Chris Hsiung 熊
@hsiung_chris
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Incoming Assistant Professor @UCSF | synthetic bio, gene regulation, functional genomics, tissue biology | #ClimateCrisis
Joined April 2015
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I'm super excited to announce that I will be starting my lab at UCSF as an assistant professor this Nov. in the Institute for Human Genetics
@IHG_at_UCSF
and Dept. of Surgery
@UCSFSurgery
. We are recruiting at all levels -- see for details!
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having DAPI photoconvert to emit fluorescence in GFP channel is like your best friend stabbing you in the back
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Excited to share our (with
@LukeGilbertSF
) new preprint () on a new combinatorial functional genomics platform that enables 6-plex CRISPRi pooled screens. This platform works for multi-gene targeting and is especially suited for multi-enhancer targeting.
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"I really enjoy scrolling back and forth between a figure, its caption, and its reference in the main text in an unformatted manuscript." - said no one ever.
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the biorxiv effect: when i try to go back to find manuscripts I've mentally categorized as "old news" and realize that they remain unpublished in journals after >1 year....
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@CFBISD
your apology should be to all people of Chinese cultural heritage, not just "Asian-Americans" -- Americans are not the only people deserving of apology here. also apologize to the children whose worldview & future potential suffered at your abject educational failure.
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Our preprint reporting a multiAsCas12a CRISPRi platform for >3plex combinatorial targeting of genes and/or enhancers (including 6plex in high-throughput pooled screens) is now a peer-reviewed publication! .
Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations
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Spatial analysis is converging with pooled CRISPR screens in a recent series of preprints w/ different guide readouts:
1. RCA
2. in situ txn + FISH
3. in situ txn + in situ seq
Exciting for tissue biology!
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@soylenttx
@nhills232
@joyjuheelim
@zmt021
@CFBISD
@BlalackMS
the descriptions are very positive and emphasize the technological strengths of the U.S., in multiple sentences characterizing the U.S. as "best in the world" in these aspects.
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Thank you to the
@satijalab
for inviting me to talk about our multiAsCas12a CRISPRi combinatorial functional genomics preprint () at the Center for Integrated Cellular Analysis Virtual Journal Club
@nygenome
. Super fun to interact with students and postdocs
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Neat solution to the challenge of reading out gRNAs by FISH
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Plasmids from our multiAsCas12a study are now available on Addgene ()! Would love to hear feedback -- both positive and negative -- on how well it works in your fav cell types, because that will help us make it even better in the future! Emails/DMs welcome.
Excited to share our (with
@LukeGilbertSF
) new preprint () on a new combinatorial functional genomics platform that enables 6-plex CRISPRi pooled screens. This platform works for multi-gene targeting and is especially suited for multi-enhancer targeting.
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does anyone know how split-pool barcoding style scRNA-seq performs vs. 10x GEM-based methods for detecting lowly expressed transcripts? i think split-pool barcoding is conceptually elegant but wonder whether using fixed cells as rxn chambers results in low enzymatic efficiencies
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Elegant study on cell fate decisions in intestinal organoids
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Reforming genome organization after mitosis -- from
@HaoyueZhang5
@blobelgroup
@CreminsLab
@KellerCaponePhD
@rosshardison
et al.
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@MicrobiomDigest
thank you for your important work. however, the basis of your concern of censorship here is unclear. a quick search on Baidu shows that there is active lively discussion + outrage (though there doesn't seem to be media coverage) on the Chinese internet regarding this fraud.
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@simonbchen
thank you for sharing this piece of family history, Simon. that period of China is the untold stories of millions of suffering and drama that need to be remembered.
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The gauge of a needle is the epitome of an unecessarily counterintuitive unit of measurement....
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Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells -- from
@ABoettiger
, Xiaowei Zhuang et al.
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"I really wish this paper I'm reading uses more acronyms." - said no one ever.
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@CokerRory
@Scottcrates
@thousand_points
it is not forever, see S. Korea, China. See analysis of "Hammer and Dance" strategy here
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for RT-qPCR, has anyone tried to make home-made lysis solutions for lysis of cells compatible for direct cDNA generation (skipping RNA isolation) that work well to replace expensive "Cells-to-Ct" kits?
