News related to both research and Zhikai
My first paper in Springer Lab was published in Plant Physiology!
The nucleotide sequence is a pool of biological information, we used this to successfully predict functional genes between plant species and this paper was published in PNAS!!
Very glad to join BSA journal Applications in plant sciences as a reviewing editor!
Being invited to join the guest editorial board of Frontiers in Genetics & Frontiers in Plant Sciences to start the topic of “Decoding Connections between Phenotype and Genotype using Machine Learning” !!
Feel thrilled to be selected as a Feature Editor in Molecular Plant. Look forward to making contribution to the development of the journal!
“implant” is a R package to process high-throughput phenotyping images. Feel glad to be a co-author in this Plant Phenomics paper. Thanks co-authors!
My previous study on high-throughput phenotyping of hybrid corns was used as a illustrator in Forbes to explain heterosis in plants. See news here.
I was invited to deliver a presentation in Baibozhihui Dajiangtang. It is fun to communicate with many Scientists in the other time zone!
One of my main projects during my PhD is published in Molecular Plant and online!
Heading to the start of Mississippi River with all members in Springer’s lab. So cold, but so much fun!
Officially started a postdoc position in Prof. Nathan Springer’s lab.
Left the place I worked four and half years where I grew up and gained knowledge. Very appreciate Prof. James Schnable, who is the person providing me so much support during my PhD.
Last time for harvesting before I leave Lincoln. Feel proud to be a cornhusker!
Had a lunch with Prof. Jianming Yu’s and always learnt about from his talk. I am really a fan of Prof. Jianming Yu’s speech!
- Hooded by Prof. James Schnable. I am official to be a doctor!
- Feel excited to give a presentation in CGM about my GPWAS model, media about my presentation could be found in YouTube and Tencent.
Successfully completed my defense and became a doctor! Thank you all for your support in the past several years!
- Successfully compiled the deep learning frame for DNA sequence level prediction using a test data!
- We began to start the planting in 2019 maize nursery field!
- It is enjoyable to back in Deep South, familiar accent, familiar nice people, and familar weather! Nice!
- First time to be in North Carolina, met with famous maize experts like Jim Holland. Excited to communicate with them about my latest research.
- I could not give more thanks to the steering committee for the opportunity of short talk in 61st Maize Genetics Conference in St. Louis. That is a wonderful event on the end of my PhD study.
- Excited for my first trip to be in Donald Danforth Plant Science Center!
Announced to deliver an oral presentation in the 61st Maize Genetics Conference in St. Louis, Missouri.
Awarded the Larrick and Whitmore Graduate Student Travel for next month Maize Genetic Conference.
Excited to be announced as a Plantae Fellow in Plantae 2019 Fellow Program and see my first post summary of a deep-learning of phenotyping review paper.
My GPWAS paper was posted in preprint server and this is one of my most interested works in my PhD. Integration of hundreds of phenotypes to investigate gene properties of maize from multiple perspectives, such as evolutionary features, expression and synteny analysis. Must be a potentially valuable guide for studies in other species with similar dataset of genomics and phenomics in upcoming decades.
Attended my first PAG meeting, and presented my research on solving complexity of phenomic data using genomic data. So many people expected to see the whole story and I believe the paper should come very soon !!
Finished all of my officially registered classes during my education life with satisfied grades.
Great honor to have lunch with Prof. Steve Briggs. Not only his researches, but also plentiful advise on job hunting, performance in academia and lab management impressed me a lot.
It’s awesome to attend Prof. Sanzhen Liu’s talk. Great work on candidate pathogen resistance gene selection and mini-chromosomes characterization on pathogenic strains!
The second time joined the Plant Science Innovation retreat, the advent of big data is coming. High-throughput phenotyping, microbiomes, RNA-seq and metabolite data are being generated. Intriguingly seeing how to couple these data to generate interesting stories.
Tool for calculating Ka-Ks per gene (grass-kaks) is just initially completed.
Completed two days root sampling for rhizosphere microbe study @CRRI!!
- Genomic selection on four field traits of hybrid pearl millet published online. Just got acceptance after 1 month submission, thank you G3 journal for this super fast decision!!
