Benoit Bruneau
@benoitbruneau
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Cardiovascular disease researcher, developmental biologist, and Oakland resident. Je cherche a comprendre.
San Francisco Bay area
Joined April 2010
"single cell RNA sequencing reveals" in a paper title is the current science equivalent of "feat. Pitbull".
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Grant writing. 1% actual writing, 50% procrastination, 20% making sure nobody has done this in last year. 29% freaking out that I will never do science again. I’m OK thank you.
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PI back at the bench for the one thing he still can do better than anyone else.
Turkey sent a 51 yr old guy with no specialized lenses, eye cover or ear protection and got the silver medal
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If I see another paper titled “Single cell RNASeq reveals…”
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Thrilled to announce that I’m the new director of the Gladstone Institute of Cardiovascular Disease! A singular honour to follow in the footsteps of Deepak Srivastava and Bob Mahley. Excited to serve and help propel cardiovascular research forward!.
Congrats to @benoitbruneau who was selected as the new director of the Gladstone Institute of Cardiovascular Disease!.
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Highly recommend sending authors of a paper you enjoyed a note congratulating them on their great science. Even better if it's the first author!.
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Hey everyone! I had a head-on 65 mph collision with a drunk driver a year and half ago (truth), and all I got was a contused foot. So don't be afraid of drunk driving highway head on collisions! I feel 20 years younger!
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What the hell Jeremy? What. The. Actual. Hell?!? This broke my brain @ReiterLab. Seriously though, mind blowing.
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incredible paper! Proteomics of adult and embryonic hearts shows female hearts express different set of proteins than male hearts, and KO of one these impairs cardiac physiology only in females. Awesome work from @fconlon and Ileana Cristea's labs
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well good morning all! Martin Dominguez's and colleagues' paper is out today!
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Out now! Final v of @swetansuhota‘s amazing work, now heavily enhanced. Brm KO ES cells make mesoderm under directed differentiation conditions but rapidly switch to a neuronal fate. Self-reprogramming! Whole lab pitched in; amazing teamwork! 1/12.
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A first-author John Gurdon paper is essential reading for me no matter what it's about. This one turns out to be exactly spot on for me on top of it.
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The one on the right was the first thing I bought as a new PI in 2001. It’s going in my office. My cold dead hands my dudes
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Out today, our paper on modeling TBX5 haploinsufficiency in human iPS cells to understand congenital heart disease regulatory networks! Updated from preprint, now with added classifier flavor and a side of spatial transcriptomics! Super proud of the team!
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This shows clearly that whatever "stem cell" is squirted in the heart to "repair" does nothing more than a macrophage mediated wound response with ECM remodeling. (previously on bioRxiv but out today in @nature)
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just submitted a "no suggestions for improvement" manuscript review. I love when I can do that.
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Very sad to report that my PhD advisor, Adolfo de Bold of the Ottawa @HeartInstitute passed away yesterday. He taught me how to be a scientist. He discovered Atrial Natriuretic Factor, which established that the heart is an endocrine gland that helps regulate blood pressure.
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Deleted Mastodon account. I can’t or don’t want multiple platforms and if this one goes down so be it. I have other things to do.
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OK this time the genome is really complete, we promise.
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20 years ago today I rolled up to the McMaster building @SickKidsNews after a road trip from my postdoc in Boston with my friend Jim, a ficus, and boxes of plasmids. The lab was born that day. Feeling old but proud after a wild 20 year ride! Happy lab anniversary!.
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Tanya loved taking pictures. I'll be posting some of the ones I used to make a book for her last birthday.
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Bonkers paper! From TF cooperatively and interdependence to crystal structure to biochemistry to human genetics! Tour de force from Joanna Wysocka's team including @seungsookim10, @jussitai, @snaqvi1990, and others:
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Trainees and junior faculty are seriously constrained to network and therefore advance their careers at virtual meetings. This should not be underestimated as personal connections and visibility are really important. This is a disaster.
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Predicting genome folding from DNA sequence with Akita. Awesome work from @gfudenberg @GladstoneInst @GladPostdocs in Katie Pollard's lab. It works! It's amazing!
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Finally a noble use of machine learning! “Predicting and improving complex beer flavor through machine learning” | Nature Communications
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New preprint from the lab! Live embryo imaging of precardiac mesoderm and early heart tube formation in the mouse embryo, from gastrulation to linear heart tube. Led and executed by Martin Dominguez, with help from @alexisleighkrup and @jmmuncie. 1/14.
