Yihui Shen @DrYihuiShen Twitter profile

Pinned Tweet

Yihui Shen

9 months

Shen Lab website is up! We will be open in Jan 2024 @pennbioeng 🥳 Come join us if you are interested in imaging and metabolism🔬 Pls retweet

Shen Lab @ UPenn

www.imaging-systems-metabolism-lab.com

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Yihui Shen

@DrYihuiShen

4 months

Excited to share my postdoc work out in @nchembio ! We explored the preferences and efficiencies of ATP pathways in cells and tissues. By quantifying metabolic flux and proteomics, we found that respiration makes ATP faster per enzyme mass than glycolysis🧵

Mitochondrial ATP generation is more proteome efficient than glycolysis

Nature Chemical Biology - Aerobic glycolysis is a hallmark of fast-growing cells, but it is unclear whether glycolysis was selected for its speed. Glycolysis produces ATP slower than respiration...

www.nature.com

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Yihui Shen

@DrYihuiShen

1 year

I’m thrilled to announce that I will be joining BioE department at UPenn @pennbioeng as an assistant professor, starting Jan 2024! My future lab is gonna have fun imaging and modeling metabolism!

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Yihui Shen

@DrYihuiShen

2 years

Why would fast-growing cells switch to aerobic glycolysis even when respiration generates more ATP? Enzyme cost? Check out our new preprint - Respiration produces ATP faster with less enzyme. Aerobic glycolysis primes yeast’s proteome for oxygen limitation

Proteome capacity constraints favor respiratory ATP generation

Cells face competing metabolic demands. These include efficient use of both limited substrates and limited proteome capacity, as well as flexibility to deal with different environments. Flexibility...

www.biorxiv.org

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Yihui Shen

@DrYihuiShen

3 years

Textbook says pentose phosphate pathway generates the reductive power for liver lipid synthesis, but it is not true. Check out this study led by @ZhaoyueZhang and @tarateslaa , where they identified the major substrate source to be serine catabolism. Congrats to all co-authors!

Nature Metabolism

@NatMetabolism

3 years

Online now! Serine catabolism generates liver NADPH and supports hepatic lipogenesis

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Yihui Shen

@DrYihuiShen

5 months

Last week has been an adventure! 1st lecture📚 @pennbioeng , 1st equipment👀, 1st lab meeting with @Caroline_Bartma lab🙌, 1st conference @SPIEtweets & 1st time as chair. Exhausted but in a wonderful way! Can’t do this without support by wonderful colleagues friends and trainees!

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Yihui Shen

@DrYihuiShen

3 months

Lunch with amazing @pennbioeng colleagues who have been so helpful and supportive in the past few months!! @noor_M0MIN @JennyNJiang @XueSherryGao And formal welcome to Sherry!

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Yihui Shen

@DrYihuiShen

4 months

This week we had a three-day mass spec training! Optimizing instrument parameters was such a fun team building activity @Caroline_Bartma 🙌🙌🙌 Look at the happy face of Hoang, who worked with a lot of mass spec data but never touched an ion transfer tube

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Yihui Shen

@DrYihuiShen

9 months

Had a great time with old and new friends in my first @BMESociety meeting #BMES2023 🙌🙌🙌 and also enjoyed my first time in Seattle ☀️☀️☀️

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Yihui Shen

@DrYihuiShen

10 months

Yay! Looking forward to exciting data from it 🙌🙌🙌

Dr. Caroline Bartman

@Caroline_Bartma

10 months

So excited to have our new mass spec getting installed! #dreamteam @DrYihuiShen

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Yihui Shen

@DrYihuiShen

1 year

Looking forward to visiting the department!

