%\item Faculty Fellow, Robert B. Dougherty Water for Food Institute\hfill2016-Present
%\item Faculty Fellow, Robert B. Dougherty Water for Food Institute\hfill2016-Present
\end{itemize}
\end{itemize}
\section*{Research Support}
\section*{Research Support}
\begin{center}
\begin{center}
\$25.6M in total federal funding as PI/co-PI 2015-Present\\
\$25.6M in total federal funding as PI/co-PI 2015-Present\\
\textit{(Excludes \$20M CRRI award)}
\textit{(Excludes \$20M NSF Center for Root and Rhizobiome Innovation award (2016) and \$20M NSF AI Institute for Resilient Agriculture award (2021).)}
\item FFAR ``\href{http://www.ncsa.illinois.edu/news/story/crops_in_silico_project_awarded_5_million}{Crops in silico: Increasing crop production by connecting models from the microscale to the macroscale.}'' (co-PI) 2019-2023. \$5M
\item FFAR ``\href{http://www.ncsa.illinois.edu/news/story/crops_in_silico_project_awarded_5_million}{Crops in silico: Increasing crop production by connecting models from the microscale to the macroscale.}'' (co-PI) 2019-2023. \$5M
\item NSF ``AI Institute for Resilient Agriculture'' (Investigator) 2021-2026 \$20M
\item NSF ``\href{https://nsf.gov/awardsearch/showAward?AWD_ID=1557417}{Center for Root and Rhizobiome Innovation.}'' (Investigator \& Management Team Member) 2016-2021. \$20M
\item NSF ``\href{https://nsf.gov/awardsearch/showAward?AWD_ID=1557417}{Center for Root and Rhizobiome Innovation.}'' (Investigator \& Management Team Member) 2016-2021. \$20M
%\item DOE-JGI Community Sequencing Program ``Expanding grass genome comparators.''
%\item DOE-JGI Community Sequencing Program ``Expanding grass genome comparators.''
Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$undergraduate author, $^\S$corresponding author
Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$undergraduate author, $^\S$corresponding author
\end{center}
\end{center}
...
@@ -304,9 +309,9 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
...
@@ -304,9 +309,9 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\begin{etaremune}
\begin{etaremune}
\subsection*{Faculty Publications}
\subsection*{Faculty Publications}
\item\textbf{Miao C}, \textbf{Guo A}$^\ddagger$, 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}\textit{(Accepted)}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.10.27.355495}{10.1101/2020.12.19.423626}
\itemDiao 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)}}
\itemHurst JP, \textbf{Schnable JC}, Holding DR$^\S$ (2021) Tandem duplicate expression patterns are conserved between maize haplotypes of the $\alpha$-zeingene family. \textsc{Plant Direct}\textit{(Accepted)}
\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}
\item\textbf{Sun G}$^\S$, \textbf{Mural RV}, \textbf{Turkus JD}, \textbf{Schnable JC} (2021) Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel. \textsc{Phytopathology} doi: \href{https://doi.org/10.1094/PHYTO-04-21-0160-R}{10.1094/PHYTO-04-21-0160-R}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.04.02.438220}{10.1101/2021.04.02.438220}
\item\textbf{Sun G}$^\S$, \textbf{Mural RV}, \textbf{Turkus JD}, \textbf{Schnable JC} (2021) Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel. \textsc{Phytopathology} doi: \href{https://doi.org/10.1094/PHYTO-04-21-0160-R}{10.1094/PHYTO-04-21-0160-R}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2021.04.02.438220}{10.1101/2021.04.02.438220}
...
@@ -316,14 +321,16 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
...
