **just maybe** this is a good time to bring down the journal pay walls
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The idea presented here is to collect a dry swab and forgo having to put the swab into viral transport media. This is not a new innovation. We spoke with
@SmallRedOne
who told us that her group has been collecting dry swabs in Wales for more than a decade. (5/n)
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@sciencemagazine
@joselmcfaline
@vram142
@JShendure
@coletrapnell
I promised myself I would keep the twitter to a minimum until I update the GitHub README . There you'll not only find all of our analyses, but also the order forms to order hash-oligos.
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that feeling when Supplemental Figure 2B is actually the most consequential figure
Back to my favorite scatterplot...
We now have more than 750 counties, with a pretty good mix of sizes (but there are thousands of other counties still counting!)
Biden currently overperforming Clinton by 1.7 points on average
Regression equation: Biden = 1.04 * Clinton + .005
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So proud!! Check out my wife's company and mission. She's implementing her PhD work and trying to bring affordable drinking water to people that need it worldwide.
Thanks
@venturewell
for highlighting and supporting my work, I am so excited to get started and to launch the SAFR pilot through Global Water Labs!
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We're going to continue collecting swabs and stress testing this, but one thing I've become acutely aware of is that each facility needs to start performing experiments and filing for paperwork to get FDA approval for new testing. (8/n)
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Hetero 894-mer 🫠
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Preventative quarantine log (day 3) -had a thought when I woke up this morning, what will happen to my HEK293T cells?
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My lovely wife is a finalist for
@SVPSeattle
’s fast pitch! Check out her pitch here give her company Global Water Labs a vote. It only takes a second :)
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I usually don’t click these bioRxiv articles without recommendation, but this title drew me in immediately
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Currently, swabs are collected and placed in a solution called viral transport media. This media has generally been used to keep the virus alive, presumably for viral culture. Unfortunately, the high salt concentration or another aspect of these solutions inhibits PCR (3/n)
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I had a fantastic time learning from
@davidkmyang
and the rest of the
@8vc
team. If you have any questions about it or if you’re ever in Seattle, reach out! I’m always excited to have conversations about the future of biotech
@ElliotHershberg
@JamesADiao
@Kristinali
@chloehsu0
@saigourisankar
@SRsrivatsan
Highlight was bringing together this group as well as the 5 fellows from last year into SF. Excited for the next cohort - if you're a PhD student or postdoc with an entrepreneurial interest, be on the lookout for our application cycle / DM me to get on the mailing list!
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Getting this information out there early will hopefully get others to test, try and adopt.(9/n)
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Just added ~100 more shots 💉, hope today is another record setter
Today is another big day for US vaccinations:
3 days of ~3 million
CDC corrected (due to Δ cutoff):
Friday 2.92 million
Saturday 2.98 million
Sunday 2.96 million
Now 27% of all adults with ≥ 1 dose
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@fredhutch
My vision is that these data will be used to train models that can then generate new instances of biology so far unexplored by evolution -- think
@UWproteindesign
's RFdiffusion but for cells and tissues. The future is going to be crazy and cool.
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@sciencemagazine
@joselmcfaline
@vram142
@JShendure
@coletrapnell
I can't emphasize how cool I think this technology and combinatorial indexing are. We're currently working on a page to build a more connected and communicative community around the family of "sci" (single-cell combinatorial indexing) techniques.
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To get the viral RNA out of this solution, current testing facilities perform RNA extraction on the viral transport media. Right now there are huge shortages of both RNA extraction reagents and viral transport media. (4/n)
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This is such a huge problem in medical education and it’s a reflection of this society’s values. Show us more black and brown patients
1/ I am a third-year medical student. Yesterday, I was assigned a new patient. I hadn’t met them yet, but knew they had presented with liver-related symptoms. In preparation for morning rounds, I flipped through their chart and checked their lab work.
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Thank you
@VirusesImmunity
!! This is super useful.
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Mapping connections
CICERO joins elements
With single cell ATAC
#ChromatinHaiku
@ChromatinHaiku
@HPliner
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My favorite part of this project was working with
@LSaund11
🥰🥰🥰. Science is so much easier when you have a friend to share in the bad and in the good parts of the endeavor.
