“Functional Modeling of Plant Growth Dynamics” our paper with statisticians Yumou Qiu and Yuhang Xu was selected by the Editorial Board of The Plant Phenome Journal as their 2020 Paper of the Year.
On October 2nd Chenyong Miao taught a Phenome Force sponsored workshop on using scikit learn for semantic segmentation.
- Our new paper on leaf angle measurements from video data comes out in Applications in Plant Sciences and the story is profiled in Nebraska Today’s Pocket Science.
Guangchao Sun wins the CROPS award for his talk on the mechanisms of stress tolerance in a crop wild relative during in PSI’s regional (remote) seminar series this summer.
Madison Tunnell a 2020 remote REU student in the lab, presents at the UNL summer research fair as she wraps up her project.
Chenyong is officially awarded the Widaman Distinguished Graduate Fellowship. Well deserved. Congratulations!
Lodging and greensnap. Planting errors and poor germination. Such is life in field research. This is why field plans should always build in more replication and redundancy than one expects to need. Thankfully our resilience was enough to save the day.
Jon Turkus joins the lab from Michigan State!
Michael Tross, who rotated in the last this spring, decides to stick around and do his thesis research with us. Here’s hoping for a fun and productive set of years.
New funding from the USDA! In a grant lead by our collaborator Liang Dong at Iowa State, we were funded to develop new cyberphysical systems to use water and nitrogen more efficiently. (Source.)
- It was a crazy month. Somehow corn got planted in the midst of a lockdown and pandemic. The fact that we succeeded was enough to make Nebraska Today.
Mackenzie Zweiner is the photo of the week for Nebraska Today, continuing to prep seeds for her field this summer in her parent’s sun room after everyone was kicked off campus.
The other shoe we’ve been waiting for drops and UNL goes to complete on campus shutdown. Christine is essential personnel and still able to access the building. Many of the undergrads who worked so hard to make this field season possible go on (thankfully paid!) leave.
Chenyong completes his qualifying exam and advances to PhD candidacy.
James Schnable is elected to to the Maize Genetics Cooperation Board of Directors.
University moves to mandatory work from home for those able to work from home. Fortunately many of us are able to work from home. Unfortunately, some of us cannot. Undergraduates log long hours in separate rooms all through spring break preparing seed for field season knowing a shutdown order could come at any time.
The lab was going to attend the maize genetics conference in Hawaii. But COVID-19 had other plans. Conference cancelled.
Daniel Carvalho publishes the second chapter of his PhD. Aime Valetin is a co-author and this is his very first time publishing a scientific paper. Congrats, Aime!
Ravi Mural joins the lab as a postdoc, fresh off a PhD in soybean breeding.
Xiaoxi Meng’s last day in lab. She’s headed to Minnesota for a postdoc at the intersection of genomics, machine learning, and potatoes.
Guangchao Sun, Nate Korth, Chenyong Miao, and James Schnable all attended the 2020 Plant and Animal Genome conference in San Diego, CA. Guangchao gave his first presentation at an international conference as a member of the Schnable Lab in the Crop Genomics for Global Food Security session. James also spoke in the Systems Biology and Ontology session.
- Interview with James Schnable on Plantae as part of the “Faculty Jobs: Myths and Realities” series.
Brandi Sigmon receives the LK Crowe Advising Award!
James Schnable speaks at the University of Guelph Plant Sciences Symposium.
Bryce Askey, an REU student with the lab this summer, publishes his first peer reviewed paper EVER in Applications in Plant Sciences.
James Schnable is the inaugural Charles O. Gardner Professor of maize quantitative genetics.
Zhikai Liang’s last day in the lab. Zhikai leaves us to start a postdoc in the Springer lab at UMN.
Xiuru Dai’s last day in lab. She’s headed back to Shandong Agriculture University to finish up her PhD.
A bunch of congressional staff take a tour of our cornfield, and hear about how #cornhuskercorn provides value to the state of Nebraska and the USA as a whole.
Chenyong Miao gives his first talk at a national conference! Plant organ semantic segmentation at MLCAS 2019.
Daniel Carvalho’s last day in the lab. He’s headed to the Federal University of Minas Gerais in Brazil!
