TY - JOUR AU - Jiao, W. -. B. AU - Schneeberger, K. PY - 2017 DA - 2017// TI - The impact of third generation genomic technologies on plant genome assembly JO - Curr Opin Plant Biol VL - 36 UR - https://doi.org/10.1016/j.pbi.2017.02.002 DO - 10.1016/j.pbi.2017.02.002 ID - Jiao2017 ER - TY - JOUR AU - Bevan, M. W. AU - Uauy, C. AU - Wulff, B. B. H. AU - Zhou, J. AU - Krasileva, K. AU - Clark, M. D. PY - 2017 DA - 2017// TI - Genomic innovation for crop improvement JO - Nature VL - 543 UR - https://doi.org/10.1038/nature22011 DO - 10.1038/nature22011 ID - Bevan2017 ER - TY - JOUR AU - Alonso-Blanco, C. AU - Andrade, J. AU - Becker, C. AU - Bemm, F. AU - Bergelson, J. AU - Borgwardt, K. M. PY - 2016 DA - 2016// TI - 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana JO - Cell VL - 166 UR - https://doi.org/10.1016/j.cell.2016.05.063 DO - 10.1016/j.cell.2016.05.063 ID - Alonso-Blanco2016 ER - TY - STD TI - The 3,000 Rice Genomes Project. The 3,000 rice genomes project. GigaScience. 2014;3(1):7, 2047-217X. ID - ref4 ER - TY - JOUR AU - Zhou, Z. AU - Jiang, Y. AU - Wang, Z. AU - Gou, Z. AU - Lyu, J. AU - Li, W. PY - 2015 DA - 2015// TI - Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3096 DO - 10.1038/nbt.3096 ID - Zhou2015 ER - TY - JOUR AU - Song, Q. AU - Hyten, D. L. AU - Jia, G. AU - Quigley, C. V. AU - Fickus, E. W. AU - Nelson, R. L. PY - 2015 DA - 2015// TI - Fingerprinting soybean germplasm and its utility in genomic research JO - G3 VL - 5 UR - https://doi.org/10.1534/g3.115.019000 DO - 10.1534/g3.115.019000 ID - Song2015 ER - TY - JOUR AU - Lee, Y. -. G. AU - Jeong, N. AU - Kim, J. H. AU - Lee, K. AU - Kim, K. H. AU - Pirani, A. PY - 2015 DA - 2015// TI - Development validation and genetic analysis of a large soybean SNP genotyping array JO - Plant J VL - 81 UR - https://doi.org/10.1111/tpj.12755 DO - 10.1111/tpj.12755 ID - Lee2015 ER - TY - STD TI - Henry VJ, Bandrowski AE, Pepin A-S, Gonzalez BJ, Desfeux A. OMICtools: an informative directory for multi-omic data analysis. Database. Oxford University Press (OUP); 2014;2014:bau069. ID - ref8 ER - TY - JOUR AU - Massart, S. AU - Candresse, T. AU - Gil, J. AU - Lacomme, C. AU - Predajna, L. AU - Ravnikar, M. PY - 2017 DA - 2017// TI - A framework for the evaluation of biosecurity commercial, regulatory, and scientific impacts of plant viruses and Viroids identified by NGS technologies JO - Front Microbiol. VL - 8 UR - https://doi.org/10.3389/fmicb.2017.00045 DO - 10.3389/fmicb.2017.00045 ID - Massart2017 ER - TY - JOUR AU - Leekitcharoenphon, P. AU - Kaas, R. S. AU - Thomsen, M. C. AU - Friis, C. AU - Rasmussen, S. AU - Aarestrup, F. M. PY - 2012 DA - 2012// TI - snpTree - a web-server to identify and construct SNP trees from whole genome sequence data JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-S7-S6 DO - 10.1186/1471-2164-13-S7-S6 ID - Leekitcharoenphon2012 ER - TY - JOUR AU - Marburger, D. A. AU - Smith, D. L. AU - Conley, S. P. PY - 2016 DA - 2016// TI - Revisiting planting date and cultivar effects on soybean sudden death syndrome development and yield loss JO - Plant Dis VL - 100 UR - https://doi.org/10.1094/PDIS-12-15-1411-RE DO - 10.1094/PDIS-12-15-1411-RE ID - Marburger2016 ER - TY - JOUR AU - Rincker, K. AU - Cary, T. AU - Diers, B. W. PY - 2017 DA - 2017// TI - Impact of soybean cyst nematode resistance on soybean yield JO - Crop Sci VL - 57 UR - https://doi.org/10.2135/cropsci2016.07.0628 DO - 10.2135/cropsci2016.07.0628 ID - Rincker2017 ER - TY - STD TI - Sohn H-B, Kim S-J, Hwang T-Y, Park H-M, Lee Y-Y, Markkandan K, et al. Barcode system for genetic identification of soybean [Glycine max (L.) Merrill] cultivars using InDel markers specific to dense variation blocks. Front Plant Sci. 2017;8:520. ID - ref13 ER - TY - STD TI - Cook DE, Andersen EC. VCF-kit: assorted utilities for the variant call format. Bioinformatics. 2017;33(10):1581–2. ID - ref14 ER - TY - JOUR AU - Crossa, J. AU - Pérez-Rodríguez, P. AU - Cuevas, J. AU - Montesinos-López, O. AU - Jarquín, D. AU - los, C. G. PY - 2017 DA - 2017// TI - Genomic selection in plant breeding: methods models, and perspectives JO - Trends Plant Sci VL - 22 UR - https://doi.org/10.1016/j.tplants.2017.08.011 DO - 10.1016/j.tplants.2017.08.011 ID - Crossa2017 ER - TY - JOUR AU - Lee, G. -. A. AU - Crawford, G. W. AU - Liu, L. AU - Sasaki, Y. AU - Chen, X. PY - 2011 DA - 2011// TI - Archaeological soybean (Glycine max) in East Asia: does size matter?. Newsom LA, editor JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0026720 DO - 10.1371/journal.pone.0026720 ID - Lee2011 ER - TY - JOUR AU - Pedregosa, F. AU - Varoquaux, G. AU - Gramfort, A. AU - Michel, V. AU - Thirion, B. AU - Grisel, O. PY - 2011 DA - 2011// TI - Scikit-learn: machine learning in Python JO - J Mach Learn Res VL - 12 ID - Pedregosa2011 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Li, H. PY - 2011 DA - 2011// TI - A statistical framework for SNP calling mutation discovery, association mapping and population genetical parameter estimation from sequencing data JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr509 DO - 10.1093/bioinformatics/btr509 ID - Li2011 ER - TY - JOUR AU - Tarasov, A. AU - Vilella, A. J. AU - Cuppen, E. AU - Nijman, I. J. AU - Prins, P. PY - 2015 DA - 2015// TI - Sambamba: fast processing of NGS alignment formats JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv098 DO - 10.1093/bioinformatics/btv098 ID - Tarasov2015 ER - TY - JOUR AU - Oliphant, T. E. PY - 2007 DA - 2007// TI - Python for scientific computing JO - Comput Sci Eng VL - 9 UR - https://doi.org/10.1109/MCSE.2007.58