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@michaelmina_lab
@QIAGEN
@CDCgov
Lab medicine and mol bio colleague here -- Is this a serious bottleneck? In research it is well-established that cell lysates can directly be used for RT-qPCR, for example see protocols . Was under the impression diagnostics also do not use RNA purification
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I wanted to understand the supposed narrative that China contributed to a massive delay in response to COVID19. So I took a closer look at the timeline taken at face value from this article, which is critical of China's early response .... 1/n
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@ACasadevall1
its not that people don't know how to use old school methods it's that those methods dont scale to the demand for clinical testing in terms of labor. in fact i'm surprised they arent doing one-step direct to RT, and wonder how china and korea achieved their scale of testing
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"I prefer PDF file over comma-separated text file for accessing tabular data in the supplement of papers." - said no one ever.
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@michaelmina_lab
@QIAGEN
@CDCgov
i cannot imagine China, Korea, etc can achieve their speed of testing with RNA purification steps. there are commercial "cells-to-Ct" kits such as by ThermoFisher that i've used for non-clinical research and they work well, its just one stupidly expensive proprietary lysis buffer
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happy lunar new year! especially to the many international students and scholars who routinely spend years away from their family on this holiday, and all the Chinese people who sacrificed their celebration last year in their fight against COVID19. 新年好!
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@Newsweek
Buried in article "To be sure, there's no evidence that SARS-Cov-2 came from the Wuhan lab, nor that the virus is the product of engineering. Most scientists believe...that a natural origin is the most likely explanation. But neither have they ruled out these possibilities."
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@tony_zy
How do doctors and nurses help without being mobilized to the frontline in Wuhan while local doctors and nurses are overwhelmed? How do they help without enough hospital space? How do scientists help if they werent funded or their tests blocked by bureaucracy?
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our txn after mitosis paper officially out!
@arjunrajlab
@blobelgroup
@KellerCaponePhD
@CarolineBartma1
@paul_ginart
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A new, potentially druggable, target for therapeutic reactivation of fetal globin -- maybe one day improve the lives of sickle cell anemia and thalassemia patients. congrats
@grevetjd
@blobelgroup
@jiejie_stella
@rosshardison
@KellerCaponePhD
et al.
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@PrometheusAM
@florian_krammer
Using "critisizing the regime not the people" is not a good excuse when the criticism for either is wrong. The Chinese gov responds to incentives like anyone else. Right now they r strongly incentivized to produce accurate numbers to fight the virus. Anything else backfires.
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@drdevangm
@arjunrajlab
a modified lottery system, including an initial relaxed cut-off for selecting likely meritorious proposals by peer review, has been articulated by
@ACasadevall1
and Ferric Fang
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"The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far" 😮
Loss of ETS sites in the ZRS enhancer of Shh has been linked to limb reduction in snakes. Here is another example of independent ETS site mutations in the ZRS linked to fin reduction in some lungfishes. Congrats to all authors of this tour de force study!
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Mitosis nostalgia for me -- Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition
@blobelgroup
@CreminsLab
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@dearclarissa
History? Anyone overtly anti-Japanese would've been dead? Positive selective memory due to 50yr Japanese propaganda favoring compliant ethnic Chinese Taiwanese in exchange for better treatment e.g. serve in imperial army, kill other Asians + own ethnicity
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Funny and true. However, a little know fact is that CRISPRi using KRAB fusions are relatively weaker in HEK293T compared to other cell types.
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@Caroline_Bartma
@arjunrajlab
the whole CD-19 CAR-T thing relies on the fact that we don't need B cells to live, so I think the fundamental cancer bio question, after immunologists figure out getting CAR-T to kill well, is whether there are truly cancer-specific cell surface targets for essential solid organs
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@TRyanGregory
what are your thoughts regarding their new inhaled mucosal vaccine developed by CanSino? is there any known data on efficacy?
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Visualizing DNA folding and RNA in embryos at single-cell resolution -- congrats to my lab mates Leslie Mateo
@SedonaMurphy
@toniai12
Carly Walker
@ABoettiger
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A reproducible phenomenon! :) -- Transcription spikes transiently upon mitotic exit
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our preprint on transcription after mitosis
@arjunrajlab
@blobelgroup
@CarolineBartma1
@paul_ginart
@KellerCaponePhD
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mind already blown just by this sentence in intro... "Dinoflagellate genomes are often huge (up to ≥200 gigabases), genes are organized into tandem gene arrays, individual messenger RNAs are generated through trans-splicing and transcriptional regulation is largely absent"
Excited that our work exploring chromatin organization in dinoflagellates is out now in Nature Genetics!