Zhikai and Daniel both walked at the summer 2019 Commencement.
A new grant from DOE for the lab: Combining machine learning and crop models to characterize genes in Sorghum.
Daniel Carvalho presenting on his research at a special symposium recognizing the contributions of Brazilian scientists to research at UNL.
- James Schnable was in San Jose and received the ASPB Early Career Award at the annual American Society of Plant Biologists meeting.
Thank you to Bryce Askey for the photo
- On August 23, 2019, Aime Valentin Nishimwe presented his UCARE summer 2019 research project with the title, “Understanding Rwanda’s Soil Quality and Management Practices” with Dr. Rebecca Young as his advisor.
Big thanks to Justina Clark,Director of Undergraduate Research Undergraduate Education & Student Success, for stopping by!
Coming together with the Alfano, Yang and Sigmon labs, we dug up 3,000 maize roots in three days. It was exhausting but time in the cornfield at least makes me appreciate computational biology more.
Daniel Carvalho passed his final defense (July 25th)! Way to go!
On July 22nd, Zhikai Liang passed his final defense becoming the first PhD student to successfully graduate from the Schnable Lab. Congrats!
- The paper on our robotic phenotyping collaboration with the Ge lab is both published and picks up media attention. A story on the robot for the Lincoln Journal Star is picked up nationally and runs in papers from San Francisco to Miami.
- Congratulations to Christine and Guangchao who each welcomed healthy baby girls into the world.
- Welcome to the Schnable Lab Natalie Belz (Scripps College, CA) and Bryce Askey (University of Florida). Natalie and Bryce are both NSF supported undergrad students who will spend the summer here as part of the Research Experience for Undergraduates program.
Our first lab meeting to include this summer’s REU students.
- In the midst of the rainiest planting season across the corn belt in 40+ years, the whole lab pulled together to prep seeds and get seed in the ground on the rare days when fields were dry enough for our planter. Read more about just how bad this year has already been for corn in this Washington Post article.
Most of the lab is extremely busy prepping seed for our field season if it ever stops raining long enough to plant.
James Schnable presents at the Crops in Silico meeting at UIUC. No video but you can download the slide deck here.
Preston Hurst graduates! Preston spent his last two years in the lab earning an MS. He’s now moving upstairs to David Holding’s group to work on genome editing in maize and sorghum.
Ashley Foltz, an alum of the REU program in the Schnable Lab is admitted back to UNL to work on her masters in the School of Biological Sciences.
James Schnable is notified that the university has officially recommended him for promotion to Associate Professor and tenure. In the same month, he was selected as the 2019 winner of the American Society of Plant Biologists Early Career award.
- Almost the entire lab attended the Maize Genetics Conference in St. Louis, MO, where Zhikai Liang’s abstract on GPWAS was selected for a short talk and Guangchao Sun, Xiaoxi Meng, Chenyong Miao, Preston Hurst, Xiuru Dai, and Tom Hoban all presented posters.
Top row L-> R: Tom Hoban, Xiuru Dai, Chenyong Miao, Preston Hurst. Bottom row L-> R Xiaoxi Meng, Zhikai Liang, Brandi Sigmon. Not pictured: Guangchao Sun, Nate Korth, James Schnable.
- Daniel Carvalho and James Schnable both gave invited talks at the Nebraska Plant Science Symposium, and Chenyong Miao recieved a prize in the poster competition at the same event. Thank you to the amazing organizing committee (including Preston Hurst) and all of the symposium sponsors. You can watch the video of Prof. Schnable’s talk (https://go.unl.edu/6m06)[here].
- James Schnable returned to his old alma mater for a seminar. Thanks for the invite Cornell, and thank you for hosting me Buckler Lab!
2019, February - March
- On February 28- March 2, 2019, Aime Nishimwe attended AFA Technology Institute in Orlando Florida.
- At the conference, he had the opportunity to learn a lot about current trends in agritechnology, and he also networked with different agri-tech companies like Winfield United, Helena, and Bayer CropScience.
- James Schnable, Brandi Sigmon, and Daniel Carvalho all attended Phenome in Tucson Arizona. Brandi was awarded an all expenses paid travel award by the Phenome organizing committee. James received the NAPPN Plant Phenotyping Early Career Award during the conference.