Thank to my friend to put me on their 2018 school admission brochure of Agriculural College in Nanjing Agriculture University in China.
03-21-2018 to 03-27-2018
Traveled back China, gave three talks in both 2nd Asian-Pacific Plant Phenotyping Conference and other two institutes in East China about high-throughput plant phenotyping. Hope can develop more in future.
Passed my PhD candidancy exam using a project on exploring response different to high-planting density between domesticated and wild species, moved closer to be a doctor !!
Joined 2018 Genomes-to-fields collaborator meeting in Ames, and also be honor to visit DuPontPioneer in Johnson. Scientists are trying various ways on making corn better.
My review paper on subgenome dominance is accepted !! Enriched a lot of new knowledge on plant genomic area from evolutionary side, that will be helpful for boarding my researches in future.
Had lunch with Prof. Jeffrey Ross-Ibarra and joined his seminar. A room fulled with people listened to his talk with clear logic to link his researches to a full big story. Really appealing!
- Very glad to join the host of field Spider-cam phenotyping facilites visiting with David Han’s group from China, who is a really nice person to know.
- Presented my published GigaScience paper for discovering maize high-throughput phenotyping data from automatic greenhouse in PSI annual report.
Was tagged in Nebraska Food For Health Center’s project to link sorghum researches to human health.
Joined the MidWest Big Data Summer School in Iowa State and felt great to visit Prof. Patrick Schnable’s Lab with advanced technologies on both genotyping and phenotyping.
- My mentored undergraduate student Thomas Hoban had his first presentation in spring research fair about sorghum roothairless mutant screening.
- Hosted the visit of pearl millet breeder SK Gupta from ICRISAT in India with graduate student lunch and discussed with my ongoing pearl millet hybrid genomic selection project.
- My self constructed RNA-seq library were completed and sent out this month. It is a long journey to follow a 10-pages modified protocol to finish this work. But everything fortunately was made smoothly. Glad to see how domesticated and relative wild species performance on simulated high planting density conditions.
Attended 59th maize genetics conference in St. Louis, MO. Presented my lastest methods on phenotype extraction from high-throughput image data in the conference.
Had lunch with Prof. Michael Freeling, who is the major advisor of my advisor. He wanted to chanllenge something that he is not that good at after he made the super accomplishment in the academia. Yup, that is we always want to see ourself in mirror in order to make a better self.
Sent out my 500 leaf samples of hybrid corns out to Danforth Center @BaxterLab for measuring ionomic data just after they run out experiment from automatic greenhouse.
- Rescued 10-years root hairless mutant and planted to grow and we will harvest thousands of mutant seeds later.
- Farewell, Kyle! The REU student from BYU I mentored this summer for GWAS on image-based seed trait extractions of maize diversity panel. The guy also interested on learning multiple languages.
- Joined Purdue Plant Science Symposium, and presented our idea on tracking individual leaf extension from high-throughput images.
- Completed the organization of sorghum diversity panel field work this summer, sampled, phenotype measured and seeds harvested !! Figured out to use tablet to record phenotype data in field study.
- My 140 varieties of hybrid corns from exPVP lines run out of automatic greenhouse and we collected a batch of ground-truth phenotypes for further validation with computer vision methods.
Using Lemnatec Automatic greenhouse system to estimate the water use efficiency of various species and varieties within each species. Sorghum and millets on right side apparently use water in a more efficient way than maize, valuable to dig in.
First time to attend a professional conference and be proud to give my first time oral presentation in 58th maize genetics conference holden in Jacksonville, Florida. My very first author paper’s link related to this topic is here. Regretably I am hidden in front of my slides …
Finished the report of Popcorn population study before Winter Holiday. Landed on a new world that I haven’t touched before.
- Started to record plant growthes of 6 selected grass species. Excited to see plant growth in time lapse and leaf extension !!!
- The very first phenotyping experiment on a small population including public and private maize sectors completed this month. I used raw data generated from this system to test its stability as well as settings when for further operating this system.
Transit from bench work to computer work and it is the first wet lab experiment I did in Schnable Lab. Data collection is a first step, modified a large-scale DNA extraction methods, and successfully extracted large amount of DNA for Paspalum, Dichanthelium and Urochloa.