Commit fe6df4a5 authored by James Schnable's avatar James Schnable
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crri paper

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......@@ -125,8 +125,9 @@
\section*{Employment}
\begin{itemize}
\item University of Nebraska-Lincoln
\\Professor, Department of Agronomy and Horticulture\hfill 2022-Present
\\Charles O. Gardner Professor of Maize Quantitative Genetics \hfill 2019-Present
\\Associate Professor, Department of Agronomy and Horticulture \hfill 2019-Present
\\Associate Professor, Department of Agronomy and Horticulture \hfill 2019-2022
\\Assistant Professor, Department of Agronomy and Horticulture \hfill 2014-2019
\item Chinese Academy of Agricultural Sciences\\
NSF PGRP Fellowship Supported Visiting Scholar \hfill 2014
......@@ -137,7 +138,7 @@ NSF PGRP Fellowship Supported Postdoctoral Researcher \hfill 2013
%EDUCATION
\section*{Education}
\begin{itemize}
\item PhD Plant Biology \hfill 2008-2012\\University of California-Berkeley (Advisor: Michael Freeling)
\item PhD Plant Biology \hfill 2008-2012\\University of California-Berkeley
\item BA Biology \hfill 2004-2008\\Cornell University
\end{itemize}
......@@ -235,7 +236,7 @@ Hongyu Jin (PhD, Complex Biosystems),
Michael Tross (PhD, Complex Biosystems),
Nate Korth (co-advised, PhD, Food Science),
Fangyi Li (co-advised, PhD, Complex Biosystems),
Kahheetah Barnoskie (co-advised MS, Agronomy \& Horticulture),
%Kahheetah Barnoskie (co-advised MS, Agronomy \& Horticulture),
Kyle Linders (co-advised MS, Agronomy \& Horticulture)
\item \textbf{Thesis Committees:}
%Abbas Atefi (PhD, Biological Systems Engineering),
......@@ -250,8 +251,8 @@ Qinnan Yang (PhD, Food Science),
J. Preston Hurst (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),
%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),
......@@ -289,8 +290,6 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\addtolength{\leftskip}{9mm}
\subsection*{Preprints}
\noindent \textbf{Mural RV}, \textbf{Sun G}, \textbf{Grzybowski M}, \textbf{Tross MC}, \textbf{Jin H}, \textbf{Smith C}, Newton L, Andorf CM, Woodhouse MR, Thompson AM, \textbf{Sigmon B}, \textbf{Schnable JC}$^\S$ Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2022.02.25.480753}{10.1101/2022.02.25.480753}\\
\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. \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.08.18.456832}{10.1101/2021.08.18.456832} \\
\noindent Yang Q, Van Haute M, \textbf{Korth N}, Sattler S, Toy J, Rose D, \textbf{Schnable JC}, Benson A$^\S$ Complex trait analysis of human gut microbiome-active traits in \textit{Sorghum bicolor}: a new category of human health traits in food crops. \textsc{Research Square} doi: \href{https://doi.org/10.21203/rs.3.rs-1490527/v1}{10.21203/rs.3.rs-1490527/v1}
......@@ -299,30 +298,39 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\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{https://doi.org/10.1101/2022.01.28.478212}{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} \\
\noindent Zhang Z$^\S$, Chen C, Rutkoski J, \textbf{Schnable JC}, Murray S, Wang L, Jin X, Stich B, Crossa J, Hayes B. Harnessing Agronomics Through Genomics and Phenomics in Plant Breeding: A Review. \textsc{preprints.org} doi: \href{https://www.preprints.org/manuscript/202103.0519/v1}{10.20944/preprints202103.0519.v1}
\subsection*{Other Manuscripts in Review}
%\subsection*{Other Manuscripts in Review}
%\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 \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 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 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 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 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 Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu J, Wang K, Xin B, Zhao H, Song W, Hufford MB, \textbf{Schnable JC}, Ware DH, Jin W, Lai J$^\S$ A complete telomere-to-telomere assembly of the genome of maize. \textit{(In Review)}
%\noindent Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu J, Wang K, Xin B, Zhao H, Song W, Hufford MB, \textbf{Schnable JC}, Ware DH, Jin W, Lai J$^\S$ A complete telomere-to-telomere assembly of the genome of maize. \textit{(In Review)}
\begin{etaremune}
\subsection*{Faculty Publications}
\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{https://doi.org/10.1002/ppj2.20030}{10.1002/ppj2.20030} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.05.24.445447}{10.1101/2021.05.24.445447}
\item Meier M, Xu G, Lopez-Guerrero, Li G, \textbf{Smith C}, \textbf{Sigmon B}, Herr J, Alfano J, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ (2022) Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance. \textsc{eLife} \textit{(Accepted)}
\item \textbf{Mural RV}, \textbf{Sun G}, \textbf{Grzybowski M}, \textbf{Tross MC}, \textbf{Jin H}, \textbf{Smith C}, Newton L, Andorf CM, Woodhouse MR, Thompson AM, \textbf{Sigmon B}, \textbf{Schnable JC}$^\S$ (2022) Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize. \textsc{Gigascience} doi: \textit{(Accepted)} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2022.02.25.480753}{10.1101/2022.02.25.480753}
\item \textbf{Korth N}, Parsons L, Van Haute M, Yang Q, Hurst JP, \textbf{Schnable JC}, Holding DR, Benson AK$^\S$ The unique seed protein composition of quality protein popcorn promotes growth of beneficial bacteria from the human gut microbiome. \textsc{Frontiers in Microbiology} doi: \href{https://www.frontiersin.org/articles/10.3389/fmicb.2022.921456/abstract}{10.3389/fmicb.2022.921456}
\item \textbf{Mural RV}, \textbf{Schnable JC}$^\S$ (2022) Can the grains offer each other helping hands? Convergent molecular mechanisms associated with domestication and crop improvement in rice and maize. \textsc{Molecular Plant} doi: \href{https://doi.org/10.1016/j.molp.2022.04.003}{10.1016/j.molp.2022.04.003}\\
\textit{Peer Reviewed Invited Perspective}
\item Boatwright JL, Sapkota S, \textbf{Jin H}, \textbf{Schnable JC}, Brenton Z, Boyles R, Kresovich S$^\S$ (2022) Sorghum Association Panel whole-genome sequencing establishes pivotal resource for dissecting genomic diversity. \textsc{The Plant Journal} doi: \href{https://doi.org/10.1111/tpj.15853}{10.1111/tpj.15853} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.12.22.473950}{10.1101/2021.12.22.473950}
\item Rodene E, Xu G, Delen SP, \textbf{Smith C}, Ge Y, \textbf{Schnable JC}, Yang J$^\S$ (2022) 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{https://doi.org/10.1002/ppj2.20030}{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{https://doi.org/10.1038/s41467-022-28449-8}{10.1038/s41467-022-28449-8}
......@@ -720,6 +728,9 @@ Science Advances
\begin{itemize}
%Michigan Plant Science Symposium
%Nexus symposium
\item IPPN-CEPPG Workshop on Environment Simulation and Phenotyping, Gatersleben, Germany\hfill 2022
\item Michigan State Genome Sciences Symposium (Student Organized), East Lansing, MI, USA\hfill 2022
\item Nexus Informatics, Kansas City, MO, USA\hfill 2022
\item Molecular Plant Virtual Seminar Series \hfill 2022 \textit{(Remote, COVID)}
\item DIGICROP 2022 \hfill 2022 \textit{(Remote, COVID)}
\item Machine Learning for Cyber-Agricultural Systems (Keynote) \hfill 2021 \textit{(Remote, COVID)}
......
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