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Schnable} +\renewcommand\thefootnote{\textcolor{unlred}{\arabic{footnote}}} + + +% Replace this with a link to your CV if you like, or set it empty +% (as in \def\footerlink{}) to remove the link in the footer: +%\def\footerlink{https://github.com/rossibarra/CV/blob/master/CV.pdf?raw=true} + +%Add in-line comments +\newcommand{\ignore}[1]{} + +% The following metadata will show up in the PDF properties +\hypersetup{ + colorlinks = true, + urlcolor = unlred, + pdfauthor = {\name}, + pdfkeywords = {comparative genomics, maize, grasses}, + pdftitle = {\name: Curriculum Vitae}, + pdfsubject = {Curriculum Vitae}, + pdfpagemode = UseNone +} + +\geometry{ + body={6.5in, 9in}, + left=1.0in, + top=1.0in +} + +% Customize page headers +\pagestyle{myheadings} +\markright{\name} +\thispagestyle{empty} + +% Custom section fonts +\usepackage{sectsty} +\sectionfont{\rmfamily\mdseries\Large} +\subsectionfont{\rmfamily\mdseries\itshape\large} + +% Other possible font commands include: +% \ttfamily for teletype, +% \sffamily for sans serif, +% \bfseries for bold, +% \scshape for small caps, +% \normalsize, \large, \Large, \LARGE sizes. + +% Don't indent paragraphs. +\setlength\parindent{0em} + +% Make lists without bullets +%\renewenvironment{itemize}{ +% \begin{list}{}{ +% \setlength{\leftmargin}{1.5em} +% } +%}{ +% \end{list} +%} + +\begin{document} + +% Place name at left +\centerline{\huge \textsc{Curriculum Vitae}} +\vspace{0.25in} +\centerline{\huge \textsc{\name}} +%Updated transliteration of Schnable, thanks to Zhikai Liang +\centerline{\begin{CJK*}{UTF8}{gbsn}詹姆斯 . 施耐博\end{CJK*}} + +% Alternatively, print name centered and bold: +%\centerline{\huge \bf \name} + +\vspace{0.25in} + +%ADDRESS +\begin{minipage}{0.5\linewidth} + \begin{center} +% \href{http://bigdata.unl.edu/}{Quantitative Life Sciences Initiative}\\ +% \href{http://www.unl.edu/psi/}{Center for Plant Science Innovation}\\ +% \href{https://foodforhealth.unl.edu/}{Nebraska Food for Health Center}\\ +% \href{http://agronomy.unl.edu}{Department of Agronomy \& Horticulture}\\ +% \href{http://www.unl.edu}{University of Nebraska-Lincoln} \\ + Quantitative Life Sciences Initiative\\ + Center for Plant Science Innovation\\ + Department of Agronomy \& Horticulture\\ + University of Nebraska-Lincoln\\ + +\end{center} +\end{minipage} +\begin{minipage}{0.5\linewidth} + \begin{center} + \begin{tabular}{ll} + Office: & E207 Beadle Center \\ + Phone: & (402) 472-4540 \\ +% Fax: & \\ + Email: & \href{mailto:schnable@unl.edu}{schnable@unl.edu} \\ + Web: & \href{http://www.schnablelab.org/}{schnablelab.org}\footnote{Clickable hyperlinks are in \textcolor{unlred}{blue} throughout} +% \\ + \end{tabular} +\end{center} +\end{minipage} + +%EMPLOYMENT +\section*{UNL Employment} +\begin{itemize} +\item University of Nebraska-Lincoln +\\Associate Professor, Department of Agronomy and Horticulture \hfill 2019-Present +\\Assistant Professor, Department of Agronomy and Horticulture \hfill 2014-2019 +\end{itemize} +\vspace{-0.25in} +\section*{Advising} +\subsection*{2020 Undergraduate Researcher Advisees:} +\begin{enumerate} +\item Thomas Hoban (graduated in summer 2020) +\item Aime Nishimwe (CUSP scholar, published as co-author in 2020) +\item Isaac Stevens +\item Elijah Frost +\item Alice Guo (in review paper as co-author in 2020) +\item Logan Duryee +\item Olivier Mizero (CUSP scholar) +\item Alexis Finch +\item Luke Micek +\item Aldi Airori +\item Jocelyne Horanituze (CUSP scholar) +\item Nate Pester (graduated in summer 2020, attending med school at UNMC) +\item Leighton Wheeler (graduated in summer 2020) +\item Sierra Conway +\item Madison Tunnell (remote REU student from Kansas State University) +\item Isabel Sigmon +\item Clay Christenson +\item Jean D’Amour Kwizerimana (CUSP Scholar)\\ \\ +\noindent \textit{Alex Enerson (former advisee, graduated in 2019, published as co-author in 2020)}\\ \\ +\noindent \textit{Alejandro Pages (former advisee, graduated in 2019, published as co-author in 2020)} +\subsection*{2020 Graduate Advisees:} +\item Chenyong Miao (PhD) (Graduated Dec 2020) +\item Hongyu Jin (PhD) +\item Michael Tross (PhD) +\item Mackenzie Zweiner (MS) +\item Kahheetah Barnoskie (MS) +\item Nate Korth (co-advised, PhD) +\item Fangyi Li (co-advised, PhD) +\item Santos Yenandy Barrera Lemus (co-advised, PhD) +\item Michael Richter (rotating PhD student in 2020) +\subsection*{2020 Postdoctoral Advisees:} +\item Guangchao Sun +\item Marcin Grzybowski +\item Ravi Mural +\item Xiaoxi Meng (attained new postion at University of Minnesota in 2020) +\subsection*{2020 Faculty Mentees:} +\item Brandi Sigmon (Assistant Professor of Practice, Plant Pathology) +\end{enumerate} +\vspace{-0.25in} +\subsection*{2020 Thesis Committee Service:} +\begin{itemize} +\item Yen Ning Chai (PhD, Agronomy \& Horticulture) +\item Mallory Suhr (PhD, Food Science) +\item Qinnan Yang (PhD, Food Science) +\item Ronghao Wang (PhD, Statistics) +\item J. Preston Hurst (PhD, Agronomy \& Horticulture) +\item Leandra Parsons (PhD, Agronomy \& Horticulture) +\item Rituaj Khound (PhD, Agronomy \& Horticulture) +\item Sergio Manuel Gabriel Peralta (PhD, Plant Pathology) +\item Shimin Chen (PhD, Food Science) +\item Zachery Shomo (PhD, Biochemistry) +\item Jared Haupt (PhD, Biochemistry) +\item Sairam Behera (PhD, Computer Science) +\item Sarah Johnson (PhD, Agronomy \& Horticulture) +\item Michael Meier (PhD, Agronomy \& Horticulture) +\item Semra Palali (PhD, Agronomy \& Horticulture) +\end{itemize} + +\section*{2020 Classroom Instruction:} +\begin{itemize} +\item LIFE 891\hfill"Big Questions in Complex Biosystems"\hfill In Person \hfill Enrollment: 3 +\item AGRO 896-791\hfill"Network Science Applied to Agronomical and Biological Sciences"\hfill Online; Joint with Federal University of Minas Gerais, Brazil \hfill Total Enrollment (UNL Enrollment): 20 (1) +\end{itemize} + +\section*{Grant Funding} +\begin{enumerate} +\subsection*{New in 2020} +\item USDA-NIFA ``\href{https://portal.nifa.usda.gov/web/crisprojectpages/1022298-high-intensity-phenotyping-sites.html}{High Intensity Phenotyping Sites: Transitioning To A Nationwide Plant Phenotyping Network.}'' (co-PI) 2020-2023. \$3.0M +\item USDA-NIFA ``\href{https://portal.nifa.usda.gov/web/crisprojectpages/1022122-cps-medium-collaborative-research-field-scale-single-plant-resolution-agricultural-management-using-coupled-molecular-and-macro-sensing-and-multi-scale-data-fusion-and-modeling.html}{CPS: Medium: Field-scale, single plant-resolution agricultural management using coupled molecular and macro sensing and multi-scale data fusion and modeling}'' (co-PI) 2020-2023 \$1.05M +\item ARPA-E ``\href{https://arpa-e.energy.gov/?q=news-item/arpa-e-announces-165-million-technologies-supporting-biofuels-supply-chain}{Soil Organic Carbon Networked Measurement System (SOCNET)}'' (co-PI) 2020-2023 \$1.9M +\item USDA-NIFA ``High Intensity Phenotyping Sites: A Multi-Scale, Multi-Modal Sensing and Sense-Making Cyber-Ecosystem for Genomes to Fields'' (co-PI) (2020-2023) \$2.7M +\item ARPA-E ``CORN- Crop Optimization Realized through Neuralnets'' (co-PI) 2020-2022 \$620k +\item Nebraska Corn Board ``Genomes to Fields (G2F) - Predicting Final Yield Performance in Variable Environments.'' (PI) 2016-2021. \$250k (Competitive annual renewal in 2020) +\item ICRISAT ``Identifying Novel Loci Controlling Priority Traits in Pearl Millet and Sorghum using Supervised Classification Algorithms.'' (PI) 2020-2021 \$50k + +\subsection*{Ongoing in 2020} +\item DOE ``\href{https://news.unl.edu/newsrooms/today/article/nebraska-team-merges-machine-learning-plant-genetics-to-maximize-sorghum/}{TGCM: (T)rait, (G)ene, and (C)rop Growth (M)odel directed targeted gene characterization in sorghum}.'' (PI) 2019-2022. \$2.7M +\item NSF ``\href{https://www.nsf.gov/awardsearch/showAward?AWD_ID=1838307}{RoL: FELS: EAGER: Genetic constraints on the increase of organismal complexity over time.}'' (PI) 2018-2021. \$300k +\item USDA-NIFA ``\href{https://portal.nifa.usda.gov/web/crisprojectpages/1008702-identifying-mechanisms-conferring-low-temperature-tolerance-in-maize-sorghum-and-frost-tolerant-relatives.html}{Identifying mechanisms conferring low temperature tolerance in maize, sorghum, and frost tolerant relatives.}'' (PI) 2015-2020. \$455k +\item NSF ``\href{https://www.nsf.gov/awardsearch/showAward?AWD_ID=1844707}{BTT EAGER: A wearable plant sensor for real-time monitoring of sap flow and stem diameter to accelerate breeding for water use efficiency.}'' (co-PI) 2019-2021. \$300k +\item NSF ``\href{https://www.nsf.gov/awardsearch/showAward?AWD_ID=1826781}{RII Track-2 FEC: Functional analysis of nitrogen responsive networks in Sorghum.}'' (co-PI) 2018-2022. \$4M +\item ARPA-E ``\href{https://unews.utah.edu/protecting-the-field-of-dreams/}{Low cost wireless chemical sensor networks.}'' (co-PI) 2019-2022. \$2.2M +\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 ``\href{https://nsf.gov/awardsearch/showAward?AWD_ID=1557417}{Center for Root and Rhizobiome Innovation.}'' (Investigator \& Management Team Member) 2016-2021. \$20M +\item Wheat Innovation Foundation ``A Low-Cost, High-Throughput Cold Stress Perception Assay for Sorghum Breeding.'' (co-PI) 2019-2021. \$205k +\end{enumerate} +\subsection*{Submitted in 2020} +\begin{itemize} +\item DOE "Plant resilience to extreme short‐term climatic events: discovery through integrated mechanistic models and machine learning" \$15M (co-PI) \textbf{Status:} \textcolor{red}{Declined} +\item USDA-NIFA "Scaling Soil Health Indicators From Fields to Regions." \$500k (co-PI) \textbf{Status:} \textcolor{red}{Declined} +\item ARPA-E "SURF: Smart Underground RFID For In-Soil CO2 Measurement" \$2.0M (co-PI) \textbf{Status:} \textcolor{red}{Declined} +\item NSF "REU Site: Integrated Development of Bioenergy Systems" \$416k (participant) \textbf{Status:} Pending +\item NSF "AI Institute for Resilient Agriculture (AIIRA)" \$20M (co-PI) \textbf{Status:} Pending +\end{itemize} + + + +%PROFESSIONAL SERVICE +\addtolength{\leftskip}{-9mm}\section*{2020 Service/Citizenship} +\subsection*{University} +\begin{itemize} +\item Consortium for Integrated Translational Biology (CITB)\hfill2014-Present +\item UNL Faculty Greenhouse Committee\hfill2015-Present +\item Nebraska Food for Health Center Faculty Advisory Committee\hfill2017-Present +\item Department of Agronomy and Horticulture Awards Committee\hfill2019-Present +\item Department of Agronomy and Horticulture Graduate Admissions Committee\hfill2019-Present +\end{itemize} + +\subsection*{Professional} +\begin{itemize} +%find and add other associate editorship +\item \textbf{Guest Editor:} The Plant Cell\hfill2019-Present +\item Data Management Subcommittee, Maize Genetics Research Collaboration Network \hfill 2018-Present +\item MaizeGDB Advisory Committee\hfill 2018-Present +\item \textbf{Grant Reviewer:} NSF (panel \& ad hoc), USDA (panel) +\end{itemize} + +%SEMINARS +\section*{2020 Invited Talks:} +\subsection*{At External Institutions} +%\begin{itemize} +% \item Miami University, Oxford, OH, USA \textit{\hfill(Sept. 2019)} +% \item University of Massachusetts Amherst, Oxford, OH, USA\textit{\hfill(Sept. 2019)} +%\end{itemize} +\begin{itemize} +\item University of Missouri, Columbia, MO, 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 University of Bonn, Bonn, Germany\hfill2020 \textit{(Remote, COVID)} +\item King Abdullah University of Science and Technology, Jeddeh, Saudi Arabia \hfill 2020 \textit{(Remote, COVID)} +\end{itemize} +\subsection*{At External Conferences} +\begin{center} +\emph{Invited presentations only. Excludes presentations selected based on abstracts or applications.