ARPA-E Open announces a new grant to the Schnable Lab and collaborators in Computer Science and Engineering at the University of Utah to develop field deployable early warning sensors to detect volatile compounds released by plants. Special thanks to the Hanseup Kim Research Group for leading this effort.
Zhikai and Chenyong attend the 27th Annual Plant and Animal Genome Conference in San Diego each presenting posters on their work resolving different quantitative genetics challenges presented by high throughput phenotyping data.
Nate Korth receives the NFHC award for his initial doctoral dissertation research studying the interaction of crop plant genetics and the human gut microbiome.
Zhikai Liang’s paper on genomic prediction in pearl millet, funded by a USAID Linkages grant with ICRISAT receives the “Best Research Article of 2018” award from their Asia research division.
- And that’s a wrap for 2018, folks. Happy new year from all of us.
- James Schnable submits his promotion and tenure package.
Daniel Carvalho is awarded the Henry M. Beachell Fellowship. Article here.
Brandi Sigmon an assistant professor of practice and an expert on evolutionary development in maize and sorghum joins the lab.
Chenyong Miao’s first paper as a first author in the Schnable Lab (a collaborative effort with the Yang Lab) comes out in Plant Biotechnology Journal.
Multiple lab members present their research at the University of Nebraska Plant Science Retreat.
- We take possession of our new office space, now with even more desks and with a window.
NSF awards a new grant to study the nitrogen responsive gene regulatory networks in sorghum to us, collaborators here at UNL, and collaborators at HudsonAlpha in Huntsville, Alabama. Check out the great work happening in lead PI Jeremy Schmutz’s group, Kankshita Swaminathan’s lab, Tom Clemente’s Lab, Jinliang Yang’s Lab (a Schnable lab alum!), and Yufeng Ge’s lab
Welcome to the lab Xiaoxi Meng! Xiaoxi is coming to the lab having finished a PhD in biochemistry working on rice at Mississippi State. Follow her on twitter.
- Last day in the lab for many of the undergraduates who joined us for the summer. Going away celebrations includes both a nice dinner and intramural soccer game.
NSF decides to fund “Genetic Constraints on the Increase of Organismal Complexity Over Time.” This is the Schnable Lab’s very first grant with James Schnable as a solo PI.
Daniel Carvalho, Chenyong Miao, and James Schnable attend the 3rd Annual Broomcorn Millet conference organized by lab collaborator Dipak Santra in Ft. Collins, Co.
Connor Pedersen’s last day. After graduating this spring he stuck around to help with one last field season before heading off for his new job at Los Alamos.
Working with the Yang, Sigmon, and Alfano labs we dug up 1000 maize root samples for the CRRI project. By the end (almost) everyone was really happy that we’re a heavily computational lab.
- Our first paper in pearl millet, a collaboration with ICRISAT (with Zhikai as lead author) was published in G3. Also check out Daniel’s really fun animated GIF of the whole pearl millet lifecycle.
- A successful planting in at UNL’s Havelock farm. 80,000 total kernels put into the ground over two days. Fortunate to have Schnable Lab alumni as a professor here at UNL to make this happen.
R->L Christine (Schnable Lab), Connor (Schnable Lab), Sam (Yang Lab), Jinliang Yang, Josh (Ag & Hort Field team). Photo Credit: Raghu (Yang Lab)
- Our lab becomes a victim our our own success and is evicted from our office space over the summer while renovations take place to double the number of student desks.
- With help and guidance from Jinliang Yang, his lab, and the Alfano lab, we’re preparing for our first real field season since the Schnable Lab at UNL was founded.
- Holly Podliska presents on her UCARE project over the past year, linking experimentally measured cold and freezing tolerance of grass species to botanical records of where the same species have been observed in the wild. Unfortunately we’re losing her at the end of the semester when she moves on to student teaching.
- Connor Pedersen wins another prize at the UNL spring research fair for his own poster on linking greenhouse and field phenotypes.
- Sunil Kumar leaves the lab for his real first postdoc in the Niedehuth Lab at Michigan State. He carries with him Pete2, a the same Tripsacum clone Jinliang Yang brought to the Schnable Lab from California.