Penn Bioengineering

@pennbioeng

1 year

Don't forget this upcoming #PennBioengineering seminar! Tomorrow, February 9 in Raisler Lounge Refreshments will be served! “Probing Metabolism Across Scales” @PennRadiology @PennCBP @DrYihuiShen

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Yihui Shen

@DrYihuiShen

10 months

We made it 🙌🙌🙌

Dr. Caroline Bartman

@Caroline_Bartma

10 months

Running our first test sample on the mass spec @DrYihuiShen 🎉😍

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Yihui Shen

@DrYihuiShen

8 months

@DelgoffeLab Our metabolic flux analysis shows about 6-fold increase in ATP production with CD3/CD8 activation in vitro. Paper under revision, stay tuned!

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Yihui Shen

@DrYihuiShen

2 years

I almost forgot how stimulating it was to talk about stimulated Raman scattering since graduation! Thanks @PhotonicsMedia for organizing the event! Credit goes to the whole Raman community that pushes the frontier of the technique.

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Yihui Shen

@DrYihuiShen

5 months

Come to hear our thoughts on why yeast makes alcohol and why tumors love glucose!

Matthew Swaffer

@mpswaffer

5 months

We’re back with more Cell Size & Growth seminars for 2024! Please join us online next week as we restart the series with two exciting talks from Easun Arunachalam and @DrYihuiShen . More info including (free) registration and upcoming speakers:

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Yihui Shen

@DrYihuiShen

3 months

Hearing the history and future of both Penn BE and synthetic biology today is super inspiring and exciting!

Ravi.Radhakrishnan

@raviradhak

3 months

Join us today. Penn Bioengineering presents the: 50th Anniversary Distinguished Lecture by James J. Collins, Ph.D. titled "Synthetic Biology: Programmable Biology" And enjoy some art! @pennbioeng

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Yihui Shen

@DrYihuiShen

3 months

Imaging friends! Come join us at Penn for the 3rd Britton Chance International Symposium on Metabolic Imaging and Spectroscopy on July 17-20th! Travel awards available for trainees and junior faculty. Abstract due April 1st. Pls spread the word!

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Yihui Shen

@DrYihuiShen

2 years

LC-MS help! I have two different samples ran on orbitrap with same method (same injection time, same noise, same day). Similar intensity but HUGE difference in peak quality. How could this happen? #TeamMassSpec

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Yihui Shen

@DrYihuiShen

4 years

We are looking for a someone to join our team as a Research Specialist. Apply if you are trained in biochemistry and/or molecular biology, and are interested in yeast metabolism! ( #Princeton , New Jersey) #job

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Yihui Shen

@DrYihuiShen

1 year

Really enjoyed the brainstorming and open discussion. It is so good to catch up with many friends!

CABBI

@CABBIbio

1 year

Thanks to our #CABBI scientists, researchers, and students who gathered at the 2023 retreat to share their field work and lab and modeling research! The meeting fostered new collaborations and insights supporting #bioenergy advances!🌱🤝 Highlights ➡️

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Yihui Shen

@DrYihuiShen

1 year

@Caroline_Bartma Ribosome is definitely a clear distinction. Also there is a gradient of cholesterol from low in ER to medium in Golgi and high in plasma membrane, which is important for vesicular transport

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Yihui Shen

@DrYihuiShen

5 months

Supportive mentor @dr_ohsopretty and a supportive community @CABBIbio !

The McReynolds Lab!

@mcreynolds_lab

5 months

Amazing opportunity to join us and contribute to our @CABBIbio funded work! Please help spread the word!

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Yihui Shen

@DrYihuiShen

1 year

How wonderful we can keep collaborating, DR. BARTMAN lol 🙌🙌🙌

Dr. Caroline Bartman

@Caroline_Bartma

1 year

DR. SHEN AT PENN! SO EXCITED 🥳🥳🥳 if you're looking for an engineering lab studying metabolic flux in T cells (and other cell types), check out Yihui's lab!!

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Yihui Shen

@DrYihuiShen

4 years

When I tried to design an experiment on sugar cane metabolism...

