Commit 218fceaa authored by James Schnable's avatar James Schnable
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JSchnable.tex

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......@@ -233,17 +233,16 @@ NSF PGRP Fellowship Supported Postdoctoral Researcher \hfill 2013
\item \textbf{Current Graduate Advisees:}
Hongyu Jin (PhD, Complex Biosystems),
Michael Tross (PhD, Complex Biosystems),
Mackenzie Zweiner (MS, Agronomy \& Horticulture),
Kahheetah Barnoskie (MS, Agronomy \& Horticulture),
Nate Korth (co-advised, PhD, Food Science),
Fangyi Li (co-advised, PhD, Complex Biosystems),
Santos Yenandy Barrera Lemus (co-advised, PhD, 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),
Yen Ning Chai (PhD, Agronomy \& Horticulture),
%Waseen Huassain (PhD, Agronomy \& Horticulture),
Ying Ren (PhD, Agronomy \& Horticulture),
Mallory Suhr (PhD, Food Science),
%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),
......@@ -266,6 +265,8 @@ Chenyong Miao (PhD, Agronomy \& Horticulture),
Preston Hurst (MS, Agronomy \& Horticulture),
Xianjun Lai (PhD, Sichuan Agriculture University),
Xiuru Dai (PhD, Shandong Agriculture University),
Santos Yenandy Barrera Lemus (co-advised, PhD, Agronomy \& Horticulture)
Mackenzie Zweiner (MS, Agronomy \& Horticulture),
Bhushit Agarwal (co-advised, MS, Computer Science \& Engineering),
Srinidhi Bashyam (co-advised, MS, Computer Science \& Engineering)
\item \textbf{Undergraduate Researchers:}
......@@ -279,7 +280,7 @@ Srinidhi Bashyam (co-advised, MS, Computer Science \& Engineering)
\section*{Publications}
\begin{center}
\textbf{H-Index:} \textbf{\href{https://scholar.google.com/citations?user=cik4JVYAAAAJ}{35}} \\
\textbf{H-Index:} \textbf{\href{https://scholar.google.com/citations?user=cik4JVYAAAAJ}{36}} \\
Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$undergraduate author, $^\S$corresponding author
\end{center}
......@@ -288,11 +289,17 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\addtolength{\leftskip}{9mm}
\subsection*{Preprints}
\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 \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 \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 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}
\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 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{https://doi.org/10.1101/2022.02.09.479784}{10.1101/2022.02.09.479784}\\
\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}\\
......@@ -304,28 +311,24 @@ 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 \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 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 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)} \\
\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{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 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 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 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}
\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 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}
......@@ -575,7 +578,8 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\subsection*{Peer Reviewed Conference Papers}
\begin{etaremune}
\item Khan SH, Tope S, Dalpati R, Kim KH, Noh M, Bulbul A, \textbf{Mural RV}, Banerjee A, \textbf{Schnable JC}, Ji M, Mastrango C, Zang L, Kim H. (2021) Development of a gas sensor for green leaf volatile detection. \textsc{Transducers 2021} doi: \href{https://doi.org/10.1109/Transducers50396.2021.9495597}{10.1109/Transducers50396.2021.9495597}
\item Khan SH, Karkhanis M, Hatasaka B, Tope S, Noh S, Bulbul A, Banerjee A, Ji M, Mastrangelo CH, Kim H, Dalapati R, Zang L, \textbf{Mural RV}, \textbf{Schnable JC}, Kim K (2022) Field deployment of a nanogap gas sensor for crop damage detection. \textsc{35th International Conference on Micro Electro Mechanical Systems Conference (MEMS)} Berlin, Germany doi: \href{https://doi.org/10.1109/MEMS51670.2022.9699614}{10.1109/MEMS51670.2022.9699614}
\item Khan SH, Tope S, Dalpati R, Kim KH, Noh M, Bulbul A, \textbf{Mural RV}, Banerjee A, \textbf{Schnable JC}, Ji M, Mastrango C, Zang L, Kim H (2021) Development of a gas sensor for green leaf volatile detection. \textsc{Transducers 2021} doi: \href{https://doi.org/10.1109/Transducers50396.2021.9495597}{10.1109/Transducers50396.2021.9495597}
\item Gaillard M, \textbf{Miao C}, \textbf{Schnable JC}, Benes B (2020) Sorghum Segmentation by Skeleton Extraction. \textsc{Computer Vision Problems in Plant Phenotyping (CVPPP 2020)} Glasgow, UK
\item Sankaran S, Zhang C, \textbf{Hurst JP}, Marzougui A, Sivakumar ANV, Li J, \textbf{Schnable JC}, Shi Y (2020) Investigating the potential of satellite imagery for high-throughput field phenotyping applications. \textsc{SPIE Defense + Commercial Sensing} California, USA doi: \href{https://doi.org/10.1117/12.2558729}{10.1117/12.2558729}
\item Al-Zadjali A, Shi Y, Scott S, Deogun JS, and \textbf{Schnable JC} (2020) Faster-R-CNN based deep learning for locating corn tassels in UAV imagery. \textsc{SPIE Defense + Commercial Sensing} California, USA doi: \href{https://doi.org/10.1117/12.2560596}{10.1117/12.2560596}
......@@ -714,6 +718,10 @@ Science Advances
\emph{Invited presentations only. Excludes presentations selected based on abstracts or applications.}
\end{center}
\begin{itemize}
%Michigan Plant Science Symposium
%Nexus symposium
\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)}
\item Plant Science Symposium West Africa (Student Organized) \hfill 2021 \textit{(Remote, COVID)}
\item Soybean Breeders Workshop \hfill 2021 \textit{(Remote, COVID)}
......
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