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Cool paper from Pennacchio lab. But 4.5 years (years! almost 5!) in revision! Yikes.
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WOW! increased pH in embryonic tail bud leads to increased b-catenin signaling to favour mesodermal induction. I'd say that's a pretty *basic* mechanism! @PourquieOlivier lab
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And yes that’s why we need basic research. Boom. Done.
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16 yo F1 following in his papa’s footsteps (at least for the summer!) @GladstoneInst @TheConklinLab
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25 page 10,000 word response to reviewers. I hope they love it.
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Hot off the press! First copy of the volume Paul @GroupRiley and I put together. Thanks to all the authors who made this a great adventure. All chapters online here:
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My lab is so awesome. They came in on the weekend to decorate my new office. So touched. I’m a really lucky guy. (yes, two Justins and on the wall both Ryans, Keanu, poutine, Drake, Sandra Oh, and more)
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In new issue of Cell, an interview with Shinya Yamanaka. A quote I quite like as he reflects on puzzling results that led to exploring new fields "I want to advise young people to regard unexpected results as big chances to start something new and unique.
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16 years ago on this day I landed with a one way ticket from Toronto with Tanya, 7 month old Sasha, and our dog Laika. I’ve loved every day being here and running my lab at @GladstoneInst. 16 more?.
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Two years ago, a few days before everything shut down, we went out for our wedding anniversary. Since then more subdued but still celebrating 17 years!
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Transcription factor interactome and heart disease! Our PPG collaboration paper is online @CellCellPress. Led by @barbaraglezt and @moepittman involves @dsrivastava_md Katie Pollard, @BrianBlackUCSF, @KroganLab @BruceConklin and many others.
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and in other funding news, thrilled to announce that Katie Pollard and I have been awarded a @4DNucleome project! Thrilled to be part of this excellent group
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Already a year gone by. Feels like yesterday.
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I’ve published my paper just by thinking about it. This is great!.
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Geneformer is here! Transfer learning to make fine predictions of gene regulatory networks and their alterations in disease. Amazing work from @GladstoneInst investigator Christina Theodoris @TheodorisLab and colleagues incl. @patrick_ellinor @XShirleyLiu .
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Having a relatively hard time balancing family/work and searing explosive anger. Any tips?.
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Yesterday while on a faculty call talking about PIs not getting feedback on rejected grant applications I received an email letting me know that my grant application was rejected and I wouldn’t get feedback.
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This is so terrible. That it went on for so long. And that 39 people need to figure out what to do now. Also: 39 people for one lab?.
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My wife’s side of the family is from Kyiv. Most of them emigrated when Jews were expelled from the Soviet Union in 1978. But some relatives are still there. My mother in law is with us and she is anguished in addition to the reason she is here.
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sales folks: stop emailing about setting up a meeting. We don't have time to do this especially on a cold call. Send us materials. And please DO NOT keep emailing us repeatedly we will definitely delete actively if you do this. How is it you don't understand how this works?.
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Our latest, on CTCF binding polarity and genome folding. Led by @ElphegeNoraLab and featuring @LCaccianini, @gfudenberg, Kevin So, Vasu Kameswaran, @abbynagle, @awuebersohn and many others @GladstoneInst and @institut_curie
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landed here 15 years ago with my wife, 7 month old son, mother in law, and Laika. Feels like yesterday. Thank you to @GladstoneInst for being the best place I could ever imagine doing science, @dsrivastava_md for giving me the opportunity, and everyone who made this a wild ride.
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@CraigHorbinski Disagree. Be very selective with your time. Reviewing papers will not have you noticed by senior faculty and even if it did they don’t care about your reviewing, only your science and mentoring.
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F1 accepted to college! A good school, but the one he really wants come next. So excited. Proud of him!.
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How many of you are not taking on undergrads this year or summer because of COVID-related occupancy limitations?.
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New preprint! Led by @alexisleighkrup, single cell RNAseq and ATACseq in mouse embryos with mesoderm and cardiac precursor lineage labeling, asking how Mesp1 deficiency affects cell fate and differentiation.
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CTCF helps make chromatin loops, insulates TADs! Peer reviewed version of out now!