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Yihui Shen

@DrYihuiShen

3 years

Congratulate @Caroline_Bartma on this beautiful work! I am delighted to witness her effort in pushing the technical limits and understanding cancer metabolism. If you are interested in in-vivo flux analysis and cancer energetics, check out her preprint here👇

Dr. Caroline Bartman

@Caroline_Bartma

3 years

Here is my preprint of my postdoctoral work! TLDR, we developed methods to quantify TCA and glucose usage flux in tumors, and found tumors have suppressed TCA flux. Using these measures, we calculated that tumors make+use ATP slower than healthy tissues.

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Yihui Shen

@DrYihuiShen

8 months

Students from underrepresented and disadvantaged groups, apply to this program if you are considering graduate school!

Arjun Raj

@arjunrajlab

8 months

The Penn Bioengineering PhD program offers support during the application process. If you are interested in Penn BE, or even just graduate school in general, please take advantage. We are here to help! Link:

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Yihui Shen

@DrYihuiShen

1 year

So interesting “the level of microbiome-derived metabolites … is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux”

Huiluo Cao 曹慧荦

@hlcao

1 year

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota | Nature Biotechnology

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Yihui Shen

@DrYihuiShen

2 years

If you are interested in the technique, please also check out @TheMinLab @Lu_Wei8 @StimulatedRaman 😃

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Yihui Shen

@DrYihuiShen

1 year

Lol job posting coming soon

Zhenrun Jerry Zhang

@SZhangJerry

1 year

A lab at the interface of all STEM - physics, chemistry, biology, engineering and math! All STEM graduate and postdoctoral candidates are welcome to apply!

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Yihui Shen

@DrYihuiShen

1 year

Comprehensive protein degradation rate in E.coli reveals new protein recycling mechanism yet to be defined

Meera Gupta

@guptameera94

1 year

Unlocking the secrets of protein turnover in E. coli in collaboration with Gitai, Wingreen and Silhavy labs. We quantify degradation rates of 3k proteins revealing recycling of cytoplasmic proteins under Nitrogen limitation. #Proteomics #ProteinTurnover

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Yihui Shen

@DrYihuiShen

4 months

So, if not proteome efficient, why do certain cells prefer aerobic glycolysis? We randomly picked about 20 species across the budding yeast phylum and tested their growth and metabolism. We found that excess glycolysis does not benefit aerobic growth, consistent with efficiency

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Yihui Shen

@DrYihuiShen

4 months

We first quantified metabolic fluxes in two yeasts, and mouse T cells. See how different their ATP production is! S. cere has less total ATP flux than I.orie but greater glycolytic contribution. T cell activation comes with higher total and also greater glycolytic contribution.

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Yihui Shen

@DrYihuiShen

11 months

@Caroline_Bartma Let’s call it rational host selection for immunotherapy

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Yihui Shen

@DrYihuiShen

4 months

ATP can be made through glycolysis or respiration. Despite respiration having >10X higher yield of ATP per glucose, many cells default to glycolysis regardless of oxygen availability (Warburg metabolism in cancer or Crabtree effect in Baker's yeast). But why?

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Yihui Shen

@DrYihuiShen

2 years

So excited to see this paper out! This is a refreshment of basic biochemistry, and a story of persistent search for mystery chemical. Congrats @CSRJankowski and co-authors!

Connor Jankowski PhD

@CSRJankowski

2 years

Delighted to share my latest work in the Rabinowitz Lab, now online @CR_AACR TL;DR restricting bio-availability of selenium, a dietary mineral, sensitizes cancer cells to pro-oxidant treatments like high-dose ascorbate (vitamin C)

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Yihui Shen

@DrYihuiShen

1 year

@dr_ohsopretty @mcreynolds_lab Looking forward to knowing more NAD metabolism in yeast!🙌

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Yihui Shen

@DrYihuiShen

4 months

We then quantified protein mass for main cellular tasks. Look at how costly is metabolism! The two yeasts have similar metabolic proteome mass, yet the striking difference in their ATP production is driven by the allocation -- glycolytic yeast has 3X more glycolytic proteome!