} +\end{center} +\begin{itemize} +\item DIGICROP 2020, Digital Technologies for Sustainable Crop Production (Germany)\hfill 2020 \textit{(Remote, COVID)} +\item National Association of Plant Breeders Annual Meeting, Lincoln, NE, USA\hfill 2020 \textit{(Remote, COVID)} +\item iGenomX Session, Plant and Animal Genome, San Diego, CA, USA\hfill2020 +\item Systems Biology and Ontologies Session, Plant and Animal Genome, San Diego, CA, USA\hfill2020 +\end{itemize} +\subsection*{At Internal Events} +\begin{itemize} +\item Agronomy \& Horticulture Departmental Seminar Series, UNL\hfill2020 \textit{(Remote, COVID)} +\end{itemize} + +\section*{2020 Awards and Recognition} +\begin{itemize} +\item Chenyong Miao was nominated for and recieved Widaman Distinguished Graduate Fellowship. +\item Guangchao Sun recieved 2020 CROPS presentation award. +\item James Schnable elected to the Board of Directors of the Maize Genetics Cooperation. +\item "\href{https://ianrnews.unl.edu/james-schnable-recognized-outstanding-paper}{Paper of the Year}" Award from The Plant Phenome Journal. +\item Two papers selected as "Editor's Choice" by the MaizeGDB Editorial Board. +\end{itemize} +\section*{2020 Outreach and News Coverages} +\begin{itemize} +\item Plant Physiology "\href{https://community.plantae.org/article/5447329265999677113/plant-phenomics-first-author-insights-02-04-2020}{First Author Insight}" interview with Chenyong Miao. +\item Nebraska Today Pocket Science "\href{https://news.unl.edu/newsrooms/today/article/all-the-angles-automated-image-processing-could-aid-crop-evals/}{All the angles: Automated image processing could aid crop evals}" +\item Nebraska Today "\href{https://news.unl.edu/newsrooms/today/article/planting-innovation-schnable-lab-maintains-research-momentum/}{Planting innovation: Schnable Lab maintains research momentum}" +\item Nebraska Ag Connection "\href{http://nebraskaagconnection.com/story-state.php?Id=809&yr=2020}{Researchers Build Cyber-Physical System to Monitor Crops, Drive Decisions}" +\item Plant Physiology - News and Views "\href{https://doi.org/10.1104/pp.20.00797}{Functional Principal Component Analysis: A Robust Method for Time-Series Phenotypic Data}" +\item The Plant Cell - In Brief "\href{https://doi.org/10.1105/tpc.20.00471}{Comparative Profiling Examines Roles of DNA Regulatory Sequences and Accessible Chromatin during Cold Stress Response in Grasses +}" +\item 2.1M tweet impressions to primary science/academic twitter account (@szinti) in 2020 +\end{itemize} +\section*{2020 Professional Development} +\begin{itemize} +\item Weekly joint meetings with a professor of computer science (Bedrich Benes, Purdue) and several of our respective graduate students have allowed me to expand both my own knowledge of algorithm design and 3D modeling relevant to plant phenotyping and functional/structural modeling and that of my trainees. +\item Attendance at and participation in professional conferences in my field in 2020 including "Plant and Animal Genome" (in person), Maize Genetics (virtual), and National Association of Plant Breeders (virtual). +\end{itemize} +\end{document} +% Footer diff --git a/2021_AnnualReport/JSchnable_Summary.aux b/2021_AnnualReport/JSchnable_Summary.aux new file mode 100644 index 0000000000000000000000000000000000000000..257b3fd3b596c7733e218c2ca0032615c550f3ac --- /dev/null +++ b/2021_AnnualReport/JSchnable_Summary.aux @@ -0,0 +1,18 @@ +\relax +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} +\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined +\global\let\oldcontentsline\contentsline +\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global\let\oldnewlabel\newlabel +\gdef\newlabel#1#2{\newlabelxx{#1}#2} +\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\ifx\hyper@anchor\@undefined +\let\contentsline\oldcontentsline +\let\newlabel\oldnewlabel +\fi} +\fi} +\global\let\hyper@last\relax +\gdef\HyperFirstAtBeginDocument#1{#1} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} diff --git a/2021_AnnualReport/JSchnable_Summary.log b/2021_AnnualReport/JSchnable_Summary.log new file mode 100644 index 0000000000000000000000000000000000000000..46f4c2cefb853ad624fcbf846ac57aa98f5b67eb --- /dev/null +++ b/2021_AnnualReport/JSchnable_Summary.log @@ -0,0 +1,800 @@ +This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex 2020.4.7) 12 JAN 2021 20:43 +entering extended mode + restricted \write18 enabled. + %&-line parsing enabled. +**JSchnable_Summary.tex +(./JSchnable_Summary.tex +LaTeX2e <2020-02-02> patch level 5 +L3 programming layer <2020-03-06> +(/usr/local/texlive/2020/texmf-dist/tex/latex/base/article.cls +Document Class: article 2019/12/20 v1.4l Standard LaTeX document class +(/usr/local/texlive/2020/texmf-dist/tex/latex/base/size10.clo +File: size10.clo 2019/12/20 v1.4l Standard LaTeX file (size option) +) +\c@part=\count167 +\c@section=\count168 +\c@subsection=\count169 +\c@subsubsection=\count170 +\c@paragraph=\count171 +\c@subparagraph=\count172 +\c@figure=\count173 +\c@table=\count174 +\abovecaptionskip=\skip47 +\belowcaptionskip=\skip48 +\bibindent=\dimen134 +) +(/usr/local/texlive/2020/texmf-dist/tex/latex/cjk/texinput/CJKutf8.sty +Package: CJKutf8 2015/04/18 4.8.4 + +(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/ifpdf.sty +Package: ifpdf 2019/10/25 v3.4 ifpdf legacy package. 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Schnable} +\renewcommand\thefootnote{\textcolor{unlred}{\arabic{footnote}}} + + +% Replace this with a link to your CV if you like, or set it empty +% (as in \def\footerlink{}) to remove the link in the footer: +%\def\footerlink{https://github.com/rossibarra/CV/blob/master/CV.pdf?raw=true} + +%Add in-line comments +\newcommand{\ignore}[1]{} + +% The following metadata will show up in the PDF properties +\hypersetup{ + colorlinks = true, + urlcolor = unlred, + pdfauthor = {\name}, + pdfkeywords = {comparative genomics, maize, grasses}, + pdftitle = {\name: Curriculum Vitae}, + pdfsubject = {Curriculum Vitae}, + pdfpagemode = UseNone +} + +\geometry{ + body={6.5in, 9in}, + left=1.0in, + top=1.0in +} + +% Customize page headers +%\pagestyle{myheadings} +%\markright{\name} +%\thispagestyle{empty} + +% Custom section fonts +\usepackage{sectsty} +\sectionfont{\rmfamily\mdseries\Large} +\subsectionfont{\rmfamily\mdseries\itshape\large} + +% Other possible font commands include: +% \ttfamily for teletype, +% \sffamily for sans serif, +% \bfseries for bold, +% \scshape for small caps, +% \normalsize, \large, \Large, \LARGE sizes. + +% Don't indent paragraphs. +%\setlength\parindent{0em} + +% Make lists without bullets +%\renewenvironment{itemize}{ +% \begin{list}{}{ +% \setlength{\leftmargin}{1.5em} +% } +%}{ +% \end{list} +%} + +\begin{document} + +% Place name at left +%\centerline{\huge \textsc{James Schnable: 2020 Summary}} +%Updated transliteration of Schnable, thanks to Zhikai Liang + +% Alternatively, print name centered and bold: +%\centerline{\huge \bf \name} + +\noindent\textbf{Executive Summary:} Mentored 8 graduate students and 18 undergraduate researchers. Published 21 total peer review products. Five new federal grants and 2 new non-federal grants. Nine invited seminars at external institutions or conferences. One paper recieved an award. I was elected to a community leadership role by my peers. Total course enrollment flat in a year when overall graduate enrollment declined. My 2020 mentoring and teaching FTE was 27\% exceeding my position description target of 18\%. + +\noindent\textbf{2020 Narrative:} Every member of my lab came through 2020 alive and safe. Students whose progress towards graduation depended on the 2020 field season got the data they needed. During the shotdown of campus, when university policy encouraged us to lay off undergraduate researchers, members of the lab instead pulled together to support our undergraduates and were able to train students in new computational tasks. No one was forced to miss a paycheck during the lockdown (many of the undergraduates in my lab depend on their income from lab to help make rent on a month to month basis), and the process even resulted in a new publishedable research project which is now posted to bioRxiv, including undergraduate student authorship. We don't have a mechanism for reporting on preprints in our annual evaluation process but I expect to be able to report it on my five year publication list in 2021. Over the summer, after first figuring out how to work in the fields safely, we also coordinately closely with both Craig Chandler (University Communications) and Lana Johnson (our department), to publically the regular routines of our field research so that both the public and the state legislature would continue to see throughout the spring and summer that the shutdown did not mean that the research work -- for which the project the substantial majority of IANR's total operating budget -- had ceased. + +I'm really pleased at how well the lab has come together, organzing vitual social events and emotional support over slack and zoom (including assistance from lab-alumni, which was unexpected and for which I was really grateful). Being a graduate student is hard at the best of times. Being a grad student during a pandemic, often hundreds if not thousands of miles from family is even harder. I'm also finding some students need more frequent meetings and others longer ones, both as a substitute for drop in conversations that used to happen at the office, and because people have many more sources of stress and worries about the future than they would in a normal year. It is hard for me to come up with metrics that will let you assess the quality of the mentoring I have provided to the eight graduate students (6 PhD; 2 MS) who I mentored or co-mentored in 2020. If the peer evaluation committee has ideas about what type of metrics they'd like to see on mentoring quality that could serve as leading indicators for final outcomes for my students I'd be happy to collect and provide them in future years. + +In addition, we engaged a total of eighteen undergraduates in research into plant biology, agronomy, and/or computer science in 2020, including both students enrolled here at UNL and an REU student who participated in a remote research experience over the summer. Three undergraduate researchers were authors on three separate published papers in 2020, including one current undergraduate researcher and two who graduated in 2019. Computational biology and agronomy are both fields that have struggled to recruit and retain diverse candidate pools. Among the undergraduate researchers in my lab in 2020, six of eighteen were female, twelve of eighteen were male, and four of eighteen came from groups historically underrepresented in STEM fields. Among graduate students in my lab in 2020, three of eight were female, five of eight were male, and three of eight were from groups historically underrepresented in STEM fields. + +In 2020 my research group published eighteen peer reviewed journal articles and three peer reviewed conference papers in 2020 (21 total peer reviewed products). This represents a significant increase from eleven peer reviewed papers and five conference papers in 2019, which was in turn an increase from 2018. Of papers published in 2020, ten of eighteen included a first and/or last author from my research group with six total trainees publishing one or more first author papers. Papers lead by trainees in my lab were published in journals including Molecular Plant (IF=12.1) and Plant Physiology (IF=6.9), and collaborative projects in which my lab participated published in journals including Nature Plants (IF=13.2) and The Plant Cell (IF=9.6). + +In 2020 I recieved funding as PI or co-PI for five additional federal grants up from four new federal grants funding in 2019. In total work in my lab in 2020 was supported by thirteen different active federal grants, including four from USDA-NIFA, four from the National Science Foundation, three from ARPA-E, one from FFAR, and one from