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Items: 18


The Fate of Deleterious Variants in a Barley Genomic Prediction Population.

Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC, Smith KP, Morrell PL.

Genetics. 2019 Dec;213(4):1531-1544. doi: 10.1534/genetics.119.302733. Epub 2019 Oct 25.


Epigenetic Changes in Alveolar Type II Lung Cells of A/J Mice Following Intranasal Treatment with Lipopolysaccharide.

Seiler CL, Song JM, Fernandez J, Abrahante JE, Kono TJY, Chen Y, Ren Y, Kassie F, Tretyakova NY.

Chem Res Toxicol. 2019 May 20;32(5):831-839. doi: 10.1021/acs.chemrestox.9b00015. Epub 2019 Apr 16.


Genome-wide association analysis of stalk biomass and anatomical traits in maize.

Mazaheri M, Heckwolf M, Vaillancourt B, Gage JL, Burdo B, Heckwolf S, Barry K, Lipzen A, Ribeiro CB, Kono TJY, Kaeppler HF, Spalding EP, Hirsch CN, Robin Buell C, de Leon N, Kaeppler SM.

BMC Plant Biol. 2019 Jan 31;19(1):45. doi: 10.1186/s12870-019-1653-x.


Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods.

Passow CN, Kono TJY, Stahl BA, Jaggard JB, Keene AC, McGaugh SE.

Mol Ecol Resour. 2019 Mar;19(2):456-464. doi: 10.1111/1755-0998.12965. Epub 2018 Dec 21.


The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus.

Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE.

Mol Ecol. 2018 Nov;27(22):4397-4416. doi: 10.1111/mec.14877. Epub 2018 Oct 16.


Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants.

Kono TJY, Lei L, Shih CH, Hoffman PJ, Morrell PL, Fay JC.

G3 (Bethesda). 2018 Oct 3;8(10):3321-3329. doi: 10.1534/g3.118.200563.


Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time.

Kono TJY, Brohammer AB, McGaugh SE, Hirsch CN.

G3 (Bethesda). 2018 Aug 30;8(9):3049-3058. doi: 10.1534/g3.118.200580.


The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines.

Brohammer AB, Kono TJY, Springer NM, McGaugh SE, Hirsch CN.

Plant J. 2018 Jan;93(1):131-141. doi: 10.1111/tpj.13765. Epub 2017 Dec 2.


A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants.

Čermák T, Curtin SJ, Gil-Humanes J, Čegan R, Kono TJY, Konečná E, Belanto JJ, Starker CG, Mathre JW, Greenstein RL, Voytas DF.

Plant Cell. 2017 Jun;29(6):1196-1217. doi: 10.1105/tpc.16.00922. Epub 2017 May 18.


angsd-wrapper: utilities for analysing next-generation sequencing data.

Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJ, Morrell PL, Ross-Ibarra J.

Mol Ecol Resour. 2016 Nov;16(6):1449-1454. doi: 10.1111/1755-0998.12578. Epub 2016 Aug 29.


The Role of Deleterious Substitutions in Crop Genomes.

Kono TJ, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL.

Mol Biol Evol. 2016 Sep;33(9):2307-17. doi: 10.1093/molbev/msw102. Epub 2016 Jun 14.


Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes.

Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJ, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM.

Theor Appl Genet. 2016 Sep;129(9):1725-38. doi: 10.1007/s00122-016-2735-x. Epub 2016 Jun 9.


Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley.

Nice LM, Steffenson BJ, Brown-Guedira GL, Akhunov ED, Liu C, Kono TJ, Morrell PL, Blake TK, Horsley RD, Smith KP, Muehlbauer GJ.

Genetics. 2016 Jul;203(3):1453-67. doi: 10.1534/genetics.116.190736. Epub 2016 May 10.


Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants.

Anderson JE, Michno JM, Kono TJ, Stec AO, Campbell BW, Curtin SJ, Stupar RM.

BMC Biotechnol. 2016 May 12;16(1):41. doi: 10.1186/s12896-016-0271-z.


Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans.

Anderson JE, Kono TJ, Stupar RM, Kantar MB, Morrell PL.

G3 (Bethesda). 2016 Apr 7;6(4):835-43. doi: 10.1534/g3.116.026914.


The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations.

Poets AM, Mohammadi M, Seth K, Wang H, Kono TJ, Fang Z, Muehlbauer GJ, Smith KP, Morrell PL.

G3 (Bethesda). 2015 Dec 29;6(3):609-22. doi: 10.1534/g3.115.024349.


CRISPR/Cas mutagenesis of soybean and Medicago truncatula using a new web-tool and a modified Cas9 enzyme.

Michno JM, Wang X, Liu J, Curtin SJ, Kono TJ, Stupar RM.

GM Crops Food. 2015;6(4):243-52. doi: 10.1080/21645698.2015.1106063.


SNPMeta: SNP annotation and SNP metadata collection without a reference genome.

Kono TJ, Seth K, Poland JA, Morrell PL.

Mol Ecol Resour. 2014 Mar;14(2):419-25. doi: 10.1111/1755-0998.12183. Epub 2013 Nov 16.


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