- James Schnable receives the Marcus Rhoades Early Career Award at the Maize Genetics conference in St. Malo, France.
Thanks to Elizabeth Lee for the Photo
- Halfway around the world at the same time James Schnable is at the Maize Meeting in France, Zhikai Liang is in Nanjing, China presenting on his plant phenotyping work at the 2nd Annual Asia-Pacific Plant Phenotyping Conference.
Sarah Johnson becomes the second student to ever officially rotate in the Schnable lab. Sarah comes in with a background in plant pathology and soybean genomics and will be working on using image data to map QTLs in sorghum during her rotation.
Congratulations to Connor Pedersen, who won first prize in the undergraduate poster competition at the 2018 Nebraska Plant Breeding Symposium for his poster on a searching for computer vision traits from our greenhouse experiments which line up field measured traits from Genomes to Fields
Zhikai Liang successfully advances to PhD candidacy
Chenyong Miao presents a poster on time-series GWAS at Plant Phenome in Tucson, Arizona.
Xiuru Dai, a PhD student with one of our amazing collaborators (Pinghua Li at Shandong Agricultural University), starts a one year visit to the lab to identify additional genes involved in C4 photosynthesis using comparative genomics and machine learning
Nate Korth becomes the first student to ever officially rotate in the lab. Nate is one of the very first Nebraska Food for Health graduate fellows and is interested in research at the intersection of Food Science, Quantitative Genetics and the Human Gut Microbiome 2017.
- The lab bids farewell to Yang Zhang (lab member #1), as she leaves for a new staff scientist position at St. Jude Children’s hospital.
- Daniel Carvalho advances to PhD candidacy.
- Sunil Kumar joins the lab for a short term postdoc focused on becoming one of the world’s experts on Tripsacum genomics – it’s a small community – before he becomes a founding member of the Niederhuth lab at MSU in the spring.
- We’re happy to welcome Guangchao Sun who just finished up his PhD in the Wilson lab to the lab. Guangchao is studying the genetic control of variation in gene expression levels across maize hybrids.
- Xianjun Lai and Lang Yan, two visiting scholars in the lab from Sichuan, China both returned home this month. Xianjun is finishing up his PhD thesis at Sichuan Agricultural University now that his three papers are all submitted, Lang is taking the skills she learned working with maize and tripsacum back to her job working on potato functional genomics.
- The Schnable lab welcomes two new members, Preston Hurst, a masters student who comes from a private sector plant breeding background and will be working on nitrogen use efficiency phenotyping in corn, and Holly Podliska a UNL UCARE student and World Food Prize Alumn who will work on reconstructing the evolution cold and freezing tolerance across panicoid grasses.
- The lab’s very first venture into root microbiome research, a collaboration with IndigoAgriculture organized through Genomes2Fields.
Jinliang Yang leaves the Schnable Lab to start his own research group here at UNL as an assistant professor.
Daniel Carvalho is awarded a prestiguous graduate fellowship from the Daugherty Water for Food Global Institute to support his work on comparative genomic analysis of independent origins of C4 photosynthesis.
- Welcome to the lab Connor Pedersen & Xiaoyang (Chloe) Ye – both undergraduate research assistants – and Nicole Hollander (a high school summer intern supported by UNL-CRRI).
- Thanks to all in the lab for a successful fascination of plants event! We packed 21 high school students into the lab office to learn how to compare syntenic orthologous genes across grain crops using CoGe.
- Farewell to Logan Olsen, a great undergraduate who has been helping with propogating diverse maize lines over the past year. He is graduating and has been immediately snatched up with an offer of a full time job.
- The Schnable Lab hosts SK Gupta, ICRISAT’s lead pearl millet breeder and our collaborator on a project to develop a genomic selection guided breeding program for pearl millet hybrids.
- Prof. Schnable presents on the lab’s work on high throughput phenotyping of water use efficency in maize and sorghum at the 2017 Water for Food Global Conference.
- Tom Hoban, a freshman undergrad in the lab gives his very first poster presentation! (Screening for new sorghum roothairless mutants.)
- The 59th annual maize genetics conference.