the Department of Energy. The new grants recieved this year included two USDA-NIFA grants for high intensity phenotyping (\$3.0M and \$2.7M), an ARPA-E grant for monitoring soil organic carbon content (\$1.9M), a USDA-NIFA grant for predictive phenomics to guide agronomic decisions (\$1.05M) and an ARPA-E supported project to use machine learning to predict agronomic outcomes in corn from molecular data (\$620k). In addition to these five new federal grants I also recieved a small \$50k linkage grant from ICRISAT (Hyderabad, India) to extend our machine learning framework for predicting loss of function phenotypes in sorghum (supported by my ongoing DOE grant) to pearl millet using field trials conducted by ICRISAT in India and Africa, and recieved a compentitive annual renewal from the Nebraska Corn Board to support my participation in Genomes to Fields. More details and links to grant summaries (when publicized) are provided in my abbreviated five year CV submitted as part of this annual report. + +In 2020, I gave a total of 9 invited seminars at external institutions (5) or conferences (4). Seven were delivered remotely as a result of COVID travel restrictions. For comparison, I had 7 invited talks in 2019. I was also elected by the maize genetics community to the board of directors for our scientific community (The Maize Genetics Cooperation) and a paper in The Plant Phenome Journal recieved that journal's Paper of the Year Award. In 2020, I recieved a total of 1,027 citations, an increase of 300 (41\%) from 2019. + +\noindent\textbf{2021 Objectives} + +\textbf{Progress towards a multi-omic model to predict maize and sorghum phenotypic outcomes in the field:} If successful, this will both help to accelerate the rate of genetic gain in plant breeding and aid growers in making and unpdating decisions about crop management throughout the growing season based on weather, crop development, and (eventually) changes in the cost of inputs (fertilizer and energy costs) and the value of outputs (crop prices). In 2020 we collected dense multi-trait datasets from large association panels of maize and sorghum at a single location. In 2021 my goal is to generate transcriptomic and metabolomic data from frozen tissue samples collected in the field last summer to provide additional variables for the predictivive models, repeat the 2020 experiment in 2021 to capture another environment, and collect data from smaller sets of lines grown across multiple locations in Nebraska. The resources for these activities will come from the new grant funding my group recieved in 2020. + +\textbf{Identification of genes controlling variation of 3D traits in maize and/or sorghum:} Crops grow, interact with their environments, capture resources, and produce harvestable outputs in 3D space. However, many of the approaches we take to measuring the phenotypes of plants, either by hand or in high throughput imaging systems, simplify them to 2D objects. In 2020 I collaborated with a computer graphics expert at Purdue University to generate and validate an approach to reconstruct the 3D structure of corn and sorghum from 2D images (see pub \#61 and conference paper \#10 on my five year publication list). In 2021 I hope to use this newly developed approach map gene controlling natural variation in leaf positioning in 3D space as canopy architecture is a trait of particular importance to crop yield and resource use efficiency. + +\textbf{Expand enrollment in the Integrated Plant Biology graduate track:} The Integrated Plant Biology PhD track provides students with the opportunity to rotate across multiple labs and increases the odds of finding good "fit" between a mentor and mentee, leading to better outcomes. At the same time, the Integrated Plant Biology track provides an opportunity to tap into pools of students currently largely inaccessible to our department. These include students from biology backgrounds where the academic culture emphasizes direct-to-PhD graduate programs. Direct to PhD is technically possible through our internal graduate program. However, the admissions committee has been historically reluctant to sign off on direct-to-PhD applications, putting faculty who are already trying to competitively recruit a PhD student who has already secured a PhD admission offer at another university at a competitive disadvantage. In 2020 I organized and held an online recruitment event for students interested in the program with a number of faculty both in and outside the department, an approach which can be expanded in 2021. + +\textbf{Pilot shared graduate instruction across institutions:} This spring, Michael Tross, a graduate student I mentor, will be taking "Breeding for Quantitative Traits in Plants" remotely with Rex Bernado of the University of Minnesota, one of the world leaders in the field. At the same time he will recieve UNL credit for the course through AGRO 896. Similarly, in 2020 UNL and Federal University of Minas Gerais students enrolled in a common course taught remotely, a collaboration with my former PhD student Daniel Carvalho. In an era of shrinking enrollments and state support, I think it is critical to explore ways we can expand these practices so our graduate students can continue to recieve world class education as our department faces the need to scale down. + +\noindent\textbf{A Small Request:} If the peer evaluation committee feels this annual report missing information I should have provided, please also tell me what I can safely omit. I'm up against length limits. Similarly, if the committee feels I should be do new or more things in 2021, please also tell me what I can safely do less of. 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26 named destinations out of 1000 (max. 500000) + 13 words of extra memory for PDF output out of 10000 (max. 10000000) + diff --git a/2021_AnnualReport/JSchnable_fiveyear_2020.out b/2021_AnnualReport/JSchnable_fiveyear_2020.out new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/2021_AnnualReport/JSchnable_fiveyear_2020.pdf b/2021_AnnualReport/JSchnable_fiveyear_2020.pdf new file mode 100644 index 0000000000000000000000000000000000000000..1e7b8a76ffc2065a2f20be6e150d7803b24faff0 Binary files /dev/null and b/2021_AnnualReport/JSchnable_fiveyear_2020.pdf differ diff --git a/2021_AnnualReport/JSchnable_fiveyear_2020.tex b/2021_AnnualReport/JSchnable_fiveyear_2020.tex new file mode 100644 index 0000000000000000000000000000000000000000..f6fabb44ef989867ea2b3fb00cf86aa1d2e1ac4e --- /dev/null +++ b/2021_AnnualReport/JSchnable_fiveyear_2020.tex @@ -0,0 +1,606 @@ +%adapted from: +%https://github.com/rossibarra/CV + +\documentclass[letterpaper]{article} +\usepackage{CJKutf8} +\usepackage{hyperref} +\usepackage{geometry} +\usepackage{etaremune} +\usepackage{fixltx2e} +\usepackage{pgf} +\usepackage{float} +\usepackage{textcomp} +%\usepackage{eurofont} +\usepackage{color} +\usepackage{verbatim} +\definecolor{unlred}{rgb}{0.0,0.0,0.71} + +% Comment the following lines to use the default Computer Modern font +% instead of the Palatino font provided by the mathpazo package. +% Remove the 'osf' bit if you don't like the old style figures. +\usepackage[T1]{fontenc} +\usepackage[sc,osf]{mathpazo} +\usepackage{setspace} +% Set your name here +\def\name{James C. Schnable} +\renewcommand\thefootnote{\textcolor{unlred}{\arabic{footnote}}} + + +% Replace this with a link to your CV if you like, or set it empty +% (as in \def\footerlink{}) to remove the link in the footer: +%\def\footerlink{https://github.com/rossibarra/CV/blob/master/CV.pdf?raw=true} + +%Add in-line comments +\newcommand{\ignore}[1]{} + +% The following metadata will show up in the PDF properties +\hypersetup{ + colorlinks = true, + urlcolor = unlred, + pdfauthor = {\name}, + pdfkeywords = {comparative genomics, maize, grasses}, + pdftitle = {\name: Curriculum Vitae}, + pdfsubject = {Curriculum Vitae}, + pdfpagemode = UseNone +} + +\geometry{ + body={6.5in, 9in}, + left=1.0in, + top=1.0in +} + +% Customize page headers +\pagestyle{myheadings} +\markright{\name} +\thispagestyle{empty} + +% Custom section fonts +\usepackage{sectsty} +\sectionfont{\rmfamily\mdseries\Large} +\subsectionfont{\rmfamily\mdseries\itshape\large} + +% Other possible font commands include: +% \ttfamily for teletype, +% \sffamily for sans serif, +% \bfseries for bold, +% \scshape for small caps, +% \normalsize, \large, \Large, \LARGE sizes. + +% Don't indent paragraphs. +\setlength\parindent{0em} + +% Make lists without bullets +\renewenvironment{itemize}{ + \begin{list}{}{ + \setlength{\leftmargin}{1.5em} + } +}{ + \end{list} +} + +\begin{document} + +% Place name at left +\centerline{\huge \textsc{Five Year Publication List}} +\vspace{0.25in} +\centerline{\huge \textsc{\name}} +%Updated transliteration of Schnable, thanks to Zhikai Liang +%\centerline{\begin{CJK*}{UTF8}{gbsn}詹姆斯 . 施耐博\end{CJK*}} + +% Alternatively, print name centered and bold: +%\centerline{\huge \bf \name} + +\vspace{0.25in} + + +\begin{center} +\textbf{H-Index:} \textbf{\href{https://scholar.google.com/citations?user=cik4JVYAAAAJ}{35}} \\ +Lab members in \textbf{bold}.\\ +Postdoc/visiting scholar$\dagger$ in Schnable Lab.\\ +Graduate student$\ddagger$ in Schnable Lab. \\ +\textcolor{red}{Undergraduate authors} in Schnable Lab.\\ +Authors contributed equally$^*$ +\end{center} + +\section*{Journal Publications 2021-2017} + +%Figure out how to emphasis italics stuff more. + +\addtolength{\leftskip}{9mm} + +\begin{etaremune} + +\subsection*{2021 Journal Publications (N=23)} + +\item \textbf{Tross MC}$\ddagger$, Gaillard M, \textbf{Zweiner M}$\ddagger$, \textbf{Miao C}, 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} +\\\textsc{Journal Impact Factor (2021 Report):} 3.0 +\\\textsc{Altmetric Score (Percentile at BioRxiv):} 24 (90th) +\\\textsc{Schnable Lab Percent Contribution:} 75\% +\\\textsc{Contribution Statement:} The Benes group (Gaillard M, Li B, \& Benes B) provided estimated leaf angle values using images collected by the Schnable lab from a previous greenhouse experiment we conducted. All other work and analyses conducted by members of the Schnable Lab. + +\item Woodhouse MR$^\S$, Sen S, Schott D, Portwood JL, Freeling M, 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} +\\\textsc{Journal Impact Factor (2021 Report):} 6.