diff --git a/JSchnable.tex b/JSchnable.tex index 9e1c29945519548ba1c818380e9731a3b5946fc5..e0beb4f357d217901c1f71e233c17f9a07f4bdca 100644 --- a/JSchnable.tex +++ b/JSchnable.tex @@ -239,25 +239,25 @@ Nate Korth (co-advised, PhD, Food Science), Fangyi Li (co-advised, PhD, Complex Biosystems), Santos Yenandy Barrera Lemus (co-advised, PhD, Agronomy \& Horticulture) \item \textbf{Thesis Committees:} -Abbas Atefi (PhD, Biological Systems Engineering), +%Abbas Atefi (PhD, Biological Systems Engineering), Yen Ning Chai (PhD, Agronomy \& Horticulture), -Waseen Huassain (PhD, Agronomy \& Horticulture), +%Waseen Huassain (PhD, Agronomy \& Horticulture), Ying Ren (PhD, Agronomy \& Horticulture), Mallory Suhr (PhD, Food Science), Qinnan Yang (PhD, Food Science), -Ronghao Wang (PhD, Statistics), -Piyush Pandey (MS, Biological Systems Engineering), -Thao Yu (MS, Statistics), +%Ronghao Wang (PhD, Statistics), +%Piyush Pandey (MS, Biological Systems Engineering), +%Thao Yu (MS, Statistics), J. Preston Hurst (PhD, Agronomy \& Horticulture), -Leandra Parsons (PhD, Agronomy \& Horticulture), +%Leandra Parsons (PhD, Agronomy \& Horticulture), Rituaj Khound (PhD, Agronomy \& Horticulture), Sergio Manuel Gabriel Peralta (PhD, Plant Pathology), Shimin Chen (PhD, Food Science), Zachery Shomo (PhD, Biochemistry), Jared Haupt (PhD, Biochemistry), -Sairam Behera (PhD, Computer Science), +%Sairam Behera (PhD, Computer Science), Sarah Johnson (PhD, Agronomy \& Horticulture), -Michael Meier (PhD, Agronomy \& Horticulture), +%Michael Meier (PhD, Agronomy \& Horticulture), Semra Palali (PhD, Agronomy \& Horticulture) \item \textbf{Graduated Advisees:} Daniel Carvalho (PhD, Agronomy \& Horticulture), @@ -271,7 +271,7 @@ Srinidhi Bashyam (co-advised, MS, Computer Science \& Engineering) \item \textbf{Undergraduate Researchers:} 7 NSF supported REU (Research Experience for Undergraduates) students; 3 UCARE (Undergraduate Creative Activities and Research Experience) students; - and 24 undergraduate students supported by regular research funding. + and 36 undergraduate students supported by regular research funding. \item \textbf{High School Researchers:} 2 students supported through the Young Nebraska Scientist program; 1 supported by regular research funding. @@ -288,9 +288,13 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg \addtolength{\leftskip}{9mm} \subsection*{Preprints} -\noindent \textbf{Tross MC}, Gaillard M, \textbf{Zweiner M}, \textbf{Miao C}, Li B, Benes B, \textbf{Schnable JC}$^\S$ 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.06.15.448566}{10.1101/2021.06.15.448566}\\ +\noindent Xu G, Lyu J, Obata T, Liu S, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding. \textsc{bioRxiv} doi: \href{10.1101/2022.02.09.479784}{https://doi.org/10.1101/2022.02.09.479784} -\noindent Rodene E, Xu G, Delen SP, \textbf{Smith C}, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ A UAV-based high-throughput phenotyping approach to assess time-series nitrogen responses and identify traits associated genetic components in maize. