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Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.
Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Muñoz-Amatriaín M, et al. Plant J. 2015 Oct;84(1):216-27. doi: 10.1111/tpj.12959. Epub 2015 Sep 21. Plant J. 2015. PMID: 26252423 Free PMC article.
Combinatorial pooling enables selective sequencing of the barley gene space.
Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Bhat PR, Wu Y, Ciardo G, Alsaihati B, Ma Y, Wanamaker S, Resnik J, Bozdag S, Luo MC, Close TJ. Lonardi S, et al. PLoS Comput Biol. 2013 Apr;9(4):e1003010. doi: 10.1371/journal.pcbi.1003010. Epub 2013 Apr 4. PLoS Comput Biol. 2013. PMID: 23592960 Free PMC article.
Development and implementation of high-throughput SNP genotyping in barley.
Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R. Close TJ, et al. BMC Genomics. 2009 Dec 4;10:582. doi: 10.1186/1471-2164-10-582. BMC Genomics. 2009. PMID: 19961604 Free PMC article.
Accurate construction of consensus genetic maps via integer linear programming.
Wu Y, Close TJ, Lonardi S. Wu Y, et al. IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):381-94. doi: 10.1109/TCBB.2010.35. IEEE/ACM Trans Comput Biol Bioinform. 2011. PMID: 20479505
On the accurate construction of consensus genetic maps.
Wu Y, Close TJ, Lonardi S. Wu Y, et al. Comput Syst Bioinformatics Conf. 2008;7:285-96. Comput Syst Bioinformatics Conf. 2008. PMID: 19642288
A linear-time algorithm for predicting functional annotations from PPI networks.
Wu Y, Lonardi S. Wu Y, et al. J Bioinform Comput Biol. 2008 Dec;6(6):1049-65. doi: 10.1142/s0219720008003916. J Bioinform Comput Biol. 2008. PMID: 19090017
Deconvoluting BAC-gene relationships using a physical map.
Wu Y, Liu L, Close TJ, Lonardi S. Wu Y, et al. J Bioinform Comput Biol. 2008 Jun;6(3):603-22. doi: 10.1142/s0219720008003564. J Bioinform Comput Biol. 2008. PMID: 18574865
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