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Research Output 2011 2017

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Article
2017
16 Citations (Scopus)

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Zhou, P., Silverstein, K. A. T., Ramaraj, T., Guhlin, J., Denny, R., Liu, J., Farmer, A. D., Steele, K. P., Stupar, R. M., Miller, J. R., Tiffin, P., Mudge, J. & Young, N. D., Mar 27 2017, In : BMC Genomics. 18, 1, 261.

Research output: Contribution to journalArticle

Medicago
Medicago truncatula
Genome
Genes
Nucleotides
16 Citations (Scopus)

Hybrid assembly with long and short reads improves discovery of gene family expansions

Miller, J. R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B. P., Liu, J., Stupar, R. M., Denny, R., Song, L., Singh, N., Maron, L. G., McCouch, S. R., McCombie, W. R., Schatz, M. C., Tiffin, P., Young, N. D. & Silverstein, K. A. T., Jul 19 2017, In : BMC Genomics. 18, 1, 541.

Research output: Contribution to journalArticle

New World Camelids
Genetic Association Studies
Medicago truncatula
Genome
Tandem Repeat Sequences
2 Citations (Scopus)
Databases
Generator
Annotation
Comparative Genomics
Genomics
19 Citations (Scopus)

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

Moll, K. M., Zhou, P., Ramaraj, T., Fajardo, D., Devitt, N. P., Sadowsky, M. J., Stupar, R. M., Tiffin, P. L., Miller, J. R., Young, N. D., Silverstein, K. A. & Mudge, J., Aug 4 2017, In : BMC Genomics. 18, 1, 578.

Research output: Contribution to journalArticle

Medicago truncatula
Fabaceae
Technology
Genome
Plant Genome
2014
74 Citations (Scopus)

Genomic signature of adaptation to climate in Medicago truncatula

Yoder, J. B., Stanton-Geddes, J., Zhou, P., Briskine, R., Young, N. D. & Tiffin, P., Jan 1 2014, In : Genetics. 196, 4, p. 1263-1275 13 p.

Research output: Contribution to journalArticle

Medicago truncatula
Climate
Genome
Haplotypes
Temperature
19 Citations (Scopus)

Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula

Nallu, S., Silverstein, K. A., Zhou, P., Young, N. D. & Vandenbosch, K. A., Jan 1 2014, In : Plant Journal. 78, 4, p. 697-705 9 p.

Research output: Contribution to journalArticle

Medicago truncatula
Cysteine
cysteine
Fabaceae
peptides
2013
72 Citations (Scopus)

Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula

Stanton-Geddes, J., Paape, T., Epstein, B., Briskine, R., Yoder, J., Mudge, J., Bharti, A. K., Farmer, A. D., Zhou, P., Denny, R., May, G. D., Erlandson, S., Yakub, M., Sugawara, M., Sadowsky, M. J., Young, N. D. & Tiffin, P. L., May 31 2013, In : PLoS One. 8, 5, e65688.

Research output: Contribution to journalArticle

Medicago truncatula
agronomic traits
Genome-Wide Association Study
Single Nucleotide Polymorphism
Genes
44 Citations (Scopus)

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

Zhou, P., Silverstein, K. A., Gao, L., Walton, J. D., Nallu, S., Guhlin, J. & Young, N. D., Nov 20 2013, In : BMC bioinformatics. 14, 1, 335.

Research output: Contribution to journalArticle

Peptides
Alignment
Genes
Gene
Genome
39 Citations (Scopus)

Phylogenetic signal variation in the genomes of medicago (Fabaceae)

Yoder, J. B., Briskine, R., Mudge, J., Farmer, A., Paape, T., Steele, K., Weiblen, G. D., Bharti, A. K., Zhou, P., May, G. D., Young, N. D. & Tiffin, P., May 1 2013, In : Systematic Biology. 62, 3, p. 424-438 15 p.

Research output: Contribution to journalArticle

Medicago
Fabaceae
genome
Genome
phylogenetics
30 Citations (Scopus)

Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula

Paape, T., Bataillon, T., Zhou, P., Kono, T., Briskine, R., Young, N. D. & Tiffin, P. L., Jul 1 2013, In : Molecular Ecology. 22, 13, p. 3525-3538 14 p.

Research output: Contribution to journalArticle

Medicago truncatula
Fabaceae
fitness
legumes
genome
2012
43 Citations (Scopus)

Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome

Paape, T., Zhou, P., Branca, A., Briskine, R., Young, N. D. & Tiffin, P. L., Sep 26 2012, In : Genome biology and evolution. 4, 5, p. 726-737 12 p.

Research output: Contribution to journalArticle

Medicago truncatula
Genetic Recombination
recombination
genome
Genome
2011
708 Citations (Scopus)

The Medicago genome provides insight into the evolution of rhizobial symbioses

Young, N. D., Debellé, F., Oldroyd, G. E. D., Geurts, R., Cannon, S. B., Udvardi, M. K., Benedito, V. A., Mayer, K. F. X., Gouzy, J., Schoof, H., Van De Peer, Y., Proost, S., Cook, D. R., Meyers, B. C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S. & 104 others, Mudge, J., Bharti, A. K., Murray, J. D., Naoumkina, M. A., Rosen, B., Silverstein, K. A., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Bergès, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J. J., Dudez, A. M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., González, A. J., Green, P. J., Hallab, A., Hartog, M., Hua, A., Humphray, S. J., Jeong, D. H., Jing, Y., Jöcker, A., Kenton, S. M., Kim, D. J., Klee, K., Lai, H., Lang, C., Lin, S., MacMil, S. L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E. L., Mun, J. H., Najar, F. Z., Nicholson, C., Noirot, C., O'Bleness, M., Paule, C. R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F., Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A. J., Sherrier, D. J., Shi, R., Sims, S., Singer, S. R., Sinharoy, S., Sterck, L., Viollet, A., Wang, B. B., Wang, K., Wang, M., Wang, X., Warfsmann, J., Weissenbach, J., White, D. D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Dénarié, J., Dixon, R. A., May, G. D., Schwartz, D. C., Rogers, J., Quétier, F., Town, C. D. & Roe, B. A., Dec 22 2011, In : Nature. 480, 7378, p. 520-524 5 p.

Research output: Contribution to journalArticle

Medicago truncatula
Medicago
Symbiosis
Fabaceae
Genome
128 Citations (Scopus)

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

Branca, A., Paape, T. D., Zhou, P., Briskine, R., Farmer, A. D., Mudge, J., Bharti, A. K., Woodward, J. E., May, G. D., Gentzbittel, L., Ben, C., Denny, R., Sadowsky, M. J., Ronfort, J., Bataillon, T., Young, N. D. & Tiffin, P. L., Oct 18 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 42, p. E864-E870

Research output: Contribution to journalArticle

Medicago truncatula
Linkage Disequilibrium
Fabaceae
Genetic Recombination
Nucleotides