I'm excited to finally share my postdoc work, co-lead with my dear friend
@SRsrivatsan
, establishing a framework for time-resolved, multi-scale phenotyping of whole zebrafish embryos. See Cole's thread for a semi-brief digest of our findings! 🐟🧬
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Congratulations
@joselmcfaline
!! Super happy for you! I’m also very grateful to have received your mentorship for the past 5 years and I’m excited for your future trainees!
I am very happy to share the official announcement!!! I look forward to starting my lab
@ColumbiaBME
.
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Thanks
@vram142
!!
Congratulations
@SRsrivatsan
et al on a spectacular study (& quite the thesis capstone =P). Spatial, cellular transcriptomics with sci-Space! So excited to see where you take this next.
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One of the best departments in terms of faculty and science vision. Also in a beautiful and historic building that has a scientific history to match. Couldn’t recommend this position more
UW Genome Sciences has an opening for a computational biologist at the assistant professor level. Deets 👇
Come and join an incredibly vibrant and collaborative scientific community in beautiful Seattle!
Please share / RT
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Fantastic talk today from
@MargaridaMCM
@uwgenome
highlighting her work . I can’t wait to see what you do next!!
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Thanks Sam!!
Congratulations,
@SRsrivatsan
,
@joselmcfaline
, and
@vram142
on sci-Plex! Amazing work from the labs of
@JShendure
and
@coletrapnell
!
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This is such an important side-by-side. It's easy to forget he absolute scale when we deal mostly in abstractions
a counterintuitive image of mRNA next to its protein via (can't retweet an image?)
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This reads like for an amazing advertisement for
@nygenome
center. Really fantastic work, bravo
@nevillesanjana
and team!
As promised, here’s an overview of our study to find host factors required for SARS-CoV-2 infection in human cells. We use a genome-wide CRISPR screen to identify genes (& key mechanisms) that might be therapeutically targetable to prevent viral infection.
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I love reading these threads as a non geneticist. The conversation here is fantastic and I wish all of Twitter were like this
@leonidkruglyak
@GENES_PK
Analogy: ppl super excited about reducing breast cancer thru high risk strategy (find and Rx BRCA1 mut carriers); clearly that’s not better than pop’n approach to reduce breast cancer incidence
Why would obesity be any different? Should evaluate both high risk and pop’n based
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@UWproteindesign
@joselmcfaline
@LSaund11
@vram142
@HelenEisenach
If you're interested in working with us, or talking since get in touch. I believe whole-heartedly that this is one of the greatest times in history to be a biologist.
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Bad take. Running some model or program doesn’t make one qualified to interpret them. This is a massive field in and of itself
@random_mommy
@JAMA_current
@UCIrvineSOM
you can read my reply in the thread with an essay I wrote 6 years ago. Nice that you are a geneticist but you are in a rarified discipline and the next generation of doctors should be well grounded in
#genomics
and bioinformatics
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One of the sharpest thinkers I know. Congratulations and best of luck
@TheNobleDust
!!!
Goodnight, Seattle. Good morning, London! Soon I’ll be starting as a new group leader
@TheCrick
. 1/6
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🍑🍑🍑🍑🍑🍑🍑🍑🍑🍑🍑🍑🍑🍑🍑
Joe Biden has surpassed President Donald Trump in Georgia, a state where no Democratic presidential hopeful has won since 1992. The race is still too close to call, but it’s a major moment as Biden has now erased Trump’s edge.
#gapol
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The human genome project is done!!
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Landing this role has been the culmination of decades of effort with the help of many wonderful advisors, collegues and collaborators along the way. Just to name a few, I couldn't imagine getting to this point without the support of my advisors
@coletrapnell
and
@JShendure
.
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Still can’t get over how cool this is. This has to be he future of scientific talks and visualizations
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“We all live and move in the crafts that we have built for ourselves” a quote from
@KarlDeisseroth
’s projections. Resonating with me atm, as I start to realize how formative my years at the NIH’s VRC were
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Congratulations
@ZernickaGoetz
and
@GianlucaAmadei1
. I remember when I first saw these data and feeling like we had entered a new era. Truly remarkable to see a decade of work result in this.