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hot take on dragon genome: "Unfortunately. authors assumed that the Komodo dragon evolved from primitive, single-celled ancestors over millions of years,” he lamented. “Rather than. Komodo dragon descended from lizard-like ancestors on board Noah’s Ark"
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@kanderson @CT_Bergstrom @KjblackJohn So we should not present at conferences by this argument. That even extra showy and self indulgent: look at me, 500 of you down there and only me up here, and I will only emphasize the cool parts and even literally wave my hands! And nobody can stop me or interrupt! Bwahahaha!.
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partial reprogramming to a fetal state promotes heart regeneration. Interesting concept, but I'd be nervous about the occasional continued cycling cell.
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So much for 20+ years of studying a KO mouse. Mesp1 KO without selection cassette has no phenotype.
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putting finishing touches on grant application. And as usual, I’m thinking “how could they NOT fund this it’s AWESOME!”. Man I never learn.
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Wow this is a big deal. Many of us always thought there had to be issues, but this is a heck of a scale of scientific fraud. About time, as so many patients’ hopes rested on these “discoveries”. A special place in hell for these people, and unfortunate for all those trainees.
BREAKING: Harvard and the Brigham call for more than 30 retractions of cardiac stem cell research
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latest from the lab: @austinchsu's brilliant work with Qiming Duan in our ongoing partnership with @saptarsi_haldar. Modulating transcription to dampen heart failure with CDK inhibitors.
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I would be King, and you'd be my Queen, and we would be Heroes, just for one day.
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I feel like a super-saturated solution. Totally stable and fine until one miserable molecule is thrown in and instantly I’m an angry precipitate.
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Game of Genomes! Our sequence and analysis of the Komodo Dragon genome is out!!! Led by @GladPostdocs @AbigailLLind, and amazing collaboration within @GladstoneInst and with @UCSF and many other colleagues across the globe
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It’s like those darn pregnancy tests. They just don’t work until one day they do. So unreliable.
Trump: Katie, she tested very good for a long period of time and then all of the sudden today she tested positive. This is why the whole concept of tests aren’t necessarily great
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Thrilled to share a new preprint from the lab! "A TBX5 dosage-sensitive gene regulatory network for human congenital heart disease" by Irfan Kathiriya et al.
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New preprint from the lab! Led by Irfan Kathiriya, we discovered that a sublineage of cardiac precursors is a compartment boundary required for interventricular septation, regulated by TBX5, which controls its integrity, and Slit2 and Netrin1 signaling 1/x.
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The new @CarcassBand album cover is something else. I want to use it as a journal cover submission!
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So distraught but need to share that Katja Brueckner passed away unexpectedly yesterday. She was a postdoc downstairs from me at HMS and led a great lab here at UCSF.
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Live imaging of the Sox2 locus shows no link between transcription and enhancer proximity. Beautiful work from my former student Jeff Alexander and colleagues at @UCSF
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And perhaps not surprising, Piezo1 is the stretch sensor that initiates cardiac hypertrophy. I’ve been wondering about who it would be since 1990 when I started my PhD in stretch and cardiac gene expression (in atria though)
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I am grieving. For the parents friends lost. For the year that we lost with cancer, for the hopes that we lost along the way, for the safety we lost in the car crash, for the goals that we lost with this new thing. I have hope, but it is fragile.
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My extensive research reveals that it takes 64,275 +/- 25,223 web site refreshes before manuscript status changes.
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Yesterday was at Tanya’s favourite spot. Beautiful but not the same without her.
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Tomorrow all day we're having a lab 20th anniversary symposium. So excited to catch up with former lab members!.
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It's out! Komodo dragon genome paper by .@AbigailLLind Katie Pollard, Pui Kwok et al .@GladstoneInst @UCSF @ZooATL Cool insights into evolution of metabolism and chemosensation. Was a really fun project
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One of the important things to consider is that different research institutions will have varied return to work policies, some more lax than others. This will create huge disparities with some able to move much faster than others. Will impact grants/papers etc. .
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mentioned to my 12 yo that I was on a call with some of my science heroes, she asks "are they old?" I replied that a few are but some are my age and she replied "OK so they're all old" Cold.
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on this Christmas Eve I accepted a manuscript for publication in @Dev_journal and I feel like a tiny part of Santa Claus. Happy Holidays everyone!.
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Inflammation droves a pro-fibrotic state in heart failure via chromatin remodeling. Another masterpiece by @m_alexanian and friends @GladstoneInst
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a thing I just wrote in response to a request for review: "Due to Elsevier and UCSF's lack of agreement leading to Elsevier cancelling access to their publications, I am not currently reviewing for Elsevier journals. I hope this can be resolved soon.".
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