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.05.24.445447}{10.1101/2021.05.24.445447} \\ +\noindent \textbf{Sun G}, Yu H, Wang P, Lopez-Guerrero MG, \textbf{Mural RV}, \textbf{Mizero ON}, \textbf{Grzybowski M}, Song B, van Dijk K, Schachtman DP, Zhang C, \textbf{Schnable JC}$^\S$ A role for heritable transcriptomic variation in maize adaptation to temperate environments. \textsc{bioRxiv} doi: \href{10.1101/2022.01.28.478212}{https://doi.org/10.1101/2022.01.28.478212} + +\noindent Boatwright JL, Sapkota S, \textbf{Jin H}, \textbf{Schnable JC}, Brenton Z, Boyles R, Kresovich S$^\S$ Sorghum Association Panel whole-genome sequencing establishes pivotal resource for dissecting genomic diversity. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.12.22.473950}{10.1101/2021.12.22.473950} + +\noindent Meier MA, Xu G, Lopez-Guerrero MG, Li G, \textbf{Smith C}, \textbf{Sigmon B}, Herr JR, Alfano J, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.11.01.466815}{10.1101/2021.11.01.466815}\\ \noindent \textbf{Miao C}, \textbf{Hoban TP}$^\ddagger$, \textbf{Pages A}$^\ddagger$, Xu Z, Rodene E, Ubbens J, Stavness I, Yang J, \textbf{Schnable JC}$^\S$ Simulated plant images improve maize leaf counting accuracy. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/706994}{10.1101/706994} \\ @@ -300,16 +304,28 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg %\noindent Wang M, Shilo S, Levy AA, Zelkowski M, Olson MA, Jiang J, \textbf{Schnable JC}, Sun Q, Pillardy J, Kianian PMA, Kianian SF, Chen C, Pawlowski WP$^\S$ Elucidating features and evolution of recombination sites in plants using machine learning. \textit{(In Review)} \\ -\noindent Kusmec A, Yeh CT, AlKhalifa N ... \textbf{Schnable JC} (26th of 38 authors) ... Willis DM, Wisser RJ, Schnable PS$^\S$ Data-driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates: a case study involving grain yield of hybrid maize. \textit{(In Review)}\\ +%\noindent \textbf{Sun G}$^*$, Yu H$^*$, Wang P, Lopez-Guerrero MG, \textbf{Mural RV}, \textbf{Mizero ON}, \textbf{Grzybowski M}, Song B, van Dijk K, Schachtman DP, Zhang C, \textbf{Schnable JC}$^\S$ A role for heritable transcriptomic variation in maize adaptation to temperate environments. \textit{(In Review)}\\ + +%\noindent \textbf{Korth N}, Parsons L, Van Haute M, Yang Q, Hurst JP, \textbf{Schnable JC}, Holding DR, Benson AK$^\S$ Identification of substrates from quality protein popcorn that promote growth of specific beneficial bacteria in the human gut microbiome. \textit{(In Review)}\\ + +%\noindent Yang Q, Van Haute M, \textbf{Korth N}, Sattler S, Toy J, \textbf{Schnable KC}, Benson AK$^\S$ Complex Trait Analysis of Human Gut Microbiome-Active Traits (MATs) in Sorghum bicolor: a new approach for genetic analysis of human health traits in food crops. \textit{(In Review)}\\ -\noindent \textbf{Sun G}, Wase N, Shu S, Jenkins J, Zhou B, Chen C, Sandor L, Plott C, Yoshinga Y, Daum C, Qi P, Barry K, Lipzen A, Berry L, Gottilla T, \textbf{Foltz A}, Yu H, O'Malley R, Zhang C, Devos KM, \textbf{Sigmon B}, Yu B, Obata T, Schmutz J$^\S$, \textbf{Schnable JC}$^\S$ Genome sequence of \textit{Paspalum vaginatum} indicates trehalose may act as a conserved trigger for increased nitrogen use efficiency in grasses. \textit{In Review} \\ +%\noindent Gen X, Lyu J, Obata T, Liu T, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ A historical balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding. \textit{(In Review)}\\ -\noindent Yu H, Sandhu J, \textbf{Sun G}, Nguyen H, Clemente T, \textbf{Schnable JC}, Walia H, Xie W, Yu B, Mower JP, Zhang C$^\S$ Pervasive misannotation of the smallest