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Yihui Shen

@DrYihuiShen

5 months

@noor_M0MIN @MJMitchell_Lab @JennyNJiang @RicGottardi Can’t agree more! What a fun wearing that matching sweatshirt and everyone knows you are new haha 😁

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Yihui Shen

@DrYihuiShen

9 months

@MJMitchell_Lab @pennbioeng OMG I would love it Michael, are you going to bring your 40 lab members 😂

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Yihui Shen

@DrYihuiShen

8 months

wow! Amazing opportunity 🤩🤩🤩

Tara TeSlaa

@tarateslaa

8 months

We would love to recruit a postdoc to work on this project. It's a unique opportunity to learn about protein-based metabolite biosensors from @schmittwitt_ and in vivo isotope tracing from me all in one project! If interested, please contact one of us!

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Yihui Shen

@DrYihuiShen

3 years

When would Princeton start vaccination

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Yihui Shen

@DrYihuiShen

3 years

3D reconstruction was so much fun 50 years ago😂 (Hoffman and Avers, ‘Mitochondrion of Yeast: Ultrastructural Evidence for One Giant, Branched Organelle per Cell’. Science, 1973).

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Yihui Shen

@DrYihuiShen

1 year

@SynBio1 It’s really hard to use Saccharomyces to make something that is not alcohol. Non-model yeast is the future!

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Yihui Shen

@DrYihuiShen

2 years

Interested in immunometabolism and new techniques? Check this out

Dr. Caroline Bartman

@Caroline_Bartma

2 years

NEW BARTMAN LAB WEBSITE JUST DROPPED: Techs/staff scientists/postdocs/students, come work with us in 2023! (pls RT)

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Yihui Shen

@DrYihuiShen

5 months

@arjunrajlab Thank you @arjunrajlab ! I have never felt so energized as now 🤩

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Yihui Shen

@DrYihuiShen

7 months

@AnthonyAngueira @PenncvARMI @PennCardiology Congrats Anthony!!

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Yihui Shen

@DrYihuiShen

1 year

@dr_ohsopretty @pennbioeng Thank you Melanie!! We could have our small yeast discussion group!

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Yihui Shen

@DrYihuiShen

9 months

Thanks to @Caroline_Bartma for great tour recommendation!

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Yihui Shen

@DrYihuiShen

9 months

@Caroline_Bartma Haha just to clarify this is not my average photo quality 😂😂😂 the focus was meant to be all the boxes

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Yihui Shen

@DrYihuiShen

3 years

@Caroline_Bartma Then you can apply what you have learned from the game and write a paper titled ‘game theory in metabolism’

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Yihui Shen

@DrYihuiShen

4 months

So, our two cents on why aerobic glycolysis occurs 👇 Optimal growth is achieved with respiration due to its efficiency. However, some cells come with copious glycolytic proteins to be robust in hypoxia. In that case, the best choice would be just using that glycolytic capacity🍻

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Yihui Shen

@DrYihuiShen

1 year

Quantitative and spatially resolved measurement of over a hundred of metabolites. Very useful resource for defining metabolic niche in the mouse gut!

Gary Siuzdak

@kadzuis

1 year

"a map of intestinal metabolism" helping to "identify metabolite–microbe associations, which provide a basis to connect the spatial occurrence of bioactive compounds" using longitudinal #activitymetabolomics @NatMetabolism @ETH_en Nice work Uwe Sauer team

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Yihui Shen

@DrYihuiShen

5 months

@Caroline_Bartma SAME! So grateful that our labs can start together 😍😍😍

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Yihui Shen

@DrYihuiShen

1 year

@pennbioeng I am so excited!