@@ -316,14 +321,16 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\item Zhou Y, Kusmec A, Mirnezami SV, Srinivasan L, Jubery TZ, \textbf{Schnable JC}, Salas-Fernandez MG, Nettleton D, Ganapathysubramanian B, Schnable PS$^\S$ (2021) Identification and utilization of genetic determinants of trait measurement errors in image-based, high-throughput phenotyping. \textsc{The Plant Cell} doi: \href{https://doi.org/10.1093/plcell/koab134}{10.1093/plcell/koab134}
\item Zhou Y, Kusmec A, Mirnezami SV, Srinivasan L, Jubery TZ, \textbf{Schnable JC}, Salas-Fernandez MG, Nettleton D, Ganapathysubramanian B, Schnable PS$^\S$ (2021) Identification and utilization of genetic determinants of trait measurement errors in image-based, high-throughput phenotyping. \textsc{The Plant Cell} doi: \href{https://doi.org/10.1093/plcell/koab134}{10.1093/plcell/koab134}
\item Atefi A, Ge Y$^\S$, Pitla S, \textbf{Schnable JC} (2021) Robotic Technologies for High-Throughput Plant Phenotyping: Reviews and Perspectives. \textsc{Frontiers in Plant Science} doi: \href{https://www.frontiersin.org/articles/10.3389/fpls.2021.611940/}{10.3389/fpls.2021.611940}\textit{(Final Version In Press)}
\item Atefi A, Ge Y$^\S$, Pitla S, \textbf{Schnable JC} (2021) Robotic Technologies for High-Throughput Plant Phenotyping: Reviews and Perspectives. \textsc{Frontiers in Plant Science} doi: \href{https://www.frontiersin.org/articles/10.3389/fpls.2021.611940/}{10.3389/fpls.2021.611940}
\item Alzadjali A, Veeranampalayam-Sivakumar A, Alali MH, Deogun JS, Scott S, \textbf{Schnable JC}, Shi Y$^\S$ (2021) Maize tassel detection from UAV imagery using deep learning. \textsc{Frontiers in Robotics and AI}\href{https://www.frontiersin.org/articles/10.3389/frobt.2021.600410/}{10.3389/frobt.2021.600410}\textit{(Final Version In Press)}
\item Alzadjali A, Veeranampalayam-Sivakumar A, Alali MH, Deogun JS, Scott S, \textbf{Schnable JC}, Shi Y$^\S$ (2021) Maize tassel detection from UAV imagery using deep learning. \textsc{Frontiers in Robotics and AI}\href{https://www.frontiersin.org/articles/10.3389/frobt.2021.600410/}{10.3389/frobt.2021.600410}
\item Meier MA, Lopenz-Guerrero MG, Guo M, Schmer MR, Herr JR, \textbf{Schnable JC}, Alfano JR, Yang J$^\S$ (2021) Rhizosphere microbiomes in a historical maize/soybean rotation system respond to host species and nitrogen fertilization at genus and sub-genus levels. \textsc{Applied and Environmental Microbiology} doi: \href{https://doi.org/10.1128/AEM.03132-20}{10.1128/AEM.03132-20}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.08.10.244384}{10.1101/2020.08.10.244384}
\item Meier MA, Lopenz-Guerrero MG, Guo M, Schmer MR, Herr JR, \textbf{Schnable JC}, Alfano JR, Yang J$^\S$ (2021) Rhizosphere microbiomes in a historical maize/soybean rotation system respond to host species and nitrogen fertilization at genus and sub-genus levels. \textsc{Applied and Environmental Microbiology} doi: \href{https://doi.org/10.1128/AEM.03132-20}{10.1128/AEM.03132-20}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.08.10.244384}{10.1101/2020.08.10.244384}
\item Serb DD, \textbf{Meng X}, \textbf{Schnable JC}, Bashir E, Michaud JP, Vara Prasad PV, Perumal R (2021) Comparative transcriptome analysis reveals genetic mechanisms of sugarcane aphid resistance in grain sorghum. \textsc{International Journal of Molecular Sciences} doi: \href{https://doi.org/10.3390/ijms22137129}{10.3390/ijms22137129}
\item Serb DD, \textbf{Meng X}, \textbf{Schnable JC}, Bashir E, Michaud JP, Vara Prasad PV, Perumal R (2021) Comparative transcriptome analysis reveals genetic mechanisms of sugarcane aphid resistance in grain sorghum. \textsc{International Journal of Molecular Sciences} doi: \href{https://doi.org/10.3390/ijms22137129}{10.3390/ijms22137129}
\item Hurst JP, \textbf{Schnable JC}, Holding DR$^\S$ (2021) Tandem duplicate expression patterns are conserved between maize haplotypes of the $\alpha$-zeingene family. \textsc{Plant Direct} doi: \href{https://doi.org/10.1002/pld3.346}{10.1002/pld3.346}
