Joshua A. Udall, Ph.D. - Publications

Affiliations: 
2003 University of Wisconsin, Madison, Madison, WI 
Area:
Agronomy Agriculture, Genetics

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Yuan D, Grover CE, Hu G, Pan M, Miller ER, Conover JL, Hunt SP, Udall JA, Wendel JF. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 8: 2003634. PMID 34026441 DOI: 10.1002/advs.202003634  0.88
2021 Grover CE, Yuan D, Arick MA, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA. The Gossypium stocksii genome as a novel resource for cotton improvement. G3 (Bethesda, Md.). PMID 33871013 DOI: 10.1093/g3journal/jkab125  0.88
2020 Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA. The Genome as a Resource for Cotton Breeding and Evolution. G3 (Bethesda, Md.). PMID 32122962 DOI: 10.1534/G3.120.401050  0.88
2019 Grover CE, Yoo MJ, Lin M, Murphy MD, Harker DB, Byers RL, Lipka AE, Hu G, Yuan D, Conover JL, Udall JA, Paterson AH, Gore MA, Wendel JF. Genetic Analysis of the Transition from Wild to Domesticated Cotton ( L.). G3 (Bethesda, Md.). PMID 31843806 DOI: 10.1534/G3.119.400909  0.88
2019 Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, Masonbrink RE, Peterson DG, Wendel JF. The Genome Sequence of Illustrates a Descending Dysploidy in Plants. Frontiers in Plant Science. 10: 1541. PMID 31827481 DOI: 10.3389/Fpls.2019.01541  0.88
2019 Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF. Genome Sequence Assemblies of and . G3 (Bethesda, Md.). PMID 31462444 DOI: 10.1534/G3.119.400392  0.88
2018 Wang M, Tu L, Yuan D, Zhu, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G, Ye Z, Huang H, Yan F, Ma Y, Zhang L, ... ... Udall JA, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics. PMID 30510239 DOI: 10.1038/S41588-018-0282-X  0.76
2017 Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, et al. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biology and Evolution. 9: 3328-3344. PMID 29194487 DOI: 10.1093/Gbe/Evx248  0.88
2017 Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, et al. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. Bmc Plant Biology. 17: 37. PMID 28158969 DOI: 10.1186/S12870-017-0981-Y  0.88
2017 Reddy UK, Nimmakayala P, Abburi VL, Reddy CV, Saminathan T, Percy RG, Yu JZ, Frelichowski J, Udall JA, Page JT, Zhang D, Shehzad T, Paterson AH. Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs. Scientific Reports. 7: 41285. PMID 28128280 DOI: 10.1038/Srep41285  0.72
2017 Hu G, Hovav R, Grover CE, Faigenboim-Doron A, Kadmon N, Page JT, Udall JA, Wendel JF. Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds. Genome Biology and Evolution. PMID 28062755 DOI: 10.1093/Gbe/Evw280  0.88
2016 Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ. The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly. The Plant Genome. 9. PMID 27898770 DOI: 10.3835/Plantgenome2015.07.0062  0.72
2016 Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA. Correction: DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. Plos Genetics. 12: e1006206. PMID 27447832 DOI: 10.1371/Journal.Pgen.1006206  0.72
2016 Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA, Grover CE, Wendel JF. Independent domestication of two Old World cotton species. Genome Biology and Evolution. PMID 27289095 DOI: 10.1093/Gbe/Evw129  0.88
2016 Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA. DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. Plos Genetics. 12: e1006012. PMID 27168520 DOI: 10.1371/Journal.Pgen.1006012  0.72
2016 Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ. The amaranth genome: Genome, transcriptome, and physical map assembly Plant Genome. 9. DOI: 10.3835/plantgenome2015.07.0062  0.88
2015 Grover CE, Gallagher JP, Jareczek JJ, Page JT, Udall JA, Gore MA, Wendel JF. Re-evaluating the phylogeny of allopolyploid Gossypium L. Molecular Phylogenetics and Evolution. 92: 45-52. PMID 26049043 DOI: 10.1016/J.Ympev.2015.05.023  0.88
2015 Huynh MD, Page JT, Richardson BA, Udall JA. Insights into transcriptomes of big and low sagebrush. Plos One. 10: e0127593. PMID 26020526 DOI: 10.1371/Journal.Pone.0127593  0.88