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"I really enjoy receiving seminar advertisements from university email listservs in the form of a PDF attachment, then manually entering the date, time, location, Zoom link, and speaker name into my calendar." - Nobody
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UNNAMED CHINA AND U.S. INTELLIGENCE SOURCES AGREE THE INVISIBLE ENEMY CONSISTS OF RIBONUCLEIC ACID
@Caroline_Bartma
PROPOSAL: super dramatic conspiracy video about covid19 but like with real science
"the virus is trying to spread itself! just by going outside you're helping its survival! WAKE UP SHEEPLE"
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interesting work showing analog epigenetic memory of transcriptional repression can be programmed
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I've really appreciated the opportunities to attend seminars by Zoom anywhere in the world at the click of a button. From the attendee's perspective I think this outweighs many disadvantages of Zoom.
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Stop assaulting the livelihoods of ethnic Chinese scientists like Gang Chen (), Anming Hu (), and now Haifan Lin.
The faculty in
@YaleCellBio
and
@YaleSCC
strongly support our colleague Haifan Lin and his entire research group in the wake of his administrative suspension by
@Yale
, a step taken without any formal charges or due process. See our statement 👇👇
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this is really cool work. the biological specificity of enhancers even when we stick them into different organisms never ceases to amaze me.
Our Jan 2023 issue is live! The cover features a gene therapy strategy from
@Ken_Poss_Lab
using zebrafish enhancers to target injury sites in small and large mammals & improve heart
#regeneration
. Read this & more here👉
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@KellerCaponePhD
I miss just sitting around chatting about random science with lab mates and people on the floor
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How do cells reestablish transcriptional output after mitosis? This study shows that some canonical gene "bookmarks" (BET proteins) surprisingly don't provide transcriptional memory, but suggests other molecules might. Will miss this epigenetics problem
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@dearclarissa
not negating the grandparents experience, but pointing out why conveying such simplistic romanticization without acknowledging the broader context of history would be offensive to others with a different heritage, if you're genuine about understanding that
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@tony_zy
i like most of your posts, and i'm being genuine here. failures, both real and exaggerated, were widely reported internationally. the bigger point is the U.S. can learn from efficiently organized societal efforts rather than only from individual efforts that make good stories.
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This
@arjunrajlab
perspective is a real gem. I feel I dodged a bullet at one point in my career when I dropped a project after ~1 year at least partially because it was too deeply dependent on skills in which I'm competent, but not the most stellar at.
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@bmart87
Onenote is great for note taking with simple UI and tables from excel sheets can be easily pasted in there without formatting issues. It is free and its longevity is backed by an entire corporate ecosystem. I find bundling note-taking with other products unhelpful for me.
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"We find that the effort researchers waste in writing proposals may be comparable to the total scientific value of the research that the funding supports, especially when only a few proposals can be funded."
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@dphansti
for TF's with very narrow peaks, the vast majority of the ChIP-seq library arise from nonspecific sticking to beads (this background acts as "spike-in"), I have found RPKM works fine. This worked for measuring global eviction of Pol II in mitosis Fig.S3.
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@tony_zy
How does anything help if ppl traveled during Chinese new years? We had an American father/daughter under self quarantine go to a school dance u think Chinese people wouldve self quarantined? We need to learn from all their failures and successes, not just individual hero worship
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An understated milestone is that Casgevy is not only the first CRISPR therapeutic, but also the first enhancer-targeting therapeutic. The remaining ~500,000+ predicted enhancers in the human genome await our exploration of their therapeutic potential.
A Welcome to the Era of Genome Editing today
@NEJM
Overview
@G_Q_Daley
Casgevy for Sickle-Cell Disease
Casgevy for Beta-Thalassemia
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Looking forward to discussing our work on multiAsCas12a at the Harvard Genome Engineering Seminar Series, thank you for the invite
@GenomeSeminars
!!
Mon. Oct. 23rd Lukas Schmidheini and Chris Hsiung -
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FYI folks who pay for BioRender: Illustrator, which you likely already pay for, has an image trace function to convert any raster graphic into vector graphic
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@Bob_Wachter
The chance of you having credible knowledge of what an actual Chinese leader thinks & how he would act is near zero. This baseless insinuation by an otherwise stellar public health communicator is pure fuel for that (very sinophobic) misinformation ecosystem you criticize.
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@Caroline_Bartma
I just want to know whether this special metabolic state is heritable through cell divisions when taken outside the mousey k thx bye - Reviewer 13
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fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
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work from Tjian lab on transcription factor binding in mitosis
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Wow. I was just thinking with the exception of hemoglobin genes I cannot think of any protein that is truly restricted in expression to one cell type. Turns out even hemoglobin is not entirely cell type specific?
