Kainer D - Search Results

1

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering.

Noshay JM, Walker T, Alexander WG, Klingeman DM, Romero J, Walker AM, Prates E, Eckert C, Irle S, Kainer D, Jacobson DA. Noshay JM, et al. Among authors: kainer d. Nucleic Acids Res. 2023 Oct 27;51(19):10147-10161. doi: 10.1093/nar/gkad736. Nucleic Acids Res. 2023. PMID: 37738140 Free PMC article.

2

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case.

Wang W, Schalamun M, Morales-Suarez A, Kainer D, Schwessinger B, Lanfear R. Wang W, et al. Among authors: kainer d. BMC Genomics. 2018 Dec 29;19(1):977. doi: 10.1186/s12864-018-5348-8. BMC Genomics. 2018. PMID: 30594129 Free PMC article.

3

Selecting optimal partitioning schemes for phylogenomic datasets.

Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A. Lanfear R, et al. Among authors: kainer d. BMC Evol Biol. 2014 Apr 17;14:82. doi: 10.1186/1471-2148-14-82. BMC Evol Biol. 2014. PMID: 24742000 Free PMC article.

4

Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence.

Harfouche AL, Jacobson DA, Kainer D, Romero JC, Harfouche AH, Scarascia Mugnozza G, Moshelion M, Tuskan GA, Keurentjes JJB, Altman A. Harfouche AL, et al. Among authors: kainer d. Trends Biotechnol. 2019 Nov;37(11):1217-1235. doi: 10.1016/j.tibtech.2019.05.007. Epub 2019 Jun 21. Trends Biotechnol. 2019. PMID: 31235329 Review.

5

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence.

Furches A, Kainer D, Weighill D, Large A, Jones P, Walker AM, Romero J, Gazolla JGFM, Joubert W, Shah M, Streich J, Ranjan P, Schmutz J, Sreedasyam A, Macaya-Sanz D, Zhao N, Martin MZ, Rao X, Dixon RA, DiFazio S, Tschaplinski TJ, Chen JG, Tuskan GA, Jacobson D. Furches A, et al. Among authors: kainer d. Front Plant Sci. 2019 Oct 8;10:1249. doi: 10.3389/fpls.2019.01249. eCollection 2019. Front Plant Sci. 2019. PMID: 31649710 Free PMC article.

6

A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks.

Cliff A, Romero J, Kainer D, Walker A, Furches A, Jacobson D. Cliff A, et al. Among authors: kainer d. Genes (Basel). 2019 Dec 2;10(12):996. doi: 10.3390/genes10120996. Genes (Basel). 2019. PMID: 31810264 Free PMC article.

7

Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?

Streich J, Romero J, Gazolla JGFM, Kainer D, Cliff A, Prates ET, Brown JB, Khoury S, Tuskan GA, Garvin M, Jacobson D, Harfouche AL. Streich J, et al. Among authors: kainer d. Curr Opin Biotechnol. 2020 Feb;61:217-225. doi: 10.1016/j.copbio.2020.01.010. Epub 2020 Feb 18. Curr Opin Biotechnol. 2020. PMID: 32086132 Review.

8

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa.

Chhetri HB, Furches A, Macaya-Sanz D, Walker AR, Kainer D, Jones P, Harman-Ware AE, Tschaplinski TJ, Jacobson D, Tuskan GA, DiFazio SP. Chhetri HB, et al. Among authors: kainer d. Front Plant Sci. 2020 Sep 9;11:545748. doi: 10.3389/fpls.2020.545748. eCollection 2020. Front Plant Sci. 2020. PMID: 33013968 Free PMC article.

9

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models.

Garvin MR, T Prates E, Pavicic M, Jones P, Amos BK, Geiger A, Shah MB, Streich J, Felipe Machado Gazolla JG, Kainer D, Cliff A, Romero J, Keith N, Brown JB, Jacobson D. Garvin MR, et al. Among authors: kainer d. Genome Biol. 2020 Dec 23;21(1):304. doi: 10.1186/s13059-020-02191-0. Genome Biol. 2020. PMID: 33357233 Free PMC article.

10

The Genetic Architecture of Nitrogen Use Efficiency in Switchgrass (Panicum virgatum L.).

Shrestha V, Chhetri HB, Kainer D, Xu Y, Hamilton L, Piasecki C, Wolfe B, Wang X, Saha M, Jacobson D, Millwood RJ, Mazarei M, Stewart CN Jr. Shrestha V, et al. Among authors: kainer d. Front Plant Sci. 2022 May 2;13:893610. doi: 10.3389/fpls.2022.893610. eCollection 2022. Front Plant Sci. 2022. PMID: 35586220 Free PMC article.

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