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 27 (95th) +\\\textsc{Schnable Lab Percent Contribution:} 40\% +\\\textsc{Contribution Statement:} Conceived of and wrote the original source code for the qTeller application. Hosted and popularized a website using the application. Contributed a draft of an unpublished earlier manuscript describing the software to the first author. Provided edits and feedback on the new manuscript drafted by the first author. + +\item Weissmann S, Huang P, Wiechert M, Furoyama K, Brutnell TP, Taniguchi M, \textbf{Schnable JC},$^\S$ Mockler TC$^\S$ (2021) DCT4 - a new member of the dicarboxylate transporter family in C\textsubscript{4} grasses. \textsc{Genome Biology and Evolution} doi: \href{https://academic.oup.com/gbe/article/doi/10.1093/gbe/evaa251/6126432?guestAccessKey=1ceb8d04-4e02-4ff3-89b5-705479ae4e47}{10.1093/gbe/evaa251} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/762724}{10.1101/762724} +\\\textsc{Journal Impact Factor (2021 Report):} 3.4 +\\\textsc{Altmetric Score (Percentile at Journal):} 1 (2nd) +\\\textsc{Schnable Lab Percent Contribution:} 35\% +\\\textsc{Contribution Statement:} Conducted comparative genomic and transcriptomic analyses. Originally identified DCT4 gene copies in sorghum and setaria (as a postdoc). Worked with the first author to draft the paper, design figures, and generate a response to reviewers (as a PI). + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 4.4 +\\\textsc{Altmetric Score (Percentile at Journal):} 1 (20th) +\\\textsc{Schnable Lab Percent Contribution:} 5\% +\\\textsc{Contribution Statement:} Conducted bioinformatic/genomic analyses using the SSR41 resequencing data. Edited portions of the manuscript for language/scientific clarity. + +\item \textbf{Miao C}$\ddagger$, \textcolor{red}{Guo A}, 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} +\\\textsc{Journal Impact Factor (2021 Report):} N/A (New Journal) +\\\textsc{Altmetric Score (Percentile at Journal):} 35 (2nd highest of 44 papers published to date) +\\\textsc{Schnable Lab Percent Contribution:} 90\% +\\\textsc{Contribution Statement:} Non-Schnable Lab authors contributed image data and/or assistance in ground truth annotation. All other work and analyses conducted by members of the Schnable Lab + +\item \textbf{Sun G}$^\S$$\dagger$, \textbf{Mural RV}$\dagger$, \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} +\\\textsc{Journal Impact Factor (2021 Report):} 4.0 +\\\textsc{Altmetric Score (Percentile at Journal):} 12 (78th percentile) +\\\textsc{Schnable Lab Percent Contribution:} 100\% +\\\textsc{Contribution Statement:} All work and analyses conducted by members of the Schnable Lab. + +\item \textbf{Mural RV}$\dagger$, \textbf{Grzybowski M}$\dagger$, \textbf{Miao C}$\ddagger$, \textbf{Damke A}$^\ddagger$, Sapkota S, Boyles RE, Salas Fernandez MG, Schnable PS, \textbf{Sigmon B}, Kresovich S, \textbf{Schnable JC}$^\S$ (2021) Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum. \textsc{Genetics} doi: \href{https://doi.org/10.1093/genetics/iyab087}{10.1093/genetics/iyab087} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.10.27.355495}{10.1101/2020.10.27.355495}\\ +\textit{Selected as the Cover Article of July Issue} +\\\textsc{Journal Impact Factor (2021 Report):} 4.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 18 (81st) +\\\textsc{Schnable Lab Percent Contribution:} 90\% +\\\textsc{Contribution Statement:} Non-Schnable lab authors contributed previously unpublished data collected at field sites in South Carolina and Iowa. All other work and analyses conducted by members of the Schnable Lab. + +\item \textbf{Grzybowski M}$\dagger$, Wijewardane NK, Atefi A, Ge Y, \textbf{Schnable JC}$^\S$ (2021) The potential of hyperspectral reflectance as a tool for quantitative genetics in crops. \textsc{Plant Communications} doi: \href{https://doi.org/10.1016/j.xplc.2021.100209}{10.1016/j.xplc.2021.100209} +\\\textsc{Journal Impact Factor (2021 Report):} NA (New Journal) +\\\textsc{Altmetric Score (Percentile at Journal):} 6 (59th) +\\\textsc{Schnable Lab Percent Contribution:} 85\% +\\\textsc{Contribution Statement:} Wijewardane NK, Atefi A \& Ge Y provided expertise and assisted with the collection of the raw hyperspectal measurements. All other work and analyses conducted by members of the Schnable Lab. + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 11.3 +\\\textsc{Altmetric Score (Percentile at Journal):} 26 (81st) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Conceived of an approach to quantifying genetically controlled measurement error. Drafted portions of the paper, edited and revised the remainder. + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 4.3 +\\\textsc{Altmetric Score (Percentile at Journal):} 2 (57th) +\\\textsc{Schnable Lab Percent Contribution:} 20\% +\\\textsc{Contribution Statement:} Worked with first author to first draft and the revise this review. + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 4.3 +\\\textsc{Altmetric Score (Percentile at Journal):} 2 (40th) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Conducted field experiments, collected ground truth data. Provided input to the final paper. + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 4.8 +\\\textsc{Altmetric Score (Percentile at Journal):} 9 (72nd) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Conceived of the key analyses that enabled us to achieve sub-genus level functional resolution in this dataset. Worked with the first author to improve statistical analyses, data visualization, and paper structure. Drafted portions of the paper, edited and revised the remainder. + +\item Serba DD, \textbf{Meng X}$\dagger$, \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} +\\\textsc{Journal Impact Factor (2021 Report):} 5.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 2 (33rd) +\\\textsc{Schnable Lab Percent Contribution:} 35\% +\\\textsc{Contribution Statement:} Extracted RNA from tissue samples collected by the lead author, constructed and sequenced RNA-seq libraries, conducted bioinformatic and statistical analyses on the resulting gene expression data. Drafted portions of the paper, edited and revised the remainder. + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 3.0 +\\\textsc{Altmetric Score (Percentile at Journal):} 8 (63rd) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Provided advice and guidance to the lead author regarding transcriptomic and comparative genomic analyses. Assisted in editing and revising the paper. + +\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} +\\\textsc{Journal Impact Factor (2021 Report):} 11.2 +\\\textsc{Altmetric Score (Percentile at Journal):} 38 (59th) +\\\textsc{Schnable Lab Percent Contribution:} 15\% +\\\textsc{Contribution Statement:} Proposed and conducted comparative genomic analysis and evolutionary reconstructions. Assisted in writing portions of the paper. Addressed reviewer concerns during revision. + +\item \textbf{Meng X}$\dagger$, \textbf{Liang Z}$\ddagger$, \textbf{Dai X}$\ddagger$, \textbf{Zhang Y}$\dagger$, Mahboub S, \textcolor{red}{Ngu DW}, 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} +\\\textsc{Journal Impact Factor (2021 Report):} 11.2 +\\\textsc{Altmetric Score (Percentile at Journal):} 68 (71st) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} All work excluding the profiling of photosynthetic impairment subsequent to cold stress (conducted by the Roston lab) was conducted by members of my research group. + +\item Sankaran S$^\S$, Marzougui A, \textbf{Hurst JP}$\ddagger$, Zhang C, \textbf{Schnable JC}, Shi Y (2021) Can high resolution satellite imagery be used in high-throughput field phenotyping? \textsc{Transactions of the ASABE} doi: \href{https://elibrary.asabe.org/abstract.asp?aid=52080&t=3&redir=aid=52080&confalias=t2&redir=[volume=0&issue=0&conf=t&orgconf=]&redirType=toc_journals.asp&redirType=toc_journals.asp}{10.13031/trans.14197} +\\\textsc{Journal Impact Factor (2021 Report):} 1.2 +\\\textsc{Altmetric Score (Percentile at Journal):} 0 (N/A) +\\\textsc{Schnable Lab Percent Contribution:} 33\% +\\\textsc{Contribution Statement:} Grew field trials, collected measurements, proposed analyses, conducted a subset of the analyses, drafted portions of the manuscript and edited the remainder. + +\item Zhu Y, Chen Y, Ali Md. A, Dong L, Wang X, Archontoulis SV, \textbf{Schnable JC}, Castellano MJ$^\S$ (2021) Continuous in situ soil nitrate sensors: a comparison with conventional measurements and the value of high temporal resolution measurements. \textsc{Soil Science Society of America Journal} doi: \href{https://doi.org/10.1002/saj2.20226}{10.1002/saj2.20226} +\\\textsc{Journal Impact Factor (2021 Report):} 2.3 +\\\textsc{Altmetric Score (Percentile at Journal):} 22 (95th) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Conducted field trials of the sensor at our eastern Nebraska field site. Contributed to writing and editing of the manuscript. + +\item \textbf{Lai X}$\ddagger$, Bendix C, \textbf{Zhang Y}$\dagger$, \textbf{Schnable JC}, Harmon FG$^\S$ (2021) 72-hour diurnal RNA-seq analysis of fully expanded third leaves from maize, sorghum, and foxtail millet at 3-hour resolution. \textsc{BMC Research Notes} doi: \href{https://doi.org/10.1186/s13104-020-05431-5}{10.1186/s13104-020-05431-5} +\\\textsc{Journal Impact Factor (2021 Report):} 1.7 +\\\textsc{Altmetric Score (Percentile at Journal):} 0 (N/A) +\\\textsc{Schnable Lab Percent Contribution:} 70\% +\\\textsc{Contribution Statement:} Members of the schnable lab extracted RNA, conducted RNA-sequencing libraries, generated the sequencing data and ran the bioinformatic analyses. Bendix grew the plants and collected tissue samples. Harmon drafted the paper. + +\item Rogers AR, Dunne JC, Romay C ... \textbf{Schnable JC} (24th of 39 authors) ... Kaeppler S, De Leon N, Holland JB$^\S$ (2021) The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. \textsc{G3:Genes|Genomes|Genetics} doi: \href{https://doi.org/10.1093/g3journal/jkaa050}{10.1093/g3journal/jkaa050}\\ +\textbf{\textit{ Selected as an Editor's Choice by MaizeGDB Editorial Board}} February 2021 +\\\textsc{Journal Impact Factor (2021 Report):} 3.2 +\\\textsc{Altmetric Score (Percentile at Journal):} 14 (88th) +\\\textsc{Schnable Lab Percent Contribution:} 5\% +\\\textsc{Contribution Statement:} Contributed data from field trials conducted across three environments in eastern and central nebraska. Provided edits and feedback on the manuscript. + +\item Jarquin D, de Leon N, Romay C ... \textbf{Schnable JC} (24th of 33 authors) ... Wisser RJ, Xu W, Lorenz A (2021) Utility of climatic information via combining ability models to improve genomic prediction for yield within the Genomes to Fields maize project. \textsc{Frontiers in Genetics} doi: \href{https://doi.org/10.3389/fgene.2020.592769}{10.3389/fgene.2020.592769} +\\\textsc{Journal Impact Factor (2021 Report):} 3.8 +\\\textsc{Altmetric Score (Percentile at Journal):} 7 (70th) +\\\textsc{Schnable Lab Percent Contribution:} 6\% +\\\textsc{Contribution Statement:} Contributed data from field trials conducted across three environments in eastern and central nebraska. Provided edits and feedback on the manuscript. + +\item DiMario RJ, Kophs AN, Pathare VS, \textbf{Schnable JC}, Cousins AB$^\S$ (2021) Phospho\textit{enol}pyruvate carboxylase kinetic variation provides opportunity to enhance C4 photosynthetic efficiency. \textsc{The Plant Journal} doi: \href{https://doi.org/10.1111/tpj.15141}{10.1111/tpj.15141} +\\\textsc{Journal Impact Factor (2021 Report):} 6.4 +\\\textsc{Altmetric Score (Percentile at Journal):} 15 (88th) +\\\textsc{Schnable Lab Percent Contribution:} 20\% +\\\textsc{Contribution Statement:} Proposed and conducted bioinformatic and comparative genomic analyses. Generated sequences used for in vitro functional characterication. Drafted a portion of the manuscript, provided edits and feedback on the remainder. + +\item Thudi M, Palakurthi R, \textbf{Schnable JC}, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Nguyen H, Sivasankar S, Close TJ, Stein N, Jackson SA, Shubo W, Varshney RK$^\S$ (2021) Genomic resources in plant breeding for sustainable agriculture. \textsc{Journal of Plant Physiology} doi: \href{https://doi.org/10.1016/j.jplph.2020.153351}{10.1016/j.jplph.2020.153351} +\\\textsc{Journal Impact Factor (2021 Report):} 3.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 25 (99th) +\\\textsc{Schnable Lab Percent Contribution:} 5\% +\\\textsc{Contribution Statement:} Drafted one section of the manuscript. Read and proposed edits to the remainder. + +\hrulefill +\subsection*{2020 Journal Publications (N=18)} + +\item \textbf{Liang Z}$\ddagger$, Qiu Y, \textbf{Schnable JC} (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 +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 52 (96th) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} All aspects of the paper with the exception of generating the original statistical method (Y. Qiu). + +\item \textbf{Miao C}$\ddagger$, Xu Y, Liu S, Schnable PS, \textbf{Schnable JC} (2020) Increased power and accuracy of causal locus identification in time-series genome-wide association in sorghum. \textsc{Plant Physiology} doi: \href{https://doi.org/10.1104/pp.20.00277}{10.1104/pp.20.00277} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.02.16.951467}{10.1101/2020.02.16.951467}\\ +\textbf{\textit{ "News and Views" highlighting this article by Y Yu}} doi: \href{https://doi.org/10.1104/pp.20.00797}{10.1104/pp.20.00797} +\\\textsc{Journal Impact Factor (2020 Report):} 6.