2015 Page JT, Udall JA. Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms. Bmc Genetics. 16: S4. PMID 25951770 DOI: 10.1186/1471-2156-16-S2-S4  0.72
2015 Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, et al. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda, Md.). 5: 1187-209. PMID 25908569 DOI: 10.1534/G3.115.018416  0.88
2014 Page JT, Liechty ZS, Huynh MD, Udall JA. BamBam: genome sequence analysis tools for biologists. Bmc Research Notes. 7: 829. PMID 25421351 DOI: 10.1186/1756-0500-7-829  0.88
2014 Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, Page JT, Jenks MA, Chapman KD, Udall JA, Gore MA, Dyer JM. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. Bmc Plant Biology. 14: 312. PMID 25403726 DOI: 10.1186/S12870-014-0312-5  0.88
2014 Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda AB, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. Bmc Genomics. 15: 945. PMID 25359292 DOI: 10.1186/1471-2164-15-945  0.88
2014 Naoumkina M, Thyssen G, Fang DD, Hinchliffe DJ, Florane C, Yeater KM, Page JT, Udall JA. The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.). Plos One. 9: e90830. PMID 24598808 DOI: 10.1371/Journal.Pone.0090830  0.88
2014 Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biology and Evolution. 6: 559-71. PMID 24558256 DOI: 10.1093/Gbe/Evu037  0.88
2014 Soliai MM, Meyer SE, Udall JA, Elzinga DE, Hermansen RA, Bodily PM, Hart AA, Coleman CE. De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. Plos One. 9: e87045. PMID 24475219 DOI: 10.1371/Journal.Pone.0087045  0.88
2014 Rambani A, Page JT, Udall JA. Polyploidy and the petal transcriptome of Gossypium. Bmc Plant Biology. 14: 3. PMID 24393201 DOI: 10.1186/1471-2229-14-3  0.72
2014 Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 127: 283-95. PMID 24170350 DOI: 10.1007/S00122-013-2217-3  0.88
2013 Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT. RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. Plos One. 8: e82634. PMID 24324815 DOI: 10.1371/Journal.Pone.0082634  0.88
2013 Page JT, Huynh MD, Liechty ZS, Grupp K, Stelly D, Hulse AM, Ashrafi H, Van Deynze A, Wendel JF, Udall JA. Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing. G3 (Bethesda, Md.). 3: 1809-18. PMID 23979935 DOI: 10.1534/G3.113.007229  0.88
2013 Page JT, Gingle AR, Udall JA. PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms. G3 (Bethesda, Md.). 3: 517-25. PMID 23450226 DOI: 10.1534/G3.112.005298  0.72
2012 Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492: 423-7. PMID 23257886 DOI: 10.1038/Nature11798  0.88
2012 Richardson BA, Page JT, Bajgain P, Sanderson SC, Udall JA. Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae) American Journal of Botany. 99: 1962-1975. PMID 23204489 DOI: 10.3732/Ajb.1200373  0.88
2012 Flagel LE, Wendel JF, Udall JA. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. Bmc Genomics. 13: 302. PMID 22768919 DOI: 10.1186/1471-2164-13-302  0.88
2012 Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 125: 311-27. PMID 22398438 DOI: 10.1007/S00122-012-1835-5  0.88
2012 Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany. 99: 291-311. PMID 22312117 DOI: 10.3732/Ajb.1100356  0.88
2012 Byers RL, Harker DB, Yourstone SM, Maughan PJ, Udall JA. Development and mapping of SNP assays in allotetraploid cotton Theoretical and Applied Genetics. 124: 1201-1214. PMID 22252442 DOI: 10.1007/S00122-011-1780-8  0.88
2012 Salmon A, Udall JA, Jeddeloh JA, Wendel J. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton G3: Genes, Genomes, Genetics. 2: 921-930. DOI: 10.1534/g3.112.003392  0.88
2011 Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biology and Evolution. 3: 1312-23. PMID 22002916 DOI: 10.1093/Gbe/Evr106  0.88
2011 Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata) Bmc Genomics. 12. PMID 21767398 DOI: 10.1186/1471-2164-12-370  0.88
2010 Rapp RA, Haigler CH, Flagel L, Hovav RH, Udall JA, Wendel JF. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. Bmc Biology. 8: 139. PMID 21078138 DOI: 10.1186/1741-7007-8-139  0.88
