Alexandersson, E., Kushwaha, S., Subedi, A., Weighill, D., Climer, S., Jacobson, D., Andreasson, E., 2020. Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. BMC Plant Biology 20, 120. https://doi.org/10.1186/s12870-020-2305-x

Weighill, D., Macaya-Sanz, D., DiFazio, S.P., Joubert, W., Shah, M., Schmutz, J., Sreedasyam, A., Tuskan, G., Jacobson, D., 2019. Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. Front. Genet. 10. doi.org/10.3389/fgene.2019.00487 

Weighill, D., Jones, P., Bleker, C., Ranjan, P., Shah, M., Zhao, N., Martin, M., DiFazio, S., Macaya-Sanz, D., Schmutz, J., Sreedasyam, A., Tschaplinski, T., Tuskan, G., Jacobson, D., 2019. Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships. Front. Genet. 10. https://doi.org/10.3389/fgene.2019.00417

Weighill, D., Tschaplinski, T.J., Tuskan, G.A., Jacobson, D., 2019c. Data Integration in Poplar: ‘Omics Layers and Integration Strategies. Front. Genet. 10. doi.org/10.3389/fgene.2019.00874 

Furches, A., Kainer, D., Weighill, D., Large, A., Jones, P., Walker, A.M., Romero, J., Gazolla, J.G.F.M., Joubert, W., Shah, M., Streich, J., Ranjan, P., Schmutz, J., Sreedasyam, A., Macaya-Sanz, D., Zhao, N., Martin, M.Z., Rao, X., Dixon, R.A., DiFazio, S., Tschaplinski, T.J., Chen, J.-G., Tuskan, G.A., Jacobson, D., 2019. Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. Front. Plant Sci. 10. https://doi.org/10.3389/fpls.2019.01249

Weighill, D., Jones, P., Shah, M., Ranjan, P., Muchero, W., Schmutz, J., Sreedasyam, A., Macaya-Sanz, D., Sykes, R., Zhao, N., Martin, M.Z., DiFazio, S., Tschaplinski, T.J., Tuskan, G., Jacobson, D., 2018. Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery. Front. Energy Res. 6. https://doi.org/10.3389/fenrg.2018.00030

Bonito, G., Benucci, G.M.N., Hameed, K., Weighill, D., Jones, P., Chen, K.-H., Jacobson, D., Schadt, C., Vilgalys, R., 2019. Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype. Front. Microbiol. 10. https://doi.org/10.3389/fmicb.2019.00481

Joubert, W., Nance, J., Climer, S., Weighill, D., Jacobson, D., 2019. Parallel accelerated Custom Correlation Coefficient calculations for genomics applications. Parallel Computing 84, 15–23. https://doi.org/10.1016/j.parco.2019.02.003

Lee, L.L., Blumer-Schuette, S.E., Izquierdo, J.A., Zurawski, J.V., Loder, A.J., Conway, J.M., Elkins, J.G., Podar, M., Clum, A., Jones, P.C., Piatek, M.J., Weighill, D., Jacobson, D.A., Adams, M.W.W., Kelly, R.M., 2018. Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses. Appl. Environ. Microbiol. 84. doi.org/10.1128/AEM.02694-17 

Tuskan, G.A., Mewalal, R., Gunter, L.E., Palla, K.J., Carter, K., Jacobson, D.A., Jones, P.C., Garcia, B.J., Weighill, D., Hyatt, P.D., Yang, Y., Zhang, J., Reis, N., Chen, J.-G., Muchero, W., 2018. Defining the genetic components of callus formation: A GWAS approach. PLoS ONE 13, e0202519. doi.org/10.1371/journal.pone.0202519 

Joubert, W., Nance, J., Weighill, D., Jacobson, D., 2018. Parallel accelerated vector similarity calculations for genomics applications. Parallel Computing 75, 130–145. doi.org/10.1016/j.parco.2018.03.009 

Joubert, W., Weighill, D., Kainer, D., Climer, S., Justice, A., Fagnan, K., Jacobson, D., 2018. Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction, in: SC18: International Conference for High Performance Computing, Networking, Storage and Analysis. Presented at the SC18: International Conference for High Performance Computing, Networking, Storage and Analysis, pp. 717–730. doi.org/10.1109/SC.2018.00060 