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 29 (91st) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} Y. Xu ran a new type of statistical analysis he had generated at Iowa State, S. Liu and PS Schnable contributed genotyping data for the sorghum population, all other aspects of the paper carried out by Schnable lab members. + +\item \textbf{Dai X}$\ddagger$, Xu Z, \textbf{Liang Z}$\ddagger$, Tu X, Zhong S, \textbf{Schnable JC}, Li P (2020) Non-homology based prediction of gene functions. \textsc{The Plant Genome} doi: \href{https://doi.org/10.1002/tpg2.20015}{10.1002/tpg2.20015} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/730473}{10.1101/730473} +\\\textsc{Journal Impact Factor (2020 Report):} 3.8 +\\\textsc{Altmetric Score (Percentile at Journal):} 16 (96th) +\\\textsc{Schnable Lab Percent Contribution:} 90\% +\\\textsc{Contribution Statement:} Z Xu, X Tu, and S Song contributed data. P Li co-mentored X Dai with Prof. Schnable. All other aspects of the paper carried out by Schnable lab members. + + +\item \textbf{Miao C}$\ddagger$, \textcolor{red}{\textbf{Pages A}}, Xu Z, Rodene E, Yang J, \textbf{Schnable JC} (2020) Semantic segmentation of sorghum using hyperspectral data identifies genetic associations. \textsc{Plant Phenomics} doi: \href{https://doi.org/10.34133/2020/4216373}{10.34133/2020/4216373} +\\\textsc{Journal Impact Factor (2020 Report):} New Journal +\\\textsc{Altmetric Score (Percentile at Journal):} 32 (93rd) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} R Rodene and J Yang contributed data. Z Xu advised on statistical analysis methods. All other aspects of the paper carried out by Schnable lab members. + +\item \textbf{Carvalho DS}$\ddagger$, \textcolor{red}{\textbf{Nishimwe AV}}, \textbf{Schnable JC} (2020) IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae. \textsc{Plant Direct} \href{https://doi.org/10.1002/pld3.203}{10.1002/pld3.203} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/689356}{10.1101/689356} +\\\textsc{Journal Impact Factor (2020 Report):} 1.7 +\\\textsc{Altmetric Score (Percentile at Journal):} 26 (92nd) +\\\textsc{Schnable Lab Percent Contribution:} 100\% +\\\textsc{Contribution Statement:} N/A + + +\item \textbf{Lai X}$\ddagger$, Bendix C, \textbf{Yan L}$\dagger$, \textbf{Zhang Y}$\dagger$, \textbf{Schnable JC}, Harmon F (2020) Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. \textsc{BMC Genomics} doi: \href{https://doi.org/10.1186/s12864-020-06824-3}{10.1186/s12864-020-06824-3}\\ +\textbf{\textit{ Selected as an Editor's Choice by MaizeGDB Editorial Board}} October 2020 +\\\textsc{Journal Impact Factor (2020 Report):} 3.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 11 (91st) +\\\textsc{Schnable Lab Percent Contribution:} 75\% +\\\textsc{Contribution Statement:} Plants were grown and RNA samples were collected in the Harmon lab. RNA-seq libraries were build and sequenced in the Schnable lab. Expression, comparative genomics, and promoter motif analysis conducted in the Schnable lab. Phylogenetic analysis of clock genes conducted in the Harmon lab. + +\item Adams J, Qiu Y, Xu Y, \textbf{Schnable JC} (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} +\\\textsc{Journal Impact Factor (2020 Report):} New Journal +\\\textsc{Altmetric Score (Percentile at Journal):} 9 (71st) +\\\textsc{Schnable Lab Percent Contribution:} 25\% +\\\textsc{Contribution Statement:} Provided the datasets employed in the paper. Originated idea for including neighborhood information for pixel classification. Drafted portions of the paper and revised the remainder. + +\item \textbf{Raju SKK}$\dagger$, Atkins M, \textcolor{red}{\textbf{Enerson A}}, \textbf{Carvalho DS}$\ddagger$, Studer AJ, Ganapathysubramanian B, Schnable PS, \textbf{Schnable JC} (2020) Leaf Angle eXtractor - A high throughput image processing framework for leaf angle measurement in maize and sorghum. \textsc{Applications in Plant Sciences} doi: \href{https://doi.org/10.1002/aps3.11385}{10.1002/aps3.11385} +\\\textsc{Journal Impact Factor (2020 Report):} 1.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 25 (73rd) +\\\textsc{Schnable Lab Percent Contribution:} 75\% +\\\textsc{Contribution Statement:} AJ Studer collaborated with JC Schnable in generating one of the several time lapse datasets analyzed. M Atkins, B Ganapathysubramanian and PS Schnable developed a new algorithm to track leaf angles in images. All other aspects of the paper conducted in the Schnable lab. + +\item Han J, Wang P, Wang Q, Lin Q, Yu G, \textbf{Miao C}$\ddagger$, Dao Y, Wu R, \textbf{Schnable JC}, Tang H, Wang K (2020) Genome-wide characterization of DNase I-hypersensitive sites and cold response regulatory landscapes in grasses. \textsc{The Plant Cell} doi: \href{https://doi.org/10.1105/tpc.19.00716}{10.1105/tpc.19.00716}\\ +\textbf{\textit{ "In Brief" highlighting this article by SKK Raju}} doi: \href{https://doi.org/10.1105/tpc.20.00471}{10.1105/tpc.20.00471} +\\\textsc{Journal Impact Factor (2020 Report):} 9.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 20 (65th) +\\\textsc{Schnable Lab Percent Contribution:} 20\% +\\\textsc{Contribution Statement:} Generating conserved noncoding sequence data, coming up with an implementing a method to compare patterns of change open chromatin data for equivalent regions of gene promoters across species. + +\item Zheng Z, Hey S, Jubery T, Liu T, Yang Y, Coffey L, \textbf{Miao C}$\ddagger$, \textbf{Sigmon B}, \textbf{Schnable JC}, Hochholdinger F, Ganapathysubramanian B, Schnable PS (2020) Shared genetic control of root system architecture between \textit{Zea mays} and \textit{Sorghum bicolor}. \textsc{Plant Physiology} doi: \href{https://doi.org/10.1104/pp.19.00752}{10.1104/pp.19.00752} +\\\textsc{Journal Impact Factor (2020 Report):} 6.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 41 (95th) +\\\textsc{Schnable Lab Percent Contribution:} 25\% +\\\textsc{Contribution Statement:} Sorghum portion of paired maize and sorghum field trials. Developing and implementing a method to compare the outcomes of GWAS analyses between maize and sorghum. + +\item Gaillard M$^*$, \textbf{Miao C}$\ddagger$$^*$, \textbf{Schnable JC}, Benes B (2020) Voxel carving based 3D reconstruction of sorghum identifies genetic determinants of radiation interception efficiency. \textsc{Plant Direct} doi: \href{https://doi.org/10.1002/pld3.255}{10.1002/pld3.255} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.04.06.028605}{10.1101/2020.04.06.028605v1} +\\\textsc{Journal Impact Factor (2020 Report):} 1.7 +\\\textsc{Altmetric Score (Percentile at Journal):} 23 (88th) +\\\textsc{Schnable Lab Percent Contribution:} 50\% +\\\textsc{Contribution Statement:} Schnable lab generated data. Benes lab analyzed data to construct 3D models. Schnable lab conducted the GWAS and analyzed the results. Writing was shared equally between the two groups. + + +\item Wang R, Qiu Y, Zhou Y, \textbf{Liang Z}$\ddagger$, \textbf{Schnable JC} (2020) A high-throughput phenotyping pipeline for image processing and functional growth curve analysis. \textsc{Plant Phenomics} doi: \href{https://doi.org/10.34133/2020/7481687}{10.34133/2020/7481687} +\\\textsc{Journal Impact Factor (2020 Report):} New Journal +\\\textsc{Altmetric Score (Percentile at Journal):} 18 (74th) +\\\textsc{Schnable Lab Percent Contribution:} 20\% +\\\textsc{Contribution Statement:} Contributed the image data used in this paper. Evaluated the outcomes of multiple iterations of the new code being developed. Drafted portions of the paper and edited the remainder. + +\item Jarquin D, Howard R, \textbf{Liang Z}$\ddagger$, Gupta SK, \textbf{Schnable JC}, Crossa J (2020) Enhancing hybrid prediction in pearl millet using genomic and/or multi-environment phenotypic information of inbreds. \textsc{Frontiers in Genetics} doi: \href{https://doi.org/10.3389/fgene.2019.01294}{10.3389/fgene.2019.01294} +\\\textsc{Journal Impact Factor (2020 Report):} +\\\textsc{Altmetric Score (Percentile at Journal):} 8 (73rd) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Diego, from our own department, should get the lion's share of credit for this paper. We had a cool dataset we were able to share with him and Reka (from Statistics). If he's claimed anything less than 70\% credit on his own report, please bump him up. + +\item \textbf{Raju SKK}$\dagger$, Thompson AM, \textbf{Schnable JC} (2020) Advances in plant phenomics: From data and algorithms to biological insights. \textsc{Applications in Plant Sciences} doi: \href{https://doi.org/10.1002/aps3.11386}{10.1002/aps3.11386} +\\\textsc{Journal Impact Factor (2020 Report):} 1.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 17 (66th) +\\\textsc{Schnable Lab Percent Contribution:} 67\% +\\\textsc{Contribution Statement:} Drafted 2/3rds of the paper, edited the remaining 1/3. + +\item Peng B, Guan K, 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} +\\\textsc{Journal Impact Factor (2020 Report):} 13.2 +\\\textsc{Altmetric Score (Percentile at Journal):} 97 (76th) +\\\textsc{Schnable Lab Percent Contribution:} 4\% +\\\textsc{Contribution Statement:} Drafted one section of the manuscript and edited and provided feedback for the remainder. + +\item Benes B, Guan K, Lang M, Long S, Lynch J, Marshall-Colon A, Peng B, \textbf{Schnable JC}, Sweetlove L, Turk M (2020) Multiscale computational models can guide experimentation and targeted measurements for crop improvement. \textsc{The Plant Journal} doi: \href{https://doi.org/10.1111/tpj.14722}{10.1111/tpj.14722} +\\\textsc{Journal Impact Factor (2020 Report):} 6.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 17 (86th) +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Drafted one section of the manuscript and edited and provided feedback for the remainder. + +\item Moisseyev G, Park K, Cui X, Freitas D, Rajagopa D, Konda A, Martin-Olenski M, Mcham M, Liu K, Du Q, \textbf{Schnable JC}, Moriyama E, Cahoon E, Chi Z (2020) RGPDB: Database of root-associated genes and promoters in maize, soybean, and sorghum. \textsc{Database} doi: \href{https://doi.org/10.1093/database/baaa038}{10.1093/database/baaa038} +\\\textsc{Journal Impact Factor (2020 Report):} 2.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 7 +\\\textsc{Schnable Lab Percent Contribution:} 7\% +\\\textsc{Contribution Statement:} Provided a purality of data. Contributed to database design decisions. Edited the manuscript. + +\item McFarland BA, AlKhalifah N, Bohn ... \textbf{Schnable JC} (34 of 54 authors) ... Xu W, Yeh CT, de Leon N (2020) Maize Genomes to Fields (G2F): 2014 –2017 field seasons' genotype, phenotype, climatic, soil and inbred ear image datasets. \textsc{BMC Research Notes} doi: \href{https://doi.org/10.1186/s13104-020-4922-8}{10.1186/s13104-020-4922-8} +\\\textsc{Journal Impact Factor (2020 Report):} 1.3 +\\\textsc{Altmetric Score (Percentile at Journal):} 25 (97th) +\\\textsc{Schnable Lab Percent Contribution:} 11\% +\\\textsc{Contribution Statement:} Secured funding for and conducted yield trials and phenotyping for hundreds of ex-PVP hybrids in eight of sixty-eight total unique environments (eastern and western nebraska with and without irrigation in 2016 and 2017) covered in this data release paper. + +\hrulefill +\subsection*{2019 Journal Publications (N=10)} + +\item Qi P, Eudy D, \textbf{Schnable JC}, Schmutz J, Raymer P, Devos KM (2019) High density genetic maps of seashore paspalum using genotyping-by-sequencing and their relationship to the \textit{Sorghum bicolor} genome. \textsc{Scientific Reports} doi: \href{https://doi.org/10.1038/s41598-019-48257-3}{10.1038/s41598-019-48257-3} +\\\textsc{Journal Impact Factor (2020 Report):} 4.0 +\\\textsc{Altmetric Score (Percentile at Journal):} 8 (67th percentile) +\\\textsc{Schnable Lab Percent Contribution:} 15\% +\\\textsc{Contribution Statement:} Draft genome sequence used to generate one of the two sets of genetic maps used in this paper. + +\item \textbf{Schnable JC} (2019) Genes and gene models, an important distinction. \textsc{New Phytologist} doi: \href{https://doi.org/10.1111/nph.16011}{10.1111/nph.16011} +\\\textsc{Journal Impact Factor (2020 Report):} 8.5 +\\\textsc{Altmetric Score (Percentile at Journal):} 45 (90th) +\\\textsc{Schnable Lab Percent Contribution:} 100\% +\\\textsc{Contribution Statement:} N/A + +\item Ge Y, Atefi A, Zhang H, \textbf{Miao C}$\ddagger$, Ramamurthy RK, \textbf{Sigmon B}, Yang J, \textbf{Schnable JC} (2019) High-throughput analysis of leaf physiological and chemical traits with VIS-NIR-SWIR spectroscopy: A case study with a maize diversity panel. \textsc{Plant Methods} doi: \href{https://doi.org/10.1186/s13007-019-0450-8}{10.1186/s13007-019-0450-8} +\\\textsc{Journal Impact Factor (2020 Report):} 3.