\item Busta L, Schmitz E, Kosma D, \textbf{Schnable JC}, Cahoon EB$^\S$ (2021) A co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistry. \textsc{Proceedings of the National Academy of Sciences of the United States of America} doi: \href{https://doi.org/10.1073/pnas.2022982118}{10.1073/pnas.2022982118}
\item Busta L, Schmitz E, Kosma D, \textbf{Schnable JC}, Cahoon EB$^\S$ (2021) A co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistry. \textsc{Proceedings of the National Academy of Sciences of the United States of America} doi: \href{https://doi.org/10.1073/pnas.2022982118}{10.1073/pnas.2022982118}
\item\textbf{Meng X}, \textbf{Liang Z}, \textbf{Dai X}, \textbf{Zhang Y}, Mahboub S, \textbf{Ngu DW}$^\ddagger$, Roston RL, \textbf{Schnable JC}$^\S$ (2021) Predicting transcriptional responses to cold stress across plant species. \textsc{Proceedings of the National Academy of Sciences of the United States of America}. doi: \href{https://doi.org/10.1073/pnas.2026330118}{10.1073/pnas.2026330118}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.08.25.266635}{10.1101/2020.08.25.266635}
\item\textbf{Meng X}, \textbf{Liang Z}, \textbf{Dai X}, \textbf{Zhang Y}, Mahboub S, \textbf{Ngu DW}$^\ddagger$, Roston RL, \textbf{Schnable JC}$^\S$ (2021) Predicting transcriptional responses to cold stress across plant species. \textsc{Proceedings of the National Academy of Sciences of the United States of America}. doi: \href{https://doi.org/10.1073/pnas.2026330118}{10.1073/pnas.2026330118}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.08.25.266635}{10.1101/2020.08.25.266635}
...
@@ -369,7 +376,7 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
...
@@ -369,7 +376,7 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\item Peng B, Guan K$^\S$, Ainsworth EA, Asseng S, Bernacchi CJ, Cooper M, Delucia EH, Elliot JW, Ewert F, Grant RF, Gustafson DI, Hammer GL, Jin Z, Jones JW, Kimm H, Lawrence DM, Li Y, Lombardozzi DL, Marshall-Colon A, Messina CD, Ort DR, \textbf{Schnable JC}, Tang J, Vallejos CE, Wu A, Yin X, Zhou W (2020) Advancing multi-scale crop modeling for agricultural climate change adaptation assessment. \textsc{Nature Plants} doi: \href{https://t.co/rl4ywzzDhy?amp=1}{10.1038/s41477-020-0625-3}
\item Peng B, Guan K$^\S$, Ainsworth EA, Asseng S, Bernacchi CJ, Cooper M, Delucia EH, Elliot JW, Ewert F, Grant RF, Gustafson DI, Hammer GL, Jin Z, Jones JW, Kimm H, Lawrence DM, Li Y, Lombardozzi DL, Marshall-Colon A, Messina CD, Ort DR, \textbf{Schnable JC}, Tang J, Vallejos CE, Wu A, Yin X, Zhou W (2020) Advancing multi-scale crop modeling for agricultural climate change adaptation assessment. \textsc{Nature Plants} doi: \href{https://t.co/rl4ywzzDhy?amp=1}{10.1038/s41477-020-0625-3}
\item Adams J, Qiu Y, Xu Y, \textbf{Schnable JC}$^\S$ (2020) Plant segmentation by supervised machine learning methods. \textsc{The Plant Phenome Journal} doi: \href{http://dx.doi.org/10.1002/ppj2.20001}{10.1002/ppj2.20001}
\item\textbf{Liang Z}, Qiu Y, \textbf{Schnable JC}$^\S$ (2020) Distinct characteristics of genes associated with phenome-wide variation in maize (\textit{Zea mays}). \textsc{Molecular Plant} doi: \href{https://doi.org/10.1016/j.molp.2020.03.003}{10.1016/j.molp.2020.03.003}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/534503}{10.1101/534503}\\
\item\textbf{Liang Z}, Qiu Y, \textbf{Schnable JC}$^\S$ (2020) Distinct characteristics of genes associated with phenome-wide variation in maize (\textit{Zea mays}). \textsc{Molecular Plant} doi: \href{https://doi.org/10.1016/j.molp.2020.03.003}{10.1016/j.molp.2020.03.003}\textsc{bioRxiv} doi: \href{https://doi.org/10.1101/534503}{10.1101/534503}\\
\textbf{\textit{ Selected as an Editor's Choice by MaizeGDB Editorial Board}} May 2020
\textbf{\textit{ Selected as an Editor's Choice by MaizeGDB Editorial Board}} May 2020
...
