Shijie_Zhao's profile picture. Microbiome, Microbial Genetics, Single-cell, Spatial Sequencing, high-throughput microbiome methods.

Jay Zhao

@Shijie_Zhao

Microbiome, Microbial Genetics, Single-cell, Spatial Sequencing, high-throughput microbiome methods.

The fundamental issue is a supply–demand imbalance of faculty positions. Yet as both postdocs and advisors usually spend their entire careers in the ivory tower, this reality is often overlooked. Many postdocs even choose to pretend this fundamental problem isn’t there.

As I’ve said multiple times , postdoc is the worst job you can have with a PhD in these times. I try hard to soften this blow for anyone in my lab and it barely scratches the surface..



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📢 Our Dept. of Systems Biology @Columbia has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate. Apply: apply.interfolio.com/177622 Suggested deadline: Dec 15, 2025. @ColumbiaSysBio

harriswangnyc's tweet image. 📢 Our Dept. of Systems Biology @Columbia has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
Apply: apply.interfolio.com/177622
Suggested deadline: Dec 15, 2025. @ColumbiaSysBio

This article used only one measure, "the total population of students active in SEVIS." The problem... it’s a lagging metric...

The US population of international students has defied predictions of a huge downturn. Data for the current academic year show that the number of overseas students — including PhD candidates and newly minted PhDs — has remained essentially flat, year-on-year.…



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Today in @NatureBiotech, we report engineered DNA recombinases with up to 53% integration efficiency and 97% genome-wide specificity at an endogenous human locus, inserting large DNA cargoes up to 12 kb for stable expression in primary human T cells, stem cells, and non-dividing…

Site-specific DNA insertion into the human genome with engineered recombinases go.nature.com/43kdvBg

NatureBiotech's tweet image. Site-specific DNA insertion into the human genome with engineered recombinases go.nature.com/43kdvBg


Really loved your approach! Ironically, I think humanity knew for ages that good leadership makes people happier and effective; the business and management fields worked that out long ago. Yet it takes a Nature piece for academia to realize the same applies to PhD supervision?

A recent study (shared below) reminded me that 𝐰𝐡𝐚𝐭 𝐦𝐚𝐤𝐞𝐬 𝐚 𝐏𝐡𝐃 𝐬𝐭𝐮𝐝𝐞𝐧𝐭 𝐡𝐚𝐩𝐩𝐲 𝐢𝐬 𝐧𝐨𝐭 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧𝐬 𝐨𝐫 𝐬𝐭𝐢𝐩𝐞𝐧𝐝𝐬, 𝐛𝐮𝐭 𝐠𝐨𝐨𝐝 𝐬𝐮𝐩𝐞𝐫𝐯𝐢𝐬𝐢𝐨𝐧. Over the years, I have supervised 53 PhD students, and I can say with…

ramgopal_rao's tweet image. A recent study (shared below) reminded me that 𝐰𝐡𝐚𝐭 𝐦𝐚𝐤𝐞𝐬 𝐚 𝐏𝐡𝐃 𝐬𝐭𝐮𝐝𝐞𝐧𝐭 𝐡𝐚𝐩𝐩𝐲 𝐢𝐬 𝐧𝐨𝐭 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧𝐬 𝐨𝐫 𝐬𝐭𝐢𝐩𝐞𝐧𝐝𝐬, 𝐛𝐮𝐭 𝐠𝐨𝐨𝐝 𝐬𝐮𝐩𝐞𝐫𝐯𝐢𝐬𝐢𝐨𝐧.

Over the years, I have supervised 53 PhD students, and I can say with…


Should people focus on the science instead of status?? What's wrong with the system?

Whoever reviewer wrote this , I have to say it’s my FAVORITE REJECTION YET! “Dr Rouskin got her PhD from UCSF and then became a Fellow at the Whitehead Institute. She has an outstanding publication record, with papers in Nature Methods, Nature, Nature Communications and Science…



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Another accomplishment achieved.

tangming2005's tweet image. Another accomplishment achieved.

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H3K4me3 is a post-transcriptional histone mark | bioRxiv biorxiv.org/content/10.110…

tangming2005's tweet image. H3K4me3 is a post-transcriptional histone mark | bioRxiv
biorxiv.org/content/10.110…

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I read this Cell paper that argues to have discovered a molecule (betaine) that mimics the geroprotective effects of exercise. This is a very valuable multi-omics resource, but the authors seemed to get caught in the rabbit hole of chasing a high-impact narrative🧵

MariosGeorgakis's tweet image. I read this Cell paper that argues to have discovered a molecule (betaine) that mimics the geroprotective effects of exercise.

