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xuebingwu.bsky.social
Xuebing Wu
@xuebingwu.bsky.social
1.6K followers 840 following 24 posts
Assistant Professor @Columbia University | Ribosome, translation, RNA, CRISPR, genomics | alum @MIT @WhiteheadInst @Tsinghua_Uni | #hiringNow xuebingwu.github.io
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Reposted by Xuebing Wu
bartellab.bsky.social
David Bartel's Lab @bartellab.bsky.social · Mar 15
Check out the latest study from our lab, led by @mhall98.bsky.social :
www.biorxiv.org/content/10.1... (1/2)
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Reposted by Xuebing Wu
srikosuri.bsky.social
Sri Kosuri @srikosuri.bsky.social · Feb 8
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Feb 3
very interesting work on ribosome cooperativity
marvintanenbaum.bsky.social
Marvin Tanenbaum @marvintanenbaum.bsky.social · Feb 3
Our paper on Stopless-ORF Circular RNAs (socRNAs) is now out in Cell. By high-res tracking and comparing translation by either single or multiple ribosomes, we find that ribosomes cooperate to overcome pausing to ensure fast and efficient translation

www.cell.com/cell/fulltex...
Long-term imaging of individual ribosomes reveals ribosome cooperativity in mRNA translation
Ribosomes cooperate through transient collisions to ensure efficient translation.
www.cell.com
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 29
wonder if we should replace 'coding' with 'canonical', i.e., lncRNA = long non-canonical RNA, as compared to long canonical RNA (mRNA)
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 29
Glad to be in the "conversation" about microproteins and other non-canonical proteins arising from noncoding translation. I look forward to continuing the discussion at the upcoming keystone symposium on microproteins
nature.com
Nature @nature.com · Jan 29
“The leaders of the Human Genome Project always knew they were just starting a conversation”

The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do

https://go.nature.com/3CupmSS
‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases
The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do.
go.nature.com
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 15
congratulations! @nadavahituv.bsky.social and @vagar.bsky.social
nadavahituv.bsky.social
Nadav Ahituv @nadavahituv.bsky.social · Jan 15
Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE.
www.nature.com/articles/s41...
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 15
sorry for steering off-topic but I think it's going to be very distant in the future for humans to escape death. and likely long before that, they will figure out how to solve the issue you brought up
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 15
the global cultural shift was in turn driven by industrial revolution. slavery existed for 1000s years around the world. there are many cultures that do not tolerate slavery. they did not end slavery globally. without Industrial Revolution to connect the world, I bet slavery still exists somewhere
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 14
To me ultimately it is new technology that drives societal progress, doesn't matter whether it's the old or the young invents those technologies. It's unclear to me whether extending health-span will slow down technology innovation. It could be the opposite.
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Reposted by Xuebing Wu
bwjones.bsky.social
BWJones @bwjones.bsky.social · Jan 13
Dear meeting organizers:

Picking the same senior PIs to keynote/give talks at meetings, who's talks I've seen a dozen times already, is not a great use of everyone's time. Nor does it highlight all of the rich talent in your field from more junior folks and peeps not at "elite" institutions.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
6, I was really surprised to find that most refseq annotated microproteins remain uncharacterized. This includes 11 out of the 13 proteins shorter than 30 amino acids, many if which are highly conserved. To me, these are low hanging fruit for function studies.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
5, should the field pivot from riboseq annotated microproteins to those annotated by mass spec? While fewer in number, ms supported microproteins still total in the 100s and could expand significantly through targeted proteomics in diverse samples.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
4, for most hits, DNA or RNA based noncoding functions have not been ruled out, which should be the default hypothesis for KO phenotypes. Most studies did not adequately rule out translation dependent but protein independent functions, ie only the act of translation is functional
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
3, eg for lncRNA derived microproteins that show KO phenotypes, the majority do not have CRISPRi KD phenotype. I'm still trying to understand this. If this observation holds, it may point toward a DNA based function rather than one mediated by the encoded microprotein.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
2, >90% cannot be detected by conventional mass spec but many are detected as MHC-I antigens, hinting at rapid degradation. While protein roles cannot be ruled out, most effects may arise from DNA, RNA, or the act of translation. KO screen cannot distinguished those.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
1, >1000 microproteins have been identified as functional hits across six CRISPR KO screens. However, large-scale complementary validation screens to rule out false positives are lacking. My estimate is that a large fraction of these hits are false positives, for several reasons.
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 7
We hope this review stimulates interest and sparks discussion in functional studies of microproteins. While we tried to be balanced in the review, there were some potentially controversial opinions that I intentionally left out. Here is a short thread to share those thoughts:
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 6
who said scientists are smart?
delphe.bsky.social
🦋 Gourdon Lab 🦠🔬 @delphe.bsky.social · Jan 6

🤔🙄🧪
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Jan 2
Excited to share our review article "Finding functional microproteins", published in @TrendsGenetics. It was fun writing it together with Alex and @FeiyueYang1 in the lab. #microprotein authors.elsevier.com/a/1kNCscQbJB...
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Dec 21
somehow this was the first thing came to my mind:

Interviewer: Can you explain this gap in your resume?

Me: I was updating my biosketch to the new format
eugenevalkov.bsky.social
Eugene Valkov @eugenevalkov.bsky.social · Dec 21
Interviewer: Can you explain this gap in your resume?

Me: It’s an in-frame deletion.
joachimgoedhart.bsky.social
Joachim Goedhart @joachimgoedhart.bsky.social · Dec 21
Interviewer: Can you explain this gap in your resume?

Me: I was thinking . . .
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Dec 20
congratulations! great to see this very interesting work in print
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Xuebing Wu @xuebingwu.bsky.social · Dec 20
I also believe that the current system of peer review and journal publishing is not working. I hope to witness and experience a system without those in my lifetime
mbeisen.bsky.social
Michael Eisen @mbeisen.bsky.social · Dec 19
In a world where publishing is a button and peer review can be carried out far more rapidly and effectively on public forums, our refusal to let go of a system that is slow, expensive and ineffective is causing substantive damage to science and society.
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Reposted by Xuebing Wu
johndoench.bsky.social
John Doench @johndoench.bsky.social · Dec 8
The total length of human DNA on the planet right now is thus: (3.4x10^-10) • (2 x 3.055x10^9) • (3x10^13) • (8.2x10^9) = 5.11 x 10^23 meters

Time to call in NASA!

1 *light-year* – the distance light travels in one year – is 9.46x10^15 meters...

So: 54 million light-years of human DNA!
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Dec 6
We are hiring a technician to help with CRISPR screens. Prior experience with CRISPR screens and large-scale cell culture is preferred but not required. Please feel free to share: jobrxiv.org/job/columbia...
Technician in Xuebing Wu lab at Columbia University in New York
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
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xuebingwu.bsky.social
Xuebing Wu @xuebingwu.bsky.social · Dec 4
I don't usually give feedback during the interview, in part b/c I need all the 30 min to evaluate the candidate. Now I feel like this is not right. Our feedback will be super useful for them. It's like grant review, reviewers did the assessment but comments are not shared with applicants.
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