@@ -500,7 +507,7 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
...
@@ -500,7 +507,7 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\subsection*{Graduate Publications}
\subsection*{Graduate Publications}
\item Woodhouse MR, Sen S, Schott D, Portwood JL, Freeling M, Walley JW, Andorf CM, \textbf{Schnable JC} (2021) qTeller: A tool for comparative multi-genomic gene expression analysis. \textsc{Bioinformatics}\textit{(Accepted Pending Minor Revision)}
\item Woodhouse MR$^\S$, Sen S, Schott D, Portwood JL, Walley JL, Andorf CM, \textbf{Schnable JC} (2021) qTeller: A tool for comparative multi-genomic gene expression analysis. \textsc{Bioinformatics}doi: \href{https://doi.org/10.1093/bioinformatics/btab604}{10.1093/bioinformatics/btab604}
\item Cheng F, Sun C, Wu J, {\bf Schnable JC}, Woodhouse MR, Liang J, Cai C, Freeling M,$^\S$ Wang X$^\S$ (2016) Epigenetic regulation of subgenome dominance following whole genome triplication in \textit{Brassica rapa}. \textsc{New Phytologist} doi: \href{http://dx.doi.org/10.1111/nph.13884}{10.1111/nph.13884}
\item Cheng F, Sun C, Wu J, {\bf Schnable JC}, Woodhouse MR, Liang J, Cai C, Freeling M,$^\S$ Wang X$^\S$ (2016) Epigenetic regulation of subgenome dominance following whole genome triplication in \textit{Brassica rapa}. \textsc{New Phytologist} doi: \href{http://dx.doi.org/10.1111/nph.13884}{10.1111/nph.13884}
...
@@ -552,7 +559,7 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
...
@@ -552,7 +559,7 @@ Lab members in \textbf{bold}, $^*$authors contributed equally, $^\ddagger$underg
\subsection*{Peer Reviewed Conference Papers}
\subsection*{Peer Reviewed Conference Papers}
\begin{etaremune}
\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}\textit{(Accepted)}
\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 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 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}
\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}
...
@@ -649,6 +656,7 @@ Science Advances
...
@@ -649,6 +656,7 @@ Science Advances
% \item University of Massachusetts Amherst, Oxford, OH, USA\textit{\hfill(Sept. 2019)}
% \item University of Massachusetts Amherst, Oxford, OH, USA\textit{\hfill(Sept. 2019)}
%\end{itemize}
%\end{itemize}
\begin{itemize}
\begin{itemize}
\item California State East Bay, Hayward, CA, USA \hfill 2021 \textit{(Remote, COVID)}
\item University of Missouri, Columbia, MO, USA\hfill2020 \textit{(Remote, COVID)}
\item University of Missouri, Columbia, MO, USA\hfill2020 \textit{(Remote, COVID)}
\item Rutgers University, New Brunswick, NJ, USA\hfill2020 \textit{(Remote, COVID)}
\item Rutgers University, New Brunswick, NJ, USA\hfill2020 \textit{(Remote, COVID)}
\item Bayer Crop Science, St. Louis, MO, USA\hfill2020 \textit{(Remote, COVID)}
\item Bayer Crop Science, St. Louis, MO, USA\hfill2020 \textit{(Remote, COVID)}
...
@@ -690,6 +698,8 @@ Science Advances
...
@@ -690,6 +698,8 @@ Science Advances
\emph{Invited presentations only. Excludes presentations selected based on abstracts or applications.}
\emph{Invited presentations only. Excludes presentations selected based on abstracts or applications.}
\end{center}
\end{center}
\begin{itemize}
\begin{itemize}
\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)}