Publications

ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies

Published in BioRxiv, 2018

We developed a nice tool to easily visualize multiple manhattan plots. This is particaully useful for phenomics datasets or longitudinal studies.

Recommended citation: Hussain W., Campbell M., Walia H., Morota G. (2018) ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies. bioRxiv. http://malachycampbell.github.io/files/Hussain_ShinyAIM_2018.pdf

Using LASSO in gene co-expression network for genome-wide identification of gene interactions responding to salt stress in rice

Published in BioRxiv, 2018

Here, we used LASSO to select gene coexpression modules associated with salinity tolerance traits.

Recommended citation: Du, Q., M.T. Campbell, H. Yu, K. Liu, H. Walia, Q. Zhang, C. Zhang. (2018) Using LASSO in gene co-expression network for genome-wide identification of gene interactions responding to salt stress in rice. bioRxiv. http://malachycampbell.github.io/files/Du_LASSO_2018.pdf

Utilizing random regression models for genomic prediction of a longitudinal trait derived from high-throughput phenotyping

Published in Plant Direct, 2018

Here we used several random regression (RR) models with Legendre polynomials for genomic prediction of shoot growth trajectories in rice (Oryza sativa).

Recommended citation: Campbell, M.T., H. Walia, and G. Morota. 2018. Utilizing random regression models for genomic prediction of a longitudinal trait derived from high-throughput phenotyping. Plant Direct (In Press) http://malachycampbell.github.io/files/Campbell_2018.pdf

A Comprehensive Image based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa)

Published in Plant Genome, 2017

We used a functional model of shoot biomass over 20 days and used model parameters for association mapping and genomic prediction.

Recommended citation: Campbell, M.T., Q. Du, K. Liu, C.J. Brien, B. Berger, C. Zhang, and H. Walia. 2017. A Comprehensive Image based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa). Plant Genome 10(2): 0 http://malachycampbell.github.io/files/Campbell_2017_pg.pdf

Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content

Published in PLoS Genetics, 2017

HKT1;1 was identified as a major regualtor of root sodium content in rice. Variants that influence the transport of sodium were found to be a component of the divergence between to two subspecies of rice for root sodium content.

Recommended citation: Campbell, M.T., N. Bandillo, F.R.A. Al Shiblawi, S. Sharma, K. Liu, Q. Du, A.J. Schmitz, C. Zhang, A.A. Very, A.J. Lorenz, and H. Walia. 2017. Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. PLoS Genet. 13(6). http://malachycampbell.github.io/files/Campbell_2017_hkt.pdf

Image Harvest: an open source platform for high throughput plant image processing and analysis

Published in Journal of Experimental Botany, 2016

We developed a software to process and anayze images derived from high throughput phenotyping platforms.

Recommended citation: Knecht, A.C., M.T. Campbell, A. Caprez, D.R. Swanson, and H. Walia. (2016). Image Harvest: an open source platform for high throughput plant image processing and analysis. J. Exp. Bot. 67(11): 3587–3599 http://malachycampbell.github.io/files/Knecht_2016.pdf

Integrating image based phenomics and association analysis to dissect the genetic architecture of temporal salinity responses in rice

Published in Plant Physiology, 2015

Here, we used image based high thoughput phenotyping and association mapping to examine the genetic basis of temporal salinity responses.

Recommended citation: Campbell, M.T., A.C. Knecht, B. Berger, C.J. Brien, D. Wang, and H. Walia. (2015). Integrating image based phenomics and association analysis to dissect the genetic architecture of temporal salinity responses in rice. Plant Physiol. 168(August): pp.00450.2015. http://malachycampbell.github.io/files/Campbell_2015_pp.pdf

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

Published in PLoS One, 2015

This paper assess natural variation for submegence tolerance in maize and identifies a QTL that influences submegence tolerance.

Recommended citation: Campbell, M.T., C.A. Proctor, Y. Dou, A.J. Schmitz, P. Phansak, G.R. Kruger, C. Zhang, and H. Walia. (2015). Genetic and molecular characterization of submergence response identifies Subtol6 as a major submergence tolerance locus in maize. PLoS One 10(3): e0120385. http://malachycampbell.github.io/files/Campbell_2015.pdf

Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat

Published in Plant Physiology, 2013

This paper looks at the effects of an introgression from Agropyron elongatum into Triticum aestivum on drought tolerance.

Recommended citation: Placido, D.F., M.T. Campbell, J.J. Folsom, X. Cui, G.R. Kruger, P.S. Baenziger, and H. Walia. (2013). Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat. Plant Physiol. 161(4): 1806-1819. http://malachycampbell.github.io/files/Placido_2013.pdf