Chenxin Li, PhD

@chenxinli2

Or just “Li” Assist. Prof. @ Plant Bio, Michigan State U. Also post data visualization Lab: GitHub:

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Chenxin Li, PhD@chenxinli2· 25d

Draft genAI guidance for classroom

PPT slide reads "Generative AI use guidance"

When you are learning:
- Minimize the use of generate AI
- Prioritize learning
- Invest time to figure out how to do stuff
- Read documentations
- When you get stuck, ask a peer, build community, and learn together

When you are working:
- Use AI responsibly.
- Never give AI sensitive, confidential, or proprietary data
- Understand AI output
- Test and validate code, regardless AI or human generated.

Chenxin Li, PhD@chenxinli2· 26d

Wrote the activity/HW! Two weeks to write 9 lectures/activities is not too bad.

Screenshot of HTML about activities using ChimeraX to view structures.

Chenxin Li, PhD@chenxinli2· 26d

Gallery for 3 other examples I prepared in ChimeraX for the lecture/homework. Details in alt text.

PDB entry 3C1B: human nucleosome with DNA wrapped around.

PDB entry 7FDO with surface shown set to 80% transparent. Arabidopsis EGL3 (pink, N-term domain) and CPC (blue/green) are shown. Alpha helices harboring the interaction motif is colored green in CPC.

Camel chymosin. Wheat color is crystal structure (PDB entry 4AA9). Blue color is AlphaFold structure. Two structures were aligned and overlaid.

Chenxin Li, PhD@chenxinli2· 26d

Viewing protein structures really tickles the data visualization part of my brain. Doing this as part of prepping for my bioinformatics class. Decided to put in a lecture on structures. This is entry 102M from PDB, sperm whale myoglobin as an example. More detail in alt text.

Polypeptide chain colored in pink against white background. The structure is mostly alpha helices with some loops. Heme is colored blue. A sulfate is colored yellow and red. His93, which coordinates the heme, is colored orange.

Chenxin Li, PhD@chenxinli2· 26d

Plants doing weird things in tissue culture. Callus growing on the wound side of a seedling explant, with roots growing out from the other side.

Green callus growing on the wound side of a seedling explant, with 2 roots growing out from the opposite side.

Chenxin Li, PhD@chenxinli2· 26d

#FluorescentFriday I saw some glowing cells from seedling explants. Hopefully these grow into transgenic shoots. We shall see.

A couple strongly glowing (green) dots from several seedling explants in a petri dish

A strongly glowing (green) dot (near the right edge of the petri dish) from several seedling explants in a petri dish

Chenxin Li, PhD@chenxinli2· 26d

#FluroscentFriday Fluorescent transgenic roots in a petri dish

Fluorescent transgenic roots (glowing green, illuminated by blue flashlight) in a petri dish

Chenxin Li, PhD@chenxinli2· 26d

I was looking up some structures for a couple proteins of interest. This is showing two transcription factors. They fit together so well!

Chenxin Li, PhD@chenxinli2· 27d

Did you know you can run bash script in RStudio? I didn't know until just now.

A screenshot with 2 code chunks of R and 1 code chunk of bash

Chenxin Li, PhD@chenxinli2· Jul 13

#MicroscopyMonday RNA-FISH of Catharanthus petal. It's like looking at stardust and/or galaxy. Blue is nuclei, purple is one gene of interest, green is another gene of interest.

Microscope image showing blue nuclei, purple dots (mRNA of a gene of interest) and green dots (mRNA of another gene of interest)

Chenxin Li, PhD@chenxinli2· Jul 13

It's a good day when you can spot shoots regenerating.

Detached Kalanchoe leaves in petri dishes of water.

Chenxin Li, PhD@chenxinli2· Jul 5

Carrot sprouting in the kitchen

A carrot with several small shoots growing from the top. Small shoots are pale orange color.

Chenxin Li, PhD@chenxinli2· Jun 30

Did you know YuGiOh has a Kalanchoe inspired card? Behold, Kalantosa, Mystical Beast of the Forest!

A yugioh that looks like a white rabbit with Kalanchoe on its back.