Our paper is finally out! After 10 years of model building we generate complete embryoids from three types of stem cells - they develop heart, brain structures and more. We show the first proof of concept knocking out a gene required for neurodevelopment
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does anyone have thoughts on the intersection of NFTs and science? would someone want to buy/own a famous gel or own an experimental result?
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🤙🏾
@uwgenome
is an amazing place to work! The people in the department are congenial, kind and always willing to lend you their time.
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@fredhutch
Development spans a massive length scale, and can unfold rather quickly. Understanding the diverse processes that occur will require many measurements at a scale that only sequencing can achieve.
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I’m interested in creating a biology paper version of this chart
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Huge update to the sci-RNA-seq protocol!!
Excited to finally release an update to the sci-RNA-seq3 protocol, building on the amazing work of my former bay-mate
@junyue_cao
, who left to start his own lab at Rockefeller.
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This is the dream team!
Huge props to everyone who was involved in generating this absolutely critical data.
@UWVirology
:
@pavitrarc
@GreningerLab
,
@seattleflustudy
:
@HelenChuMD
@lea_starita
@BrotmanBaty
@JShendure
@famulare_mike
Jan Englund Mark Rieder (and others I'm missing here) 8/8
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This software is pure brilliance. It was literally on my to-do list to install and work with it today🤘
I'm happy that kallisto | bustools is now published
@NatureBiotech
coauthored with
@pmelsted
, L. Liu, F. Gao,
@LambdaMoses
,
@lioscro
,
@VeigaBeltrame
,
@kreldjarn
,
@JaseGehring
, &
@lpachter
. A 🧵 on how to use these tools to preprocess any scRNAseq:
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Question to my virologists out there: What makes a virus seasonal vs. not at the host/pathogen or molecular level?
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Congratulations
@mwdorr
I have loved this since the very beginning. Awesome to see it out in the world!
A high throughput screen of a yeast gene-fragments based on growth selection yields dominant negative polypeptides for many genes.
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"Finally, a study with students in the age range of 9 to 13 shows that the understanding of microscopy increases significantly after working with the LEGO microscope."
Could help 30 y.o. PhD students too 🤔
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Explaining how
@McLellan_Lab
designs vaccines is one of my favorite things to do right now. Structure based vaccine design is amazing. If you’re not familiar I would check this article out.
Great article on the development of the
@moderna_tx
COVID-19 vaccine and the role my lab played in collaboration with Dr. Barney Graham and his lab at the VRC
@KizzyPhD
:
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Day 13 - still trying to figure out this weekend thing
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👏democratic👏reforms,👏the👏supreme👏court👏is👏not👏a👏democratic👏institution👏
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Really great to see
@McLellan_Lab
’s work today at the Fred Hutch. Time to fast track that RSV vaccine!
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Check put my friend Brian’s work on protein design with Foldit!! Citizen scientists can design folds previously unexplored by evolution using the power of human creativity :)
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Checkout
@lsaund11
's new pre-print that is out today! She used scRNAseq in conjunction with various genetic knockouts to map how thyroid hormone signaling contributes to pigment cell differentiation. Also checkout her fonts and colors. She especially <3's papyrus.
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It's really fun to work with
@joselmcfaline
. He was my mentor through graduate school and I'm so grateful. If you do end up applying, contact me and I can give you the scoop on how to get under his skin ;)
We are looking for a research assistant to join our lab
@ColumbiaBME
. Our lab develops and applies single-cell genomic tools to understand how cancer responds to therapy. Join us!
To apply:
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😤😤 so proud 😤😤
🎉Warm congrats to our own
@ColumbiaBME
Prof. José L. McFaline-Figueroa
@joselmcfaline
on winning a
@NSF
CAREER Award for his work to define molecular changes induced in
#cancer
cells after exposure to anti-cancer therapy. Well deserved!
Read more:
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Congratulations team!! It’s been thrilling to see this develop and so amazing to see how it has reshaped every part of the lab.
DALL-E’s amazing images are popping up all over the web. That software uses something called a diffusion model, which is trained to remove noise from static until a clear picture is formed.
Turns out diffusion models can design proteins too!