A fascinating work is published today
@Nature
by Zhang & Zhang et al. on a serendipitous discovery of haemoglobin expression outside the RBC cells--in chondrocytes--and their critical role in keeping our cartilage alive under an oxygen-deprived environment.
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I wonder if masks help with another pandemic -- mycoplasma in cell culture.
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seeing some biotech vendors like
@NEBiolabs
move toward what appears to be more sustainable non-styrofoam packaging solutions from
@TemperPack
for lab reagents seems like a great direction (my DNA ligase definitely arrived cold!)
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@arjunrajlab
@Caroline_Bartma
@blobelgroup
Very impressive job considering she had to get the immunologists excited about transcriptional bursting in an erythroid cell model :) congrats
@Caroline_Bartma
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I don't see the logic behind this mistrust in this specific context. The number of new COVID19 cases in Wuhan is now reported to be Zero. By refusing to learn as much as we can from China's experience, we're exposing ourselves to greater harm.
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CASFISH -- a rapid, multiplexable genomic imaging method without denaturation, developed by my friend
@orchid_5
!
http://t.co/U6UfzwDws1
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assumptions of global normalization procedures in genomic profiling methods can be violated in obscure ways that can really come back to bite! not usually taught in most graduate training and even further obscured in the era of single cell seq.
You were told that RNA is essential for PRC2 chromatin occupancy.
We examined key evidence that previously supported this idea: it's an artefact.🧵
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wonderful graphic on the fatality and contagiousness of the Wuhan coronavirus
So had to guesstimate the data but I think this actually works OK with a normal scale instead of a log one. The Wuhan coronavirus red box is a lot tinier on this chart but... maybe that's a good thing? I'd argue this puts it in 'correct' perspective compared to SARS, Ebola, etc.
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Microsoft Excel persistently discriminates against Septin genes :(
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The media
@Newsweek
must stop this practice of writing a SENSATIONALIST HEADLINE that contradicts its own content , which is otherwise seems to be written fairly reasonably. How do you get from this paragraph buried in the article ...
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Which class of promoters, comparing the highest transcribing promoter in each class, drives the highest level of transcription?
RNA Pol I
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RNA Pol II
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RNA Pol III
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I'm deeply grateful for
@LukeGilbertSF
for his mentorship in my scientific journey in the past few years, as well as support from
@StanfordPath
Physician Scientist Incubator and the
@arcinstitute
for support and collaboration.
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We will innovate in synthetic gene regulation & combinatorial functional genomics. By perturbing combinations of genetic elements, we aim to understand & engineer interesting & therapeutically useful emergent biological properties in tissue biology.
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I find it difficult to criticize the 4-day time frame from initial notification of a completely unknown disease to concrete public health action in shutting down the market and reporting the disease to the WHO, even while mistakes were made. 9/n
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dropped freezer box weeks ago
thought i rescued all tubes
but left you in a dusty hidden crevice
promise will never lose you again
my plasmid
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follow-up question: enhancers are transcribed by many similar molecular components yet do not show directionality -- what confers the specificity to promoters? to me this is the clearest hallmark distinguishing the two types of regulatory elements.
How do gene promoters specify productive transcriptional elongation mostly in one direction?
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@Weather_West
What is the worst possible outcome for the Bay Area? What would an Australian bushfire-like magnitude event look like?
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chuckled when i randomly came across a publication with this correction line "after first online publication: The word “novel ” was removed."
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@Caroline_Bartma
the corona virus RT-qPCR was more scarce and challenging to perform than scRNA-seq in the U.S. until very recently, and thus we can still scoop other countries in high impact journals even though they already published other similar methods.
Has anyone suggested to the CDC that qpcr is no way to publish high
Why not diagnose corona virus with single cell sequencing
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@Newsweek
please stop the practice of writing sensationalist headlines that do not capture the uncertainty conveyed in the content
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@cjmaddison
@loscharlos
@useless_priest
@LaraHawthorne
@OmicronData
@chrischirp
agree, and, if assume each re-infection has 4% independent (likely a conservative assumption) risk of resulting in long covid, the cumulative risk of long covid from getting infected 3 times would be 1-0.96^3 = ~10%. Minimizing reinfections should be high public health priority.
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how do enhancers work? the plot thickens. nice work from Orion Weiner lab at UCSF "Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity"
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Nostalgia from childhood memories of new year celebrations with grandparents and extended family. Happy lunar new year! 龍年萬事如意!
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