Chenxin Li, PhD

@chenxinli2.bsky.social

4912 Followers 2493 Following

Or just “Li” | Assist. Prof. @ Plant Bio, Michigan State U. | Also post data visualization | Lab: https://cxli233.github.io/cxLi_lab/ | GitHub: https://github.com/cxli233

A UMAP plot.
Detached leaves growing a lot of roots in a petri dish
Email from the director of MSU HPCC. It reads "Rapid growth in generative AI has dramatically increased demand for the same computing hardware used in research computing while manufacturing capacity remains constrained. As a result, CPU prices have increased roughly four- to five-fold over the past year, while GPU prices have increased by approximately two- to three-fold. Consequently, our funding will purchase substantially less computing capacity than in previous years, and we do not expect these market conditions to improve significantly in the coming year."
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.
Screenshot of HTML about activities using ChimeraX to view structures.
PDB entry 3C1B: human nucleosome with DNA wrapped around.
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.
Green callus growing on the wound side of a seedling explant, with 2 roots growing out from the opposite side.
A couple strongly glowing (green) dots from several seedling explants in a petri dish
Fluorescent transgenic roots (glowing green, illuminated by blue flashlight) in a petri dish
A blue blob on top of a pink blob.
A screenshot with 2 code chunks of R and 1 code chunk of bash
Microscope image showing blue nuclei, purple dots (mRNA of a gene of interest) and green dots (mRNA of another gene of interest)
Detached Kalanchoe leaves in petri dishes of water.
A carrot with several small shoots growing from the top. Small shoots are pale orange color.
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.
A taro held in my hand. A pink shoot is emerging. Roots that are white with yellow tips are emerging too.
The mulberry tree seen from below. Immature and mature fruits can be seen.
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.
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.
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?
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%.
Green fluorescent roots growing from detached leaves in a petri dish. Chloroplast autofluorescence can be seen in red. Not all roots are fluorescent.
Screenshot of an RMarkdown html notebook. This is the exercise section of the notebook.
Green fluorescent roots as seen under blue light. Chloroplast autofluorescence can be seen in red.
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.
A screenshot of part of the regulations.gov page on OMB-2026-0034-0001. On the left it shows 735 comments received. On the top it shows 102 comments.
A meadow with green vegetation, purple flowers, and white flowers. The sky is clear and blue.
Pond with water lily that has pink flower. A frog can be seen on the leaves.
A small rodent like mammal with brown fur, round head, and black nose next to a tree
Chipmunk on lawn, with tail facing camera
Seedlings grown in a petri dish. Green fluorescent signal can be seen on leaves.
Light golden color clear chicken stock in a glass bowl with a black ceramic spoon. White foam can be seen on top and at the edge of the surface
A screenshot of Bioicons.com, showing 3 icons contributed by James Lloyd. From left to right: Arabidopsis, moss colony, and moss gametophytes.
Structure of AtTTG1, a WD40 repeat protein: the structure is mainly beta sheets and folds into a donut shape.
A grey-ish brown rabbit eating vegetation under a tree
A walkway with lush green trees and lawn on both sides
Heatmaps (carotenoids, left) and (steroidal glycoalkaloids [SGA], right) in fruit and leaf. Each row is a metabolite, and each column is edited plant or WT control. Strong depletion can be observed in key abundant carotenoids or SGA in the fruit with minimal changes in the leaf.
AlphaFold predicted structure of AtPLT1, showing 2 AP2 domains that are predicted with high confidence and the rest of the protein predicted to be disordered and predicted with low confidence.
A phylogeny with 120+ genes. Tree on the left and MSA on the right.
A deer on a lawn seen from the side next to a fence
Photo of a wild brassica plant with yellow flowers and green leaves
Detached Kalanchoe leaves in beaker of clear liquid. Tiny shoots are visible, along with clusters of short roots.
Local synteny across 8 species/haplotypes. Gene of interest highlighted in pink ribbon. Other genes marked with grey ribbon.
Lawn at the corner of a parking lot. A rabbit eating grass and a robin chilling.
Riparian plot showing 8 genome/haplotype assemblies. The 3rd one from the top seems to have some issues: chromosomes are bigger than expected and too many unanchored genes.
Chromosomes on black background. It looks like there are 68 chromosome.
Two adult geese and four baby geese on a lawn
The design of lineage tracing experiment in Arabidopsis using two T-DNAs: (1) a base editor that binds a specific 18-bp sequence (2) a 1-kb barcode with binding sites for the base editor.
A Petri dish of seedlings in dark background illuminated by blue light, picture taken with green filter. Green fluorescent sectors can be seen.
Screenshot of part of figure 4: chematic portraying a proposed mechanism of mutation fixation within tissue layers in the shoot culture and field-grown tree clones.
Screenshot of part of figure 1: Somatic embryos exhibit high levels of mutation compared to shoots and trees. (A) Schematic of the relationship among all clones. Icons denote trees, shoot cultures, and somatic embryos. Gray icons represent dead clones. Dashed lines indicate an unknown number of clonal propagations, solid lines indicate a single clonal propagation. (B) Phylogeny of all sequenced clones constructed from de novo somatic single base substitutions (SBS) and InDels. Branch length is proportional to the number of mutations. Bootstrap support less than 1 is displayed. (C) The number of SBS and InDels present in each sample at minimum median quality scores of 20 to 40, in increasing intervals of 1.
A chipmunk emerges from a hole under a tree
Big bird with gray on the back and white in the front
Cast of FSAC-KK-11888, currently classified as Spinosaurus, displayed in a swimming posture at the Field Museum of Natural History in Chicago, Illinois. The skeleton reflects the known fossil material as of 2023. The pose is based on 2022 research claiming Spinosaurus was an aquatic specialist and displayed "subaqueous foraging behaviour."
Dark green detached zizi plant leaflets regenerating roots and developing small bumps
The solid green bars represent the funded applications, and the striped gray bars represent the unfunded applications. Most applications with overall impact scores at or below 50 were funded. Applications with an overall impact score greater than 60 were not included on this chart.
A green lawn seen through a shaded area. A groundhog can be barely seen with coat color camouflaged well with the dried grasses in the background
Green fluorescent roots growing from detached Kalanchoe leaves
Detached succulent leaves with shoot regenerated.