2010 Salmon A, Flagel L, Ying B, Udall JA, Wendel JF. Homoeologous nonreciprocal recombination in polyploid cotton. The New Phytologist. 186: 123-34. PMID 19925554 DOI: 10.1111/J.1469-8137.2009.03093.X  0.88
2010 Paterson AH, Rong Jk, Gingle AR, Chee PW, Dennis ES, Llewellyn D, Dure LS, Haigler C, Myers GO, Peterson DG, ur Rahman M, Zafar Y, Reddy U, Saranga Y, Stewart JM, ... Udall JA, et al. Sequencing and utilization of the Gossypium genomes Tropical Plant Biology. 3: 71-74. DOI: 10.1007/S12042-010-9051-4  0.88
2009 Rapp RA, Udall JA, Wendel JF. Genomic expression dominance in allopolyploids. Bmc Biology. 7: 18. PMID 19409075 DOI: 10.1186/1741-7007-7-18  0.88
2009 Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF. Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium). Genetics. 182: 503-17. PMID 19363125 DOI: 10.1534/Genetics.109.102608  0.88
2008 Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, Wendel JF. Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution & Development. 10: 567-82. PMID 18803775 DOI: 10.1111/J.1525-142X.2008.00272.X  0.88
2008 Hovav R, Chaudhary B, Udall JA, Flagel L, Wendel JF. Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton. Genetics. 179: 1725-33. PMID 18562666 DOI: 10.1534/Genetics.108.089656  0.88
2008 Hovav R, Udall JA, Chaudhary B, Rapp R, Flagel L, Wendel JF. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proceedings of the National Academy of Sciences of the United States of America. 105: 6191-5. PMID 18420816 DOI: 10.1073/Pnas.0711569105  0.88
2008 Flagel L, Udall J, Nettleton D, Wendel J. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. Bmc Biology. 6: 16. PMID 18416842 DOI: 10.1186/1741-7007-6-16  0.88
2008 Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, Hu G, Wendel JF. The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. Plos Genetics. 4: e25. PMID 18248099 DOI: 10.1371/Journal.Pgen.0040025  0.88
2008 Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF. A majority of cotton genes are expressed in single-celled fiber. Planta. 227: 319-29. PMID 17849148 DOI: 10.1007/S00425-007-0619-7  0.88
2007 Udall JA, Flagel LE, Cheung F, Woodward AW, Hovav R, Rapp RA, Swanson JM, Lee JJ, Gingle AR, Nettleton D, Town CD, Chen ZJ, Wendel JF. Spotted cotton oligonucleotide microarrays for gene expression analysis. Bmc Genomics. 8: 81. PMID 17389046 DOI: 10.1186/1471-2164-8-81  0.88
2006 Quijada PA, Udall JA, Lambert B, Osborn TC. Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 113: 549-61. PMID 16767447 DOI: 10.1007/S00122-006-0323-1  0.96
2006 Udall JA, Quijada PA, Lambert B, Osborn TC. Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 113: 597-609. PMID 16767446 DOI: 10.1007/S00122-006-0324-0  0.96
2006 Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics. 173: 1823-7. PMID 16702424 DOI: 10.1534/Genetics.106.058271  0.88
2006 Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, et al. A global assembly of cotton ESTs. Genome Research. 16: 441-50. PMID 16478941 DOI: 10.1101/Gr.4602906  0.88
2006 Zhao J, Udall JA, Quijada PA, Grau CR, Meng J, Osborn TC. Quantitative trait loci for resistance to Sclerotinia sclerotiorum and its association with a homeologous non-reciprocal transposition in Brassica napus L. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 112: 509-16. PMID 16333614 DOI: 10.1007/S00122-005-0154-5  0.96
2006 Udall JA, Wendel JF. Polyploidy and crop improvement Crop Science. 46: S-3-S-14. DOI: 10.2135/Cropsci2006.07.0489Tpg  0.88
2005 Udall JA, Quijada PA, Osborn TC. Detection of chromosomal rearrangements derived from homologous recombination in four mapping populations of Brassica napus L. Genetics. 169: 967-79. PMID 15520255 DOI: 10.1534/Genetics.104.033209  0.96
2004 Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC. Genome redundancy and plasticity within ancient and recent Brassica crop species Biological Journal of the Linnean Society. 82: 665-674. DOI: 10.1111/J.1095-8312.2004.00352.X  0.88
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