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Yihui Shen

@DrYihuiShen

1 year

@Caroline_Bartma Thank you for advertising ❤️❤️❤️

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Yihui Shen

@DrYihuiShen

4 months

But when we evaluated their hypoxic robustness as the relative growth in hypoxic culture to that in aerated culture, we found a decent correlation with aerobic glycolysis. This suggests that aerobic glycolysis does not benefit aerobic growth, but makes cell more robust to hypoxia

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Yihui Shen

@DrYihuiShen

3 years

@realTonyHui good luck!

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Yihui Shen

@DrYihuiShen

4 years

Pioneer of two-photon microscopy and FCS. I still think FCS is an elegant design even though it is less applied nowadays

Fei Xia

@_FeiXia_

4 years

Watt Webb inspired so many people, including me. Our offices are still full of his collection of scientific books on various fields ranging from pure math/physics to handbooks of biology and chemistry and they all have his signatures.

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Yihui Shen

@DrYihuiShen

5 months

@mcbride_matthew @Penn We also have so much to learn from your lab 🙌😁🤩

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Yihui Shen

@DrYihuiShen

7 months

@XueSherryGao Congrats Sherry!

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Yihui Shen

@DrYihuiShen

2 years

@pwpgomes Thanks! That’s the first I checked, both are 1 sec and the noise level is similar

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Yihui Shen

@DrYihuiShen

1 year

@MJMitchell_Lab @pennbioeng Can’t wait to work with amazing colleagues like you Michael!

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Yihui Shen

@DrYihuiShen

1 year

@Caroline_Bartma @helenjordan_ I am not ready to be honest 😂

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Yihui Shen

@DrYihuiShen

4 years

@Caroline_Bartma and facet_wrap() 🙌

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Yihui Shen

@DrYihuiShen

3 months

@rohan_palanki @MJMitchell_Lab @WPeranteau congrats Dr. Palanki🎉🎉🎉

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Yihui Shen

@DrYihuiShen

1 year

@Caroline_Bartma ❤️❤️❤️

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Yihui Shen

@DrYihuiShen

3 years

@SulianaManley @rita_strack Stimulated Raman scattering microscopy! Imaging chemical bonds with optical resolution, especially useful to visualize metabolism when that chemical bond contains an isotope

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Yihui Shen

@DrYihuiShen

3 years

Soooo cool!

Lu Wei

@Lu_Wei8

3 years

Check out our recent publication on @NatureComms : . We report a sample-expansion approach to perform super-resolved vibrational imaging, termed VISTA. With machine learning, we showed specific and multiplexed tissue imaging, but in a label-free manner!

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Yihui Shen

@DrYihuiShen

1 year

@Lu_Wei8 @NaturePhotonics @Stpotato @DongkwanLee1 so cool!

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Yihui Shen

@DrYihuiShen

2 years

@Caroline_Bartma @ronjune2 Maybe check

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Yihui Shen

@DrYihuiShen

1 year

@Lu_Wei8 @APC_2023 Wow keynote😍

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Yihui Shen

@DrYihuiShen

2 years

@Caroline_Bartma Seriously, it took me a while to read Daniel’s counterclockwise TCA

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Yihui Shen

@DrYihuiShen

4 months

@StimulatedRaman @nchembio Thank you Lingyan ❤️❤️❤️

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Yihui Shen

@DrYihuiShen

5 months

@BugajLab Thank you Lukasz!! Me too!

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Yihui Shen

@DrYihuiShen

3 months

@mcbride_matthew @DrexelUniv Congrats Matt! Nice picture!

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Yihui Shen

@DrYihuiShen

4 years

@kevolutn @Caroline_Bartma We are currently working on Issatchenkia and Rhodosporidium😁

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Yihui Shen

@DrYihuiShen

4 months

Thank you for reading through the long threads! Also huge thanks to mentors #notwitterjosh and @MartinWuhr , coauthors in the Rabinowitz lab and collaborators @CABBIbio !! Apologize for not being able to fit the whole list here

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Yihui Shen

@DrYihuiShen

2 years

@YuezhiMao @SDSU @mhg_group @UCB_Chemistry @StanfordUChem Congrats!