Greetings from Tucson, AZ home of the the first annual Phenome Conference. Read notes on the various talks in this public google doc.
Prof. Schnable receives the UNL ARD Junior Faculty Excellent in Research Award.
Welcome aboard to Jinliang Yang, an alumi of the Ross-Ibarra Lab at UC Davis, the other Schnable Lab at ISU, and the Jinsheng Lai group at CAU.
First annual progress report on our collaborative cold stress project with the Roston Lab.
ARPA-E annouces tentative funding for our collaboration with the Dong Lab at Iowa State to develop a new generation of nitrogen sensors to look at both nitrogen uptake and remobilization of corn plants in the field. Here’s the annoucement (as a PDF).
Greetings from the IPPN phenotyping meeting held at CIMMYT in Mexico City, home of the third largest ancient pyramid in the world at Teotihuacan.
- Congratulations to our awesome collaborators in the Ge Lab and many thanks to USDA NIFA for funding our EAGER grant on a new generation of plant phenotyping robots.
- The lab is happen to welcome Logan Olson and Thomas Hoban as new undergraduate research assistants. Thomas is conducting a screen for new sorghum roothairless mutants in a sorghum deletion population generated by the Holding lab, and Logan is working with the maize diversity panel being phenotyped and sequenced as part of the UNL Center for Root and Rhizobiome Innovation.
Great write up in UNL today by the always excellent Scott Schrage about our collaborative work with the Ge Lab on maize phenotyping.
Gifts from the Gates Foundation and Raikes Foundation create the new Food for Health Center at the University of Nebraska. Lead by Andy Benson, the center will seek to understand the interactions between human health and the gut microbiome by using natural biochemical phenotypic diversity in crop plants to purturb the gut micriobiome.
“Integration of omic networks in a developmental atlas of maize” led by Steve Briggs at UCSD and Justin Walley at ISU, is published in the journal Science. The Schnable lab’s contribution to this paper focused on using data from multiple grass species to predict which genes will produce both RNA and protein and which genes will produce only RNA which is not translated into protein. Departmental news coverage here.
Chenyong Miao joins the lab as a PhD student, having just completed a masters degree with Schnable Lab collaborator Haibao Tang at Fujian Agriculture and Forestery University.
- Taylor Horn (Baylor) and Kyle Johnson (BYU) join the Schnable Lab as NSF Bioenergy REU funded undergraduates.
- Daniel Carvalho wins a Milton E. Mohr Fellowship in Biotechnology.
Zhikai Liang delivers a presentation at the 55th Annual Maize Genetics Conference on identifying different subtypes of the maize inbred B73 using published RNA-seq data. You can see the preprint describing the work he presented here.
At the same meeting a small subset of the progeny and grand progeny of Mike Freeling actually managed to gather in a single location. While the members of the Schnable lab (other than the PI) missed Freeling fest, they also had the chance to meet their grand advisor during the meeting.
And that’s it for 2015 folks!
- News breaks that the lab’s first federal grant, a collaboration with the Roston Lab to study low temperature tolerance across ten related grass species, was funded by USDA-NIFA
- 17 months after James arrived in Lincoln, the Schnable Lab is starting to look respectable.
- Xianjun Lai arrives in the lab, supported by a CSC scholarship from the Chinese government to spend two years of his PhD in Lincoln.
- Daniel Carvalho is awarded a PhD fellowship by the Brazilian government to join the lab.
- Lab tour of a production maize farm just across the Missouri river in western Iowa. Fascinating experience, thanks to the Iowa Corn Growers for organizing.
- Our first attempt to grow corn plants at the new UNL automated phenotyping greenhouse. … it does not go well.
- First attempt at a field season, working with David Holding’s lab to plant several hundred rows of maize RILs.
- Zhikai Liang joins the lab from Mississippi State. His is the lab’s very first PhD student.
- Yang Zhang becomes the very first memeber of the Schnable research group. She comes from Pinghua Li’s research group at CATAS (Chinese Academy of Tropical Agricultural Sciences).
- James Schnable’s first day in the lab. He initially has no lab space, no office, no desk, and no idea what he’s doing. Year’s later, he’s worked his way up to 2/4.