microexons that are evolutionarily conserved and crucial for gene function in plants. \textit{In Review} \\ +\noindent Kusmec A, Yeh CT, AlKhalifa N ... \textbf{Schnable JC} (26th of 38 authors) ... Willis DM, Wisser RJ, Schnable PS$^\S$ Data-driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates: a case study involving grain yield of hybrid maize. \textit{(In Review)}\\ + +\noindent \textbf{Sun G}, Wase N, Shu S, Jenkins J, Zhou B, Chen C, Sandor L, Plott C, Yoshinga Y, Daum C, Qi P, Barry K, Lipzen A, Berry L, Gottilla T, \textbf{Foltz A}, Yu H, O'Malley R, Zhang C, Devos KM, \textbf{Sigmon B}, Yu B, Obata T, Schmutz J$^\S$, \textbf{Schnable JC}$^\S$ Genome sequence of \textit{Paspalum vaginatum} indicates trehalose may act as a conserved trigger for increased nitrogen use efficiency in grasses. \textit{(In Review)} \\ \begin{etaremune} \subsection*{Faculty Publications} -\item Diao X$^\S$, Zhang H, Tang s, \textbf{Schnable JC}, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H (2021) Genome-Wide DNA polymorphism analysis and molecular marker development of Setaria italica variety 'SSR41' and application in positional cloning of Setaria white leaf sheath gene SiWLS1. \textsc{Frontiers in Plant Science} \textit{\href{https://www.frontiersin.org/articles/10.3389/fpls.2021.743782/abstract}{(In Press)}} +\item Rodene E, Xu G, Delen SP, \textbf{Smith C}, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ A UAV-based high-throughput phenotyping approach to assess time-series nitrogen responses and identify traits associated genetic components in maize. \textsc{The Plant Phenome Journal} doi: \href{10.1002/ppj2.20030}{https://doi.org/10.1002/ppj2.20030} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.05.24.445447}{10.1101/2021.05.24.445447} + +\item Yu H, Sandhu J, \textbf{Sun G}, Nguyen H, Clemente T, \textbf{Schnable JC}, Walia H, Xie W, Yu B, Mower JP, Zhang C$^\S$ (2022) Pervasive misannotation of the smallest microexons that are evolutionarily conserved and crucial for gene function in plants. \textsc{Nature Communications} doi: \href{10.1038/s41467-022-28449-8}{https://doi.org/10.1038/s41467-022-28449-8} + +\item \textbf{Tross MC}$\ddagger$, Gaillard M, \textbf{Zweiner M}$\ddagger$, \textbf{Miao C}, \textbf{Grove RJ}, Li B, Benes B, \textbf{Schnable JC}$^\S$ (2021) 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves. \textsc{PeerJ} doi: \href{https://doi.org/10.7717/peerj.12628}{10.7717/peerj.12628} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.06.15.448566}{10.1101/2021.06.15.448566} + +\item Diao X$^\S$, Zhang H, Tang s, \textbf{Schnable JC}, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H (2021) Genome-Wide DNA polymorphism analysis and molecular marker development of Setaria italica variety 'SSR41' and application in positional cloning of Setaria white leaf sheath gene SiWLS1. \textsc{Frontiers in Plant Science} doi: \href{https://doi.org/10.3389/fpls.2021.743782}{/10.3389/fpls.2021.743782} \item \textbf{Miao C}, \textbf{Guo A}$^\ddagger$, Thompson AM, Yang J, Ge Y, \textbf{Schnable JC}$^\S$ (2021) Automation of leaf counting in maize and sorghum using deep learning. \textsc{The Plant Phenome Journal} doi: \href{https://doi.org/10.1002/ppj2.20022}{10.1002/ppj2.20022} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.10.27.355495}{10.1101/2020.12.19.423626}