Card text reads: Earth Beast, Lv2, 200/1400, If this card is Special Summoned by the effect of a Beast monster: You can target 1 card on the field; destroy that target.

Chenxin Li, PhD@chenxinli2· Jun 29

Taro sprouting in kitchen. This one is growing both shoot (pink) and roots (white with yellow tips).

A taro held in my hand. A pink shoot is emerging. Roots that are white with yellow tips are emerging too.

Chenxin Li, PhD@chenxinli2· Jun 27

I found a mulberry tree near my apartment building

The mulberry tree seen from below. Immature and mature fruits can be seen.

Chenxin Li, PhD@chenxinli2· Jun 27

This is a Yu-Gi-Oh! inspired color scheme. Sometimes anime just has great color designs.

A scatter plot showing body mass on x-axis and bill length of y-axis. Each data point is a penguin, colored by species. There are 3 species, colored with "tomato1", "gold", and "dodgerblue". A linear regression line was drawn for each species. There is a correlation between body mass and bill length within each species.

From left to right: "Slifer", "Ra" and "Obelisk", with red, gold, and blue themed colors.

Chenxin Li, PhD@chenxinli2· Jun 26

I made demonstrations for Central Limit Theorem and Law of Large Numbers. 1st figure for CLT: Sample means are normally distributed around population mean, even if the population is not normally distributed. 2nd figure for LLN: With increasing sample size, sample mean approaches population mean.

Distribution of mean calculated from 20,000 iterations of n = 3 samples, sampled from a uniform distribution with mean = 0. Sample means are normally distributed around 0, which is the population mean.

Line graph potting sample mean against sample sizes. Samples were drawn from a population where mean = 0. As sample size increases, the sample approaches the population mean.

Chenxin Li, PhD@chenxinli2· Jun 25

Making a fun example for my class.

Screenshot of a ppt slide. It reads "A person claims that they can tell the difference between a can of Coke vs a can of Pepsi. They were given samples of each and blind tasted them. " The result was presented as a contingency table. When a sample was claimed to be Coke, 9 times they were actually Coke, and 3 times they were Pepsi. The the sample was claimed to be Pepsi, 1 time it was actually coke, and 7 times it was Pepsi. Question: How well can this person tell the difference between Coke and Pepsi?

Chenxin Li, PhD@chenxinli2· Jun 19

I was making some slides on how to programmatically assemble figures using the patchwork package in R, with more advanced layout syntax. patchwork.data-imaginist.com

Screenshot of PPT slide showing two example. 1st example shows a figure with 3 panels in a row side-by-side, with relative widths 100%:50%:30%.

2nd example shows a figure with 2 rows and 2 columns, where relative heights are 100%:20% and relative widths are 100%:40%.

A screenshot of ppt slides showing steps to make a complex figure using hierarchical assembly.

Chenxin Li, PhD@chenxinli2· Jun 19

#FluorescentFriday Root regenerated from detached leaves. You can see not all of them were transformed with the fluorescent transgene.

Green fluorescent roots growing from detached leaves in a petri dish. Chloroplast autofluorescence can be seen in red. Not all roots are fluorescent.

Chenxin Li, PhD@chenxinli2· Jun 16

Prepping for intro bioinformatics (coding in R) that will be teaching in the spring. Will be using a combination of RMarkdown html notebook and slides.

Screenshot of an RMarkdown html notebook. This is the exercise section of the notebook.

Chenxin Li, PhD@chenxinli2· Jun 12

#FluorescentFriday Fluorescent roots emerging from detached leaves.

Green fluorescent roots as seen under blue light. Chloroplast autofluorescence can be seen in red.

Chenxin Li, PhD@chenxinli2· Jun 4

Big callus regenerating from a detached zizi plant leaflet. Roots are coming out from the callus. I think the reddish outgrowths on top will become new shoots.

Detached leaflet of zizi plant, after a few months in water. A big green callus with roots coming out. There are a few reddish outgrowth on the top side.

Chenxin Li, PhD@chenxinli2· May 31

So far there are ~700 comments received, among which 102 are posted. More will be posted when the business day comes. I made a point on the proposed changes will be counterproductive to transparent, merit-based grantmaking and good stewardship of taxpayer money.