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 25 (95th) +\\\textsc{Schnable Lab Percent Contribution:} 35\% +\\\textsc{Contribution Statement:} Conducted field component of the research. J Yang \& RK Ramamurthy conducted greenhouse component. Y Ge, A Atefi and H Zhang analyzed the data. + +\item Ali MA, Wang X, Chen Y, Jiao Y, Mahal NK, Satyanarayana M, Castellano MJ, \textbf{Schnable JC}, Schnable PS, Dong L (2019) Continuous Monitoring of Nitrate Variation Using Miniature Soil Sensor with Poly(3-octyl-thiophene) and Molybdenum Disulfide Nanocomposite. \textsc{ACS Applied Materials \& Interfaces} doi: \href{https://doi.org/10.1021/acsami.9b07120}{10.1021/acsami.9b07120} +\\\textsc{Journal Impact Factor (2020 Report):} 8.8 +\\\textsc{Altmetric Score (Percentile at Journal):} 2 +\\\textsc{Schnable Lab Percent Contribution:} 10\% +\\\textsc{Contribution Statement:} Conducted field experiments to validate the sensor described in the manuscript. + +\item Li Y, \textbf{Li D}, Jiao Y, \textbf{Schnable JC}, Li Y, Li H, Chen H, Hong H, Zhang T, Liu B, Liu Z, You Q, Tian Y, Gou Y, Guan R, Zhang L, Chang R, Zhang Z, Reif J, Zhou X, Schnable PS, Qiu L. (2019) Identification of Loci Controlling Adaptation in Chinese Soybean Landraces via a Combination of Conventional and Bioclimatic GWAS. \textsc{Plant Biotechnology Journal} doi: \href{https://doi.org/10.1111/pbi.13206}{10.1111/pbi.13206} +\\\textsc{Journal Impact Factor (2020 Report):} 8.1 +\\\textsc{Altmetric Score (Percentile at Journal):} +\\\textsc{Schnable Lab Percent Contribution:} 15\% +\\\textsc{Contribution Statement:} Designed concept and implementation strategy for bioclimactic GWAS using data on original GPS tagged collection locations of soybean lines. Outlined manuscript and edited draft written by collaborators. + +\item Atefi A, Ge Y, Pitla S, \textbf{Schnable JC} (2019) \textit{In vivo} human-like robotic phenotyping of leaf traits in maize and sorghum. \textsc{Computers and Electronics in Agriculture} doi: \href{https://doi.org/10.1016/j.compag.2019.104854}{10.1016/j.compag.2019.104854} +\\\textsc{Journal Impact Factor (2020 Report):} 3.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 142 (99th) +\\\textsc{Schnable Lab Percent Contribution:} 25\% +\\\textsc{Contribution Statement:} Co-originated concept and approaches for validation and visualization. Drafted sections of manuscript and edited others. + +\item Li L, Li X, Li L, \textbf{Schnable JC}, Gu R, J Wang (2019) QTL identification and epistatic effect analysis of seed size- and weight-related traits in \textit{Zea mays} L. \textsc{Molecular Breeding} doi: \href{https://doi.org/10.1007/s11032-019-0981-8}{10.1007/s11032-019-0981-8} +\\\textsc{Journal Impact Factor (2020 Report):} 2.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 6 (87th) +\\\textsc{Schnable Lab Percent Contribution:} 15\% +\\\textsc{Contribution Statement:} Proposed additional analyses/visualizations. Drafted portions of the manuscript and edited others. + +\item \textbf{Yan L}$\dagger$, \textbf{Kumar SKK}$\dagger$, \textbf{Lai X}$\ddagger$, \textbf{Zhang Y}$\ddagger$, \textbf{Dai X}$\ddagger$, Rodriguez O, Mahboub S, Roston RL, \textbf{Schnable JC} (2019) Parallels between artificial selection in temperate maize and natural selection in the cold-adapted crop-wild relative Tripsacum. \textsc{The Plant Journal} doi: \href{https://doi.org/10.1111/tpj.14376}{10.1111/tpj.14376} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/187575}{10.1101/187575} +\\\textsc{Journal Impact Factor (2020 Report):} 6.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 20 (84th) +\\\textsc{Schnable Lab Percent Contribution:} 90\% +\\\textsc{Contribution Statement:} O Rodriguez collected tripsacum accessions. RL Roston and S Mahboub generated lipid data. All other aspects of the paper conducted in the Schnable lab. + +\item Bai G, Ge Y, Scoby D, Leavit B, Irmak S, Graef G, \textbf{Schnable JC}, Awada T. (2019) NU-Spidercam: A large-scale, cable-driven, integrated sensing and robotic system for precision phenotyping, remote sensing, and agronomic research. \textsc{Computers and Electronics in Agriculture} doi: \\ \href{https://doi.org/10.1016/j.compag.2019.03.009}{10.1016/j.compag.2019.03.009} +\\\textsc{Journal Impact Factor (2020 Report):} 3.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 9 (76th) +\\\textsc{Schnable Lab Percent Contribution:} 15\% +\\\textsc{Contribution Statement:} Conducted 1/2 of the field experiments described in this study. + +\item Zou C, Miki D, \textbf{Li D}, Tang Q, Xiao L, \textbf{Rajput S}, Deng P, Peng L, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable P, Li F, Zhang H, Feng B, Zhu X, Liu R, \textbf{Schnable JC}, Zhu JK, Zhang H (2019) The genome of broomcorn millet. \textsc{Nature Communications} doi: \href{https://doi.org/10.1038/s41467-019-08409-5}{10.1038/s41467-019-08409-5} +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 89 (85th) +\\\textsc{Schnable Lab Percent Contribution:} 14\% +\\\textsc{Contribution Statement:} Generated a genetic map using an asian/north american cross of Panicum miliaceum which was used to order and orient the scaffolds of the genome into pseudomolecules. + +\hrulefill +\subsection*{2018 Journal Publications (N=11)} + +\item \textbf{Miao C}$\ddagger$, \textbf{Yang, J}$\dagger$, \textbf{Schnable JC} (2018) Optimizing the identification of causal variants across varying genetic architectures in crops. \textsc{Plant Biotechnology Journal} doi: \href{https://doi.org/10.1111/pbi.13023}{10.1111/pbi.13023} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/310391}{10.1101/310391} +\\\textsc{Journal Impact Factor (2020 Report):} 8.1 +\\\textsc{Times Cited To Date:} 13 +\\\textsc{Contribution Statement:} All analyses and writing conducted by lab members. + +\item Ott A, \textbf{Schnable JC}, Yeh CT, Wu L, Liu C, Hu HC, Dolgard CL, Sarkar S, Schnable PS (2018) Linked read technology for assembling large complex and polyploid genomes. \textsc{BMC Genomics} doi: \href{https://doi.org/10.1186/s12864-018-5040-z}{10.1186/s12864-018-5040-z} +\\\textsc{Journal Impact Factor (2020 Report):} 3.6 +\\\textsc{Times Cited To Date:} 15 +\\\textsc{Contribution Statement:} Conducted an analysis of a linked read genome assembly of proso millet, a previously unsequenced allotetraploid grass to assess the accuracy with which separate subgenomes were assembled and resolved using this new linked-reads technique. + +\item Liu S,$^*$ \textbf{Schnable JC},$^*$ Ott A,$^*$ Yeh CT, Springer NM, Yu J, Meuhbauer G, Timmermans MCP, Scanlon MJ, Schnable PS (2018) Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels. \textsc{Molecular Biology and Evolution} doi: \href{https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msy174/5090457?guestAccessKey=0823f03f-550f-40ac-9f4b-1c3670490e94}{10.1093/molbev/msy174} +\\\textsc{Journal Impact Factor (2020 Report):} 11.1 +\\\textsc{Times Cited To Date:} 2 +\\\textsc{Contribution Statement:} Analysis of relative correlation between recombination frequency per megabase and the relative density of either syntenic or nonsyntenic genes separately was conducted in the Schnable Lab@UNL. + +\item \textbf{Raju SKK}$\dagger$, Barnes A, \textbf{Schnable JC}, Roston RL$\S$ (2018) Low-temperature tolerance in land plants: Are transcript and membrane responses conserved? \textsc{Plant Science} doi: \href{https://doi.org/10.1016/j.plantsci.2018.08.002}{10.1016/j.plantsci.2018.08.002} +\\\textsc{Journal Impact Factor (2020 Report):} 3.6 +\\\textsc{Times Cited To Date:} 17 +\\\textsc{Contribution Statement:} Sunil and I wrote the portions of this review focused on conserved patterns transcriptional responses to cold stress across diverse plants, and worked collaboratively with the Roston lab on the combined transcript/lipid analyses. + +\item \textbf{Miao C}, Fang J, Li D, Liang P, Zhang X, \textbf{Yang J}$\dagger$, \textbf{Schnable JC}, Tang H$\S$ (2018) Genotype-Corrector: improved genotype calls for genetic mapping. \textsc{Scientific Reports} doi: \href{https://doi.org/10.1038/s41598-018-28294-0}{10.1038/s41598-018-28294-0} +\\\textsc{Journal Impact Factor (2020 Report):} 4.0 +\\\textsc{Times Cited To Date:} 7 +\\\textsc{Contribution Statement:} Improved and documented the core algorithm. Conducted tests of how much the core algorithm improved genotype call accuracy in a RIL and F2 population when using sub-optimal sequencing depth. Wrote the paper collaboratively with Haibao Tang. + +\item Alkhalifah N, Campbell DA, Falcon CM, ... \textbf{Schnable JC} (31 of 44 authors) ... Spalding EP, Edwards J, Lawrence-Dill CJ (2018) Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. \textsc{BMC Research Notes} doi: \href{https://doi.org/10.1186/s13104-018-3508-1}{10.1186/s13104-018-3508-1} +\\\textsc{Journal Impact Factor (2020 Report):} 1.3 +\\\textsc{Times Cited To Date:} 13 +\\\textsc{Contribution Statement:} Data collection from grow outs of Genomes to Fields hybrids at Nebraska field sites, assisted in writing the manuscript itself. + +\item \textbf{Liang Z}$\ddagger$, Gupta SK, Yeh CT, \textbf{Zhang Y}$\dagger$, \textcolor{red}{\textbf{Ngu DW}},Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupkta R, \textbf{Yang J}, Varshney RK, Schnable PS, \textbf{Schnable JC} (2018) Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids. \textsc{G3: Genes Genomes Genetics} doi: \href{https://doi.org/10.1534/g3.118.200242}{10.1534/g3.118.200242}\\ +\textbf{\textit{Selected as the outstanding scientific article of 2018 by ICRISAT's research program in Asia.}} +\\\textsc{Journal Impact Factor (2020 Report):} 2.8 +\\\textsc{Times Cited To Date:} 14 +\\\textsc{Contribution Statement:} Built the libraries, analyzed the SNP data, conducted the GS tests, wrote the paper. Field data and extracted DNA contributed by ICRISAT collaborators. Sequencing and SNP calling contributed by ISU collaborators. + +\item Xu Y, Qiu Y, \textbf{Schnable JC} (2018) Functional modeling of plant growth dynamics. \textsc{The Plant Phenome Journal} doi: \href{https://doi.org/10.2135/tppj2017.09.0007}{10.2135/tppj2017.09.0007} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/190967}{10.1101/190967}\\ +\textbf{\textit{Recieved the "Outstanding Paper Award" from TPPJ editorial board in 2020.