Bryan, A.C., Zhang, J., Guo, J., Ranjan, P., Singan, V., Barry, K., Schmutz, J., Weighill, D., Jacobson, D., Jawdy, S., Tuskan, G.A., Chen, J.-G., Muchero, W., 2018. A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. G3: Genes, Genomes, Genetics 8, 2631–2641. doi.org/10.1534/g3.118.200188 

Decker, S.R., Harman-Ware, A.E., Happs, R.M., Wolfrum, E.J., Tuskan, G.A., Kainer, D., Oguntimein, G.B., Rodriguez, M., Weighill, D., Jones, P., Jacobson, D., 2018. High Throughput Screening Technologies in Biomass Characterization. Front. Energy Res. 6. https://doi.org/10.3389/fenrg.2018.00120

Yang, X., Hu, R., Yin, H., Jenkins, J., Shu, S., Tang, H., Liu, D., Weighill, D., Cheol Yim, W., Ha, J., Heyduk, K., Goodstein, D.M., Guo, H.-B., Moseley, R.C., Fitzek, E., Jawdy, S., Zhang, Z., Xie, M., Hartwell, J., Grimwood, J., Abraham, P.E., Mewalal, R., Beltrán, J.D., Boxall, S.F., Dever, L.V., Palla, K.J., Albion, R., Garcia, T., Mayer, J.A., Don Lim, S., Man Wai, C., Peluso, P., Van Buren, R., De Paoli, H.C., Borland, A.M., Guo, H., Chen, J.-G., Muchero, W., Yin, Y., Jacobson, D.A., Tschaplinski, T.J., Hettich, R.L., Ming, R., Winter, K., Leebens-Mack, J.H., Smith, J.A.C., Cushman, J.C., Schmutz, J., Tuskan, G.A., 2017. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications 8, 1–15. doi.org/10.1038/s41467-017-01491-7 

Zheng, K., Wang, X., Weighill, D., Guo, H.-B., Xie, M., Yang, Y., Yang, J., Wang, S., Jacobson, D.A., Guo, H., Muchero, W., Tuskan, G.A., Chen, J.-G., 2016. Characterization of DWARF14 Genes in Populus. Scientific Reports 6, 1–11. https://doi.org/10.1038/srep21593

Abraham, P.E., Yin, H., Borland, A.M., Weighill, D., Lim, S.D., De Paoli, H.C., Engle, N., Jones, P.C., Agh, R., Weston, D.J., Wullschleger, S.D., Tschaplinski, T., Jacobson, D., Cushman, J.C., Hettich, R.L., Tuskan, G.A., Yang, X., 2016. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave. Nature Plants 2, 1–10. https://doi.org/10.1038/nplants.2016.178

Weighill, D., Jacobson, D.A., 2015. 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. PLOS Computational Biology 11, e1004079. doi.org/10.1371/journal.pcbi.1004079 

Beckner Whitener, M.E., Carlin, S., Jacobson, D., Weighill, D., Divol, B., Conterno, L., Du Toit, M., Vrhovsek, U., 2015. Early fermentation volatile metabolite profile of non-Saccharomyces yeasts in red and white grape must: A targeted approach. LWT - Food Science and Technology 64, 412–422. doi.org/10.1016/j.lwt.2015.05.018 

Bengtsson, T., Weighill, D., Proux-Wéra, E., Levander, F., Resjö, S., Burra, D.D., Moushib, L.I., Hedley, P.E., Liljeroth, E., Jacobson, D., Alexandersson, E., Andreasson, E., 2014. Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach. BMC Genomics 15, 315. doi.org/10.1186/1471-2164-15-315 

Weighill, D., Jacobson, D., 2017. Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology, in: Nookaew, I. (Ed.), Network Biology, Advances in Biochemical Engineering/Biotechnology. Springer International Publishing, Cham, pp. 143–183. doi.org/10.1007/10_2016_46 

Weighill, D., 2019. Network and multi-scale signal analysis for the integration of large omic datasets: applications in Populus trichocarpa. (Doctoral Dissertation). University of Tennessee, Knoxville, United States. trace.tennessee.edu/utk_graddiss/5380/ 

Weighill, D., 2014. Exploring the topology of complex phylogenomic and transcriptomic networks (Master's Thesis). Stellenbosch University, South Africa. scholar.sun.ac.za/handle/10019.1/95800