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Glad you enjoyed it, this totally made my day 🙃
I just attended the third part of the Spatial Transcriptomics
@isscr
event and it was superb. All of the speakers really were FANTASTIC but
@SRsrivatsan
presentation was something more! It is my favourite of the year so far 🤩🤩
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Couldn’t be happier for a fantastic team. So excited to see what comes next and how this scales
Today we publish a paper in
@ScienceMagazine
that expands nanopore readings to the proteome:
a nanopore-based scanner to read off PROTEINS at the single-molecule level! 🤩
Awesome experiments by postdoc Henry Brinkerhoff of our
#CDlab
, with MD simulations of
@aksimentievLab
1/x
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The future of vaccines has never been so bright! Congratulations
@kanekiyom
@DanLikeProteins
@KingLabIPD
and others! Can't wait to see the next generation of vaccines come into use
Happy to announce that our work on broadly protective nanoparticle-based influenza vaccines has been published in Nature!
Supraseasonal flu vaccine = protects against seasonal flu even when that year's strain prediction is off, plus some more
1/9
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This is surreal. I was in shock when I heard the news. As a kid, Kobe taught me that 99% of the hard work is done off the court
Can't believe this is happening. Kobe inspired me to watch and play the game before I could make a layup and to work my hardest in all of my endeavors. Rest in heaven Mamba.
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genomics has come a long way too. Currently, reading this
@JShendure
article
which makes this very obvious. Not sure I would recognize these instruments at all
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@RonZhu2015
bravo! I’m floored watching
@ElowitzLab
present Multifate — one of the most captivating talks I’ve ever seen
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😅🤙
why are the only acceptable hobbies for academics running and rock climbing. i will never want to do either of those things and i don't trust people who enjoy them
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Congrats
@HPliner
!! Hopefully scRNAseq-ers are going to save time wasted annotating cell types and instead dig into interesting biology! Curious as to whether the community will use these trained models to inform antibody marker selection for FACs.
Very proud to announce "Garnett", a software system for rapidly annotating cells according to type in single-cell RNA-seq. Written by
@HPliner
with
@JShendure
. Software: and preprint:
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They may be able to take advantage of this really great feature in zoom where the host can mute one of the participants
Only thing worse than last presidential debate: next presidential debate on Zoom.
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Congratulations, I am so freakin proud!
Another exciting day for structure-based vaccine antigen design! The Moderna vaccine also encodes for the prefusion-stabilized (S-2P) spike that we (
@goodwish916
) designed back in 2017 as part of a collaboration with Barney Graham,
@KizzyPhD
,
@WardLab1
, and others.
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If you dont follow
@trvrb
, do it. His work exemplifies open science, science communication, and rigor. I've learned so much by observing him engage with other scientists and the public.
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Fantastic conversation between Trevor Bedford and Margaret Brennan describing the new variants, vaccination and immune pressure.
@FaceTheNation
@margbrennan
@fredhutch
Thank you
@margbrennan
and
@FaceTheNation
for having me. Looking forward to this discussion.
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~12 hours of microscopy 🔬🏎️💨
Lab 1: course managers, Jacqueline & Andrew, as well as course facilitator Bridget teaching our
#OMIBS2022
students about sample preparation!
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Very cool combination of combinatorial indexing and droplet microfluidics! I guess this is another Datlinger/Bock paper that’s a must know
Very excited to share our new preprint describing a method for ultra-high throughput single-cell RNA-seq
#scRNAseq
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I also did a short postdoc
@UWproteindesign
working under David Baker, where I learned what it feels like to really dream and create. Hopefully, I can capture and amplify that essence in my own lab.
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Congratulations Erika!! Excited for to see what you build in this next phase 🤖🦾🦾
Happy to report that I've joined the faculty of
@TheCrick
Institute in London as a Principle Investigator! I lead the Biodesign Lab, where we use 🤖 Robotics-Accelerated Evolution 🧬 to push the limits of biotech for use on Earth 🌎 and in Space 🪐
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What if our government explained it this clearly?
This is how Angela Merkel explained the effect of a higher
#covid19
infection rate on the country's health system.
This part of today's press conf was great, so I just added English subtitels for all non-German speakers.
#flattenthecurve
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