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Yihui Shen

@DrYihuiShen

4 months

@AsaelRoichman @nchembio Thank you Asael!!

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Yihui Shen

@DrYihuiShen

9 months

@mcbride_matthew @RutgersU @Eagles @Phillies Congrats on submitting the grant! (Especially with the chaos of shutdown lol)

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Yihui Shen

@DrYihuiShen

4 months

We then leveraged data generated in lab by @Caroline_Bartma to evaluate proteome efficiency in mouse tissues and tumors in vivo. Tissues and even tumors generate 90% of ATP from respiration, yet tumors do express a substantial glycolytic proteome compared to respiratory

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Yihui Shen

@DrYihuiShen

8 months

@noor_M0MIN Happy birthday Noor!🎂🎉

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Yihui Shen

@DrYihuiShen

9 months

@BanerjeeShivali @pennbioeng Thank you Shivali!! Good luck with job searching😃

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Yihui Shen

@DrYihuiShen

5 months

@noor_M0MIN @pennbioeng @Caroline_Bartma @SPIEtweets 🙌🙌🙌

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Yihui Shen

@DrYihuiShen

3 years

@Caroline_Bartma 😂😂Don’t worry, will be taken out when the manuscript is published

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Yihui Shen

@DrYihuiShen

1 year

@Caroline_Bartma Oh to complicate things more lol there are rough and smooth ER, only the rough ER is studded with ribosomes

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Yihui Shen

@DrYihuiShen

1 year

Triangles? Seriously?

Rita Strack

@rita_strack

1 year

why is this mito full of triangles

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Yihui Shen

@DrYihuiShen

5 months

@pennbioeng @Caroline_Bartma @SPIEtweets 😍😍😍

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Yihui Shen

@DrYihuiShen

1 year

@Caroline_Bartma Happy birthday! 🎂🎊🥳

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Yihui Shen

@DrYihuiShen

9 months

@raviradhak @pennbioeng @PennCPE4H @PennEngineers Thanks Ravi!! Appreciate your help with setting everything up!

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Yihui Shen

@DrYihuiShen

4 months

@cholsoon_jang @nchembio Thank you Cholsoon!!

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Yihui Shen

@DrYihuiShen

1 year

@drGregBowman @pennbioeng Thank you!!

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Yihui Shen

@DrYihuiShen

4 months

Similar in mouse T cells! T cells come preloaded with lots of glycolytic proteins before it is activated

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Yihui Shen

@DrYihuiShen

2 years

@Caroline_Bartma Huge congrats!!! The Bartman lab is gonna make great science!

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Yihui Shen

@DrYihuiShen

3 months

@hmbaghdassarian Thank you!! Looking forward to reading the review 🤩

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Yihui Shen

@DrYihuiShen

5 months

@mcbride_matthew @Caroline_Bartma @Penn an idea for the logo: BMS, to be confused with the pharma company lol

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Yihui Shen

@DrYihuiShen

4 months

We started by asking, maybe glycolysis is more proteome efficient? The rational is that given a limited proteome size, increasing efficiency of one task (metabolism) allows the cell more capacity to do other tasks (biosynthesis). However, the answer is no. Here is why

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Yihui Shen

@DrYihuiShen

10 months

@Caroline_Bartma I will add one

L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity - PubMed

Metabolic activity is intimately linked to T cell fate and function. Using high-resolution mass spectrometry, we generated dynamic metabolome and proteome profiles of human primary naive T cells...

pubmed.ncbi.nlm.nih.gov

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Yihui Shen

@DrYihuiShen

1 year

@ElizabethAMurp2 @CABBIbio Thank you Elizabeth! It’s been a wonderful journey with so much great science in CABBI!

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Yihui Shen

@DrYihuiShen

1 year

@BugajLab @pennbioeng Thank you Lucas!! Catch up soon 😃

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