This is a very valuable multi-omics resource, but the authors seemed to get caught in the rabbit hole of chasing a high-impact narrative🧵

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This rate of validation suggests that affinity reagents such as antibodies should be considered non-specific until proven otherwise: 357 validated antibodies out of 1,124 tested. .

slavov_n's tweet image. This rate of validation suggests that affinity reagents such as antibodies should be considered non-specific until proven otherwise:  

357 validated antibodies out of 1,124 tested.  

.

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Grateful to work with the wonderful @Vilcek Foundation and the super talented @HIROKI_OTSUKA on a short manga highlighting our research and my journey as an immigrant scientist! 🧪🦠🧬 vilcek.org/news/microbes-…


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Good news. After 2 rounds of venetoclax, GO, + chemo, my daughter has had a complete response. No detectable signs of the tumor that had completely shut her eye, which she was dangerously close to losing. 🙏🏾 to the amazing team @StJude & the community for helping us get here.

srikosuri's tweet image. Good news. After 2 rounds of venetoclax, GO, + chemo, my daughter has had a complete response. No detectable signs of the tumor that had completely shut her eye, which she was dangerously close to losing. 🙏🏾 to the amazing team @StJude & the community for helping us get here.

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1/ Still using read.csv() to load big files in R? That’s like trying to fill a pool with a teacup. Here’s how to go 40x faster.


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She nailed it!


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I'm late to review the "Illusion of Thinking" paper, so let me collect some of the best threads by and critical takes by @scaling01 in one place and sprinkle some of my own thoughts in as well. The paper is rather critical of reasoning LLMs (LRMs): x.com/MFarajtabar/st…

🧵 1/8 The Illusion of Thinking: Are reasoning models like o1/o3, DeepSeek-R1, and Claude 3.7 Sonnet really "thinking"? 🤔 Or are they just throwing more compute towards pattern matching? The new Large Reasoning Models (LRMs) show promising gains on math and coding benchmarks,…

MFarajtabar's tweet image. 🧵 1/8 The Illusion of Thinking: Are reasoning models like o1/o3, DeepSeek-R1, and Claude 3.7 Sonnet really "thinking"? 🤔 Or are they just throwing more compute towards pattern matching?

The new Large Reasoning Models (LRMs) show promising gains on math and coding benchmarks,…


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Just published! Even NASA cleanrooms—designed to be ultra-clean—harbor resilient, novel bacteria. 26 new species were found, some forming biofilms, resisting radiation, and producing biotech-relevant compounds. Check it here: microbiomejournal.biomedcentral.com/articles/10.11…

JuniaSchultz's tweet image. Just published!
Even NASA cleanrooms—designed to be ultra-clean—harbor resilient, novel bacteria. 26 new species were found, some forming biofilms, resisting radiation, and producing biotech-relevant compounds.
Check it here: microbiomejournal.biomedcentral.com/articles/10.11…

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I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs. Plant, Bacterial, Archaeal Bioeng Custom Lab Hardware Turn Key Genetic Design Please RT 💚


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Editing 14 genes is no small feat, but I am not seeing enough evidence that "it is a dire wolf". Our community needs to communicate better to the public, now mor than ever, and imo that includes not exaggerating what we can deliver.

TIME's new cover: The dire wolf is back after over 10,000 years. Here's what that means for other extinct species ti.me/4jlJB54

TIME's tweet image. TIME's new cover: The dire wolf is back after over 10,000 years. Here's what that means for other extinct species ti.me/4jlJB54


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⚡️Really thrilled that #textgrad is published in @nature today!⚡️ We present a general method for genAI to self-improve via our new *calculus of text*. We show how this optimizes agents🤖, molecules🧬, code🖥️, treatments💊, non-differentiable systems🤯 + more!

james_y_zou's tweet image. ⚡️Really thrilled that #textgrad is published in @nature today!⚡️

We present a general method for genAI to self-improve via our new *calculus of text*.

We show how this optimizes agents🤖, molecules🧬, code🖥️, treatments💊, non-differentiable systems🤯 + more!
james_y_zou's tweet image. ⚡️Really thrilled that #textgrad is published in @nature today!⚡️

We present a general method for genAI to self-improve via our new *calculus of text*.

We show how this optimizes agents🤖, molecules🧬, code🖥️, treatments💊, non-differentiable systems🤯 + more!

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In 1999, I was assigned to design the expansion pack to Age of Empires 2. I chose The Conquerors as the theme, and wishing to have 4 civs (as we had on Rise of Rome), I chose the Spanish, the Aztecs, the Huns, and the Mayans. The project went ahead extremely well. We were…

SandyofCthulhu's tweet image. In 1999, I was assigned to design the expansion pack to Age of Empires 2. I chose The Conquerors as the theme, and wishing to have 4 civs (as we had on Rise of Rome), I chose the Spanish, the Aztecs, the Huns, and the Mayans. 

The project went ahead extremely well. We were…

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