}} +\\\textsc{Journal Impact Factor (2020 Report):} Not yet assigned. +\\\textsc{Times Cited To Date:} 7 +\\\textsc{Contribution Statement:} Conceived of the experiment to test subsampling on different days. Wrote the paper + +\item \textbf{Carvalho DS}$\ddagger$, \textbf{Schnable JC}, Almeida AMR (2018) Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes. \textsc{Evolutionary Bioinformatics} doi: \href{https://doi.org/10.1177/1176934318764683}{10.1177/1176934318764683} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/195669}{10.1101/195669} +\\\textsc{Journal Impact Factor (2020 Report):} 2.1 +\\\textsc{Times Cited To Date:} 2 +\\\textsc{Contribution Statement:} Conducted the majority of the analyses. Wrote the paper. + +\item \textbf{Lai X}$\ddagger$, \textbf{Yan L}$\dagger$, Lu Y, \textbf{Schnable JC} (2018) Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. \textsc{The Plant Journal} doi: \href{https://doi.org/10.1111/tpj.13806}{10.1111/tpj.13806} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/184424}{10.1101/184424} +\\\textsc{Journal Impact Factor (2020 Report):} 6.1 +\\\textsc{Times Cited To Date:} 11 +\\\textsc{Contribution Statement:} All experiments, analysis, and writing conducted by lab members. + +\item Nani TF, \textbf{Schnable JC}, Washburn JD, Albert P, Pereira WA, Sobrinho FS, Birchler JA, Techia VH (2018). Location of low copy genes in chromosomes of \textit{Brachiaria} spp. \textsc{Molecular Biology Reports} doi: \href{https://doi.org/10.1007/s11033-018-4144-5}{10.1007/s11033-018-4144-5} +\\\textsc{Journal Impact Factor (2020 Report):} 2.1 +\\\textsc{Times Cited To Date:} 3 +\\\textsc{Contribution Statement:} Identified candidate low copy genes which were used to design probes for hybridization. + +\hrulefill +\subsection*{2017 Journal Publications (N=12)} + +\item \textbf{Liang Z}$\ddagger$, \textbf{Schnable JC} (2017) Functional divergence between subgenomes and gene pairs after whole genome duplications. \textsc{Molecular Plant} doi: \href{http://doi.org/10.1016/j.molp.2017.12.010}{10.1016/j.molp.2017.12.010} +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Times Cited To Date:} 29 +\\\textsc{Contribution Statement:} All experiments, analysis, and writing conducted by lab members. + +\item \textbf{Liang Z}$\ddagger$, Pandey P, Stoerger V, Xu Y, Qiu Y, Ge Y, \textbf{Schnable JC} (2017) Conventional and hyperspectral time-series imaging of maize lines widely used in field trials. \textsc{GigaScience} doi: \href{https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/gix117/4656251?guestAccessKey=71c1c32f-78fd-42c0-99a3-38e6c4fd8100}{10.1093/gigascience/gix117} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/169045}{10.1101/169045} +\\\textsc{Journal Impact Factor (2020 Report):} 6.95 +\\\textsc{Times Cited To Date:} 25 +\\\textsc{Contribution Statement:} All analyses and writing conducted by lab members. Ge, Qiu, and Xu labs each assisted in developing new analytical approaches. Vincent Stoerger assisted with data generation. + +\item Gage J, Jarquin D, Romay M, ... \textbf{Schnable JC} (29th of 40 authors) ... Yu J, de Leon N (2017) The effect of artificial selection on phenotypic plasticity in maize. \textsc{Nature Communications} doi: \href{https://doi.org/10.1038/s41467-017-01450-2}{10.1038/s41467-017-01450-2}\\ +\textbf{\textit{Selected as an Editor's Choice by MaizeGDB Editorial Board}} December 2017 +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Times Cited To Date:} 42 +\\\textsc{Contribution Statement:} Generated and contributed yield and field phenotyping data from Nebraska field sites of Genomes to Fields project. + +\item Washburn JD, {\bf Schnable JC}, Brutnell TP, Shao Y, {\bf Zhang Y}, Ludwig M, Davidse G, Pires JC (2017) Genome-guided phylo-transcriptomic methods and the nuclear phylogentic tree of the paniceae grasses. \textsc{Scientific Reports} doi: \href{https://doi.org/10.1038/s41598-017-13236-z}{10.1038/s41598-017-13236-z} +\\\textsc{Journal Impact Factor (2020 Report):} 4.0 +\\\textsc{Times Cited To Date:} 11 +\\\textsc{Contribution Statement:} Grew plants, extracted RNA, built and sequenced libraries and shared data. Consulted with the lead author on the syntenic gene analysis. + +\item Ott A,$^*$ Liu S,$^*$ \textbf{Schnable JC}, Yeh CT, Wang C, Schnable PS (2017) Tunable Genotyping-By-Sequencing (tGBS\textregistered) enables reliable genotyping of heterozygous loci. \textsc{Nucleic Acids Research} doi: \\ \href{https://academic.oup.com/nar/article/doi/10.1093/nar/gkx853/4210942/tGBS-genotypingbysequencing-enables-reliable?guestAccessKey=0ba723ae-c6b2-4d7f-841e-cd46b4bf68f9}{10.1093/nar/gkx853} +\\\textsc{Journal Impact Factor (2020 Report):} +\\\textsc{Times Cited To Date:} 56 +\\\textsc{Contribution Statement:} Wrote portions of the manuscript, designed additional analyses to validate datasets which were executed by Alina Ott. + +\item \textbf{Lai X}$\ddagger$, \textbf{Schnable JC}, Liao Z, Xu J, Zhang G, Li C, Hu E, Rong T, Xu Y, Lu Y (2017) Genome-wide characterization of non-reference transposable elements insertion polymorphisms reveals genetic diversity in tropical and temperate maize. \textsc{BMC Genomics} doi: \href{https://doi.org/10.1186/s12864-017-4103-x}{10.1186/s12864-017-4103-x} +\\\textsc{Journal Impact Factor (2020 Report):} 3.6 +\\\textsc{Times Cited To Date:} 10 +\\\textsc{Contribution Statement:} The majority of this paper was written by Xianjun Lai during his time in the Schnable lab. I redesigned several analyses for him to carry out and helped to re-write the paper. + +\item Mei W, Boatwright L, Feng G, \textbf{Schnable JC}, Barbazuk WB (2017) Evolutionarily conserved alternative splicing across monocots. \textsc{Genetics} doi: \href{https://doi.org/10.1534/genetics.117.300189}{10.1534/genetics.117.300189}\\ +\textbf{\textit{Cover Article October 2017 Issue}} +\\\textsc{Journal Impact Factor (2020 Report):} +\\\textsc{Times Cited To Date:} 20 +\\\textsc{Contribution Statement:} Conceived and designed a new approach to identifying orthologous plant exons based on a directed acyclic graph which was robust to the insertion or deletion of entire introns. + +\item Pandey P, Ge Y, Stoerger V, \textbf{Schnable JC} (2017) High throughput in vivo analysis of plant leaf chemical properties using hyperspectral imaging. \textsc{Frontiers in Plant Science} doi \href{http://dx.doi.org/10.3389/fpls.2017.01348}{10.3389/fpls.2017.01348} +\\\textsc{Journal Impact Factor (2020 Report):} 4.4 +\\\textsc{Times Cited To Date:} 91 +\\\textsc{Contribution Statement:} Designed a different cross validation technique which was implemented by the first author. Drafted portions of the introduction and discussion and revised the manuscript. + +\item \textbf{Zhang Y}$\dagger$, \textcolor{red}{\textbf{Ngu DW}}, \textbf{Carvalho D}$\ddagger$, \textbf{Liang Z}$\ddagger$, Qiu Y, Roston RL, \textbf{Schnable JC} (2017) Differentially regulated orthologs in sorghum and the subgenomes of maize. \textsc{The Plant Cell} doi: \href{https://doi.org/10.1105/tpc.17.00354}{10.1105/tpc.17.00354} \\ +\textbf{\textit{Selected as an Editor's Choice by MaizeGDB Editorial Board}} August 2017 +\\\textsc{Journal Impact Factor (2020 Report):} 9.6 +\\\textsc{Times Cited To Date:} 34 +\\\textsc{Contribution Statement:} All analyses and writing conducted by lab members. Qiu lab assisted in developing new analytical approaches to comparing gene expression across species. Roston lab assisted in interpreting biological responses to plant cold stress. + +\item {\bf Lai X}$\ddagger$,$^*$ Behera S,$^*$ {\bf Liang Z}$\ddagger$, Lu Y, Deogun JS, {\bf Schnable JC} (2017) STAG-CNS: An order-aware conserved noncoding sequence discovery tool for arbitrary numbers of species. \textsc{Molecular Plant}. doi: \href{http://dx.doi.org/10.1016/j.molp.2017.05.010}{10.1016/j.molp.2017.05.010} +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Times Cited To Date:} 8 +\\\textsc{Contribution Statement:} I defined the problem, Sairam Behera created the algorithm, Zhikai Liang and Xianjun Lai, both from my group, conducted multiple rounds of biological validation and provided feedback to Sairam, improving the core algorithm in an iterative process. My lab wrote the paper. + +\item {\bf Lai X}$\ddagger$, {\bf Schnable JC} (2017) Harnessing the potential of the tea tree genome. \textsc{Molecular Plant}. doi: \href{http://dx.doi.org/10.1016/j.molp.2017.05.009}{10.1016/j.molp.2017.05.009} +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Times Cited To Date:} 2 +\\\textsc{Contribution Statement:} All analyses and writing conducted by lab members. + +\item Mei W, Liu S, \textbf{Schnable JC}, Yeh C, Springer NM, Schnable PS, Barbazuk WB (2017) A comprehensive analysis of alternative splicing in paleopolyploid maize. \textsc{Frontiers in Plant Science} doi: \href{http://dx.doi.org/10.3389/fpls.2017.00694}{10.3389/fpls.2017.00694} +\\\textsc{Journal Impact Factor (2020 Report):} 4.4 +\\\textsc{Times Cited To Date:} 43 +\\\textsc{Contribution Statement:} Developed approached to identifying orthologous exons across both maize subgenomes and co-orthologous genes in sorghum (an earlier iteration of the algorithm later used for paper \# 42). Consulted with the lead author on the best ways to make comparisons across subgenomes. + +\hrulefill + +\section*{Conference Articles \& Book Chapters 2021-2017} + +\subsection*{2021 Conference Articles \& Book Chapters (N=3)} + +\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} + +\hrulefill + +\subsection*{2020 Conference Articles \& Book Chapters (N=3)} + +\item Gaillard M, \textbf{Miao C}$\ddagger$, \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}$\ddagger$, 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} + +\hrulefill + +\subsection*{2019 Conference Articles \& Book Chapters (N=5)} + +\item \textbf{Miao C}$\ddagger$, \textcolor{red}{\textbf{Pages A}}, Xu Z, \textbf{Schnable JC} (2019) Sorghum organ classification in hyperspectral images using supervised machine learning classification methods. \textsc{Second International Workshop on Machine Learning for Cyber-Agricultural Systems (MLCAS 2019)} Ames, IA, USA + +\item \textcolor{red}{\textbf{Askey B}}, Yang Q, Benson AK, \textbf{Schnable JC} (2019) Computer vision phenotyping of 371 Sorghum bicolor BTx623 x ISC3620C recombinant inbred lines for QTL detection. \textsc{Second International Workshop on Machine Learning for Cyber-Agricultural Systems (MLCAS 2019)} Ames, IA, USA + +\item Jiao Y, Wang X, Chen Y, Castellano MJ, \textbf{Schnable JC}, Schnable PS, Dong L (2019) In-planta nitrate detection using insertable plant microsensor. \textsc{20th International Conference on Solid-State Sensors, Actuators and Microsystems} Berlin, Germany doi: \href{https://doi.org/10.1109/TRANSDUCERS.2019.8808527}{10.1109/TRANSDUCERS.2019.8808527} + +\item Ali MA, Wang X, Chen Y, Jiao Y, Castellano MJ, \textbf{Schnable JC}, Schnable PS, Dong L (2019) Novel all-solid-state soil nutrient sensor using nanocomposite of poly(3-octyl-thiophene) and molybdenum sulfate. \textsc{20th International Conference on Solid-State Sensors, Actuators and Microsystems} Berlin, Germany doi: \href{https://doi.org/10.1109/TRANSDUCERS.2019.8808341}{10.1109/TRANSDUCERS.2019.8808341} + +\item Clark J, Qiu Y, \textbf{Schnable JC}. (2019) Experimental design for controlled environment high throughput plant phenotyping. High Throughput Plant Phenotyping: Methods and Protocols. Editor: Argelia Lorence Publisher: Springer, New York, NY. + +\hrulefill + +\subsection*{2017 Conference Artices \& Book Chapters } + +\item Behera S, Deogun JS, \textbf{Lai X}$\ddagger$, \textbf{Schnable JC} (2017) B529 DiCE: Discovery of Conserved Noncoding Sequences Efficiently. \textsc{IEEE BIBM 2017} Kansas City, MO, USA doi: \href{http://doi.org/10.1109/BIBM.2017.8217628}{10.1109/BIBM.2017.8217628} + +\hrulefill + +\end{etaremune} + +\end{document} +% Footer diff --git a/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.aux b/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.aux new file mode 100644 index 0000000000000000000000000000000000000000..4b8111cec2b776fd99c2a7604bc64f6c0147889e --- /dev/null +++ b/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.aux @@ -0,0 +1,19 @@ +\relax +\providecommand\hyper@newdestlabel[2]{} +\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} +\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined +\global\let\oldcontentsline\contentsline +\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global\let\oldnewlabel\newlabel +\gdef\newlabel#1#2{\newlabelxx{#1}#2} +\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\ifx\hyper@anchor\@undefined +\let\contentsline\oldcontentsline +\let\newlabel\oldnewlabel +\fi} +\fi} +\global\let\hyper@last\relax +\gdef\HyperFirstAtBeginDocument#1{#1} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} +\gdef\etaremune@i{7} diff --git a/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.log b/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.log new file mode 100644 index 0000000000000000000000000000000000000000..f392212cd1b32c4fa8e8c2e9ab2fb17ac5477dfe --- /dev/null +++ b/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.log @@ -0,0 +1,852 @@ +This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex 2020.4.7) 2 NOV 2021 17:46 +entering extended mode + restricted \write18 enabled. + %&-line parsing enabled. +**JSchnable_fiveyear_2020_studentleadonly.tex +(./JSchnable_fiveyear_2020_studentleadonly.tex +LaTeX2e <2020-02-02> patch level 5 +L3 programming layer <2020-03-06> +(/usr/local/texlive/2020/texmf-dist/tex/latex/base/article.cls +Document Class: article 2019/12/20 v1.4l Standard LaTeX document class +(/usr/local/texlive/2020/texmf-dist/tex/latex/base/size10.clo +File: size10.clo 2019/12/20 v1.4l Standard LaTeX file (size option) +) +\c@part=\count167 +\c@section=\count168 +\c@subsection=\count169 +\c@subsubsection=\count170 +\c@paragraph=\count171 +\c@subparagraph=\count172 +\c@figure=\count173 +\c@table=\count174 +\abovecaptionskip=\skip47 +\belowcaptionskip=\skip48 +\bibindent=\dimen134 +) +(/usr/local/texlive/2020/texmf-dist/tex/latex/cjk/texinput/CJKutf8.sty +Package: CJKutf8 2015/04/18 4.8.4 + +(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/ifpdf.sty +Package: ifpdf 2019/10/25 v3.4 ifpdf legacy package. 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b/2021_AnnualReport/JSchnable_fiveyear_2020_studentleadonly.tex @@ -0,0 +1,165 @@ +%adapted from: +%https://github.com/rossibarra/CV + +\documentclass[letterpaper]{article} +\usepackage{CJKutf8} +\usepackage{hyperref} +\usepackage{geometry} +\usepackage{etaremune} +\usepackage{fixltx2e} +\usepackage{pgf} +\usepackage{float} +\usepackage{textcomp} +%\usepackage{eurofont} +\usepackage{color} +\usepackage{verbatim} +\definecolor{unlred}{rgb}{0.0,0.0,0.71} + +% Comment the following lines to use the default Computer Modern font +% instead of the Palatino font provided by the mathpazo package. +% Remove the 'osf' bit if you don't like the old style figures. +\usepackage[T1]{fontenc} +\usepackage[sc,osf]{mathpazo} +\usepackage{setspace} +% Set your name here +\def\name{James C. Schnable} +\renewcommand\thefootnote{\textcolor{unlred}{\arabic{footnote}}} + + +% Replace this with a link to your CV if you like, or set it empty +% (as in \def\footerlink{}) to remove the link in the footer: +%\def\footerlink{https://github.com/rossibarra/CV/blob/master/CV.pdf?raw=true} + +%Add in-line comments +\newcommand{\ignore}[1]{} + +% The following metadata will show up in the PDF properties +\hypersetup{ + colorlinks = true, + urlcolor = unlred, + pdfauthor = {\name}, + pdfkeywords = {comparative genomics, maize, grasses}, + pdftitle = {\name: Curriculum Vitae}, + pdfsubject = {Curriculum Vitae}, + pdfpagemode = UseNone +} + +\geometry{ + body={6.5in, 9in}, + left=1.0in, + top=1.0in +} + +% Customize page headers +\pagestyle{myheadings} +\markright{\name} +\thispagestyle{empty} + +% Custom section fonts +\usepackage{sectsty} +\sectionfont{\rmfamily\mdseries\Large} +\subsectionfont{\rmfamily\mdseries\itshape\large} + +% Other possible font commands include: +% \ttfamily for teletype, +% \sffamily for sans serif, +% \bfseries for bold, +% \scshape for small caps, +% \normalsize, \large, \Large, \LARGE sizes. + +% Don't indent paragraphs. +\setlength\parindent{0em} + +% Make lists without bullets +\renewenvironment{itemize}{ + \begin{list}{}{ + \setlength{\leftmargin}{1.5em} + } +}{ + \end{list} +} + +\begin{document} + +% Place name at left +\centerline{\huge \textsc{Five Year Publication List}} +\vspace{0.25in} +\centerline{\huge \textsc{\name}} +%Updated transliteration of Schnable, thanks to Zhikai Liang +%\centerline{\begin{CJK*}{UTF8}{gbsn}詹姆斯 . 施耐博\end{CJK*}} + +% Alternatively, print name centered and bold: +%\centerline{\huge \bf \name} + +\vspace{0.25in} + + +\begin{center} +\textbf{H-Index:} \textbf{\href{https://scholar.google.com/citations?user=cik4JVYAAAAJ}{30}} \\ +Lab members in \textbf{bold}.\\ +Postdoc/visiting scholar$\dagger$ in Schnable Lab.\\ +Graduate student$\ddagger$ in Schnable Lab. \\ +\textcolor{red}{Undergraduate authors} in Schnable Lab.\\ +Authors contributed equally$^*$ +\end{center} + +\section*{Journal Publications 2020-2016} + +%Figure out how to emphasis italics stuff more. + +\addtolength{\leftskip}{9mm} + +\begin{etaremune} +\subsection*{2020 Journal Publications (N=18)} + +\item \textbf{Liang Z}$\ddagger$, Qiu Y, \textbf{Schnable JC} (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 +\\\textsc{Journal Impact Factor (2020 Report):} 12.1 +\\\textsc{Altmetric Score (Percentile at Journal):} 52 (96th) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} All aspects of the paper with the exception of generating the original statistical method (Y. Qiu). + +\item \textbf{Miao C}$\ddagger$, Xu Y, Liu S, Schnable PS, \textbf{Schnable JC} (2020) Increased power and accuracy of causal locus identification in time-series genome-wide association in sorghum. \textsc{Plant Physiology} doi: \href{https://doi.org/10.1104/pp.20.00277}{10.1104/pp.20.00277} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.02.16.951467}{10.1101/2020.02.16.951467}\\ +\textbf{\textit{ "News and Views" highlighting this article by Y Yu}} doi: \href{https://doi.org/10.1104/pp.20.00797}{10.1104/pp.20.00797} +\\\textsc{Journal Impact Factor (2020 Report):} 6.9 +\\\textsc{Altmetric Score (Percentile at Journal):} 29 (91st) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} Y. Xu ran a new type of statistical analysis he had generated at Iowa State, S. Liu and PS Schnable contributed genotyping data for the sorghum population, all other aspects of the paper carried out by Schnable lab members. + +\item \textbf{Dai X}$\ddagger$, Xu Z, \textbf{Liang Z}$\ddagger$, Tu X, Zhong S, \textbf{Schnable JC}, Li P (2020) Non-homology based prediction of gene functions. \textsc{The Plant Genome} doi: \href{https://doi.org/10.1002/tpg2.20015}{10.1002/tpg2.20015} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/730473}{10.1101/730473} +\\\textsc{Journal Impact Factor (2020 Report):} 3.8 +\\\textsc{Altmetric Score (Percentile at Journal):} 16 (96th) +\\\textsc{Schnable Lab Percent Contribution:} 90\% +\\\textsc{Contribution Statement:} Z Xu, X Tu, and S Song contributed data. P Li co-mentored X Dai with Prof. Schnable. All other aspects of the paper carried out by Schnable lab members. + + +\item \textbf{Miao C}$\ddagger$, \textcolor{red}{\textbf{Pages A}}, Xu Z, Rodene E, Yang J, \textbf{Schnable JC} (2020) Semantic segmentation of sorghum using hyperspectral data identifies genetic associations. \textsc{Plant Phenomics} doi: \href{https://doi.org/10.34133/2020/4216373}{10.34133/2020/4216373} +\\\textsc{Journal Impact Factor (2020 Report):} New Journal +\\\textsc{Altmetric Score (Percentile at Journal):} 32 (93rd) +\\\textsc{Schnable Lab Percent Contribution:} 80\% +\\\textsc{Contribution Statement:} R Rodene and J Yang contributed data. Z Xu advised on statistical analysis methods. All other aspects of the paper carried out by Schnable lab members. + +\item \textbf{Carvalho DS}$\ddagger$, \textcolor{red}{\textbf{Nishimwe AV}}, \textbf{Schnable JC} (2020) IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae. \textsc{Plant Direct} \href{https://doi.org/10.1002/pld3.203}{10.1002/pld3.203} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/689356}{10.1101/689356} +\\\textsc{Journal Impact Factor (2020 Report):} 1.7 +\\\textsc{Altmetric Score (Percentile at Journal):} 26 (92nd) +\\\textsc{Schnable Lab Percent Contribution:} 100\% +\\\textsc{Contribution Statement:} N/A + + +\item \textbf{Lai X}$\ddagger$, Bendix C, \textbf{Yan L}$\dagger$, \textbf{Zhang Y}$\dagger$, \textbf{Schnable JC}, Harmon F (2020) Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. \textsc{BMC Genomics} doi: \href{https://doi.org/10.1186/s12864-020-06824-3}{10.1186/s12864-020-06824-3}\\ +\textbf{\textit{ Selected as an Editor's Choice by MaizeGDB Editorial Board}} October 2020 +\\\textsc{Journal Impact Factor (2020 Report):} 3.6 +\\\textsc{Altmetric Score (Percentile at Journal):} 11 (91st) +\\\textsc{Schnable Lab Percent Contribution:} 75\% +\\\textsc{Contribution Statement:} Plants were grown and RNA samples were collected in the Harmon lab. RNA-seq libraries were build and sequenced in the Schnable lab. Expression, comparative genomics, and promoter motif analysis conducted in the Schnable lab. Phylogenetic analysis of clock genes conducted in the Harmon lab. + +\item Gaillard M$^*$, \textbf{Miao C}$\ddagger$$^*$, \textbf{Schnable JC}, Benes B (2020) Voxel carving based 3D reconstruction of sorghum identifies genetic determinants of radiation interception efficiency. \textsc{Plant Direct} doi: \href{https://doi.org/10.1002/pld3.255}{10.1002/pld3.255} \textsc{bioRxiv} doi: \href{https://doi.org/10.1101/2020.04.06.028605}{10.1101/2020.04.06.028605v1} +\\\textsc{Journal Impact Factor (2020 Report):} 1.7 +\\\textsc{Altmetric Score (Percentile at Journal):} 23 (88th) +\\\textsc{Schnable Lab Percent Contribution:} 50\% +\\\textsc{Contribution Statement:} Schnable lab generated data. Benes lab analyzed data to construct 3D models. Schnable lab conducted the GWAS and analyzed the results. Writing was shared equally between the two groups. + +\end{etaremune} + +\end{document} +% Footer diff --git a/2021_AnnualReport/JamesSchnable_2020_Abbreviated_CV.pdf b/2021_AnnualReport/JamesSchnable_2020_Abbreviated_CV.pdf new file mode 100644 index 0000000000000000000000000000000000000000..4205c07fd82e74dd6410ffea27ed81f573607e97 Binary files /dev/null and b/2021_AnnualReport/JamesSchnable_2020_Abbreviated_CV.pdf differ diff --git a/2021_AnnualReport/JamesSchnable_2020_Summary_v2.pdf b/2021_AnnualReport/JamesSchnable_2020_Summary_v2.pdf new file mode 100644 index 0000000000000000000000000000000000000000..c70e67f34cf55c7ad61aa3867a0b9d821af0704c Binary files /dev/null and b/2021_AnnualReport/JamesSchnable_2020_Summary_v2.pdf differ diff --git a/2021_AnnualReport/Schnable_2020_fiveyearpublications.pdf b/2021_AnnualReport/Schnable_2020_fiveyearpublications.pdf new file mode 100644 index 0000000000000000000000000000000000000000..f091b8ced9b94d925699a83b4d825caeac121a9f Binary files /dev/null and b/2021_AnnualReport/Schnable_2020_fiveyearpublications.pdf differ diff --git a/2021_AnnualReport/Users:.fileloc b/2021_AnnualReport/Users:.fileloc new file mode 100644 index 0000000000000000000000000000000000000000..5711335766f190229c2fbb6addcbee76a670d5e8 --- /dev/null +++ b/2021_AnnualReport/Users:.fileloc @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> +<plist version="1.0"> +<dict> + <key>URL</key> + <string>file:///Users/jamesschnable/software/lab_cvs/2021_AnnualReport/JSchnable_fiveyear_2020.tex</string> +</dict> +</plist> diff --git a/2021_AnnualReport/texput.log b/2021_AnnualReport/texput.log new file mode 100644 index 0000000000000000000000000000000000000000..dff4b2d4ef5f37916f1e985335dba4137749cbe9 --- /dev/null +++ b/2021_AnnualReport/texput.log @@ -0,0 +1,21 @@ +This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex 2020.4.7) 12 JAN 2021 20:43 +entering extended mode + restricted \write18 enabled. + %&-line parsing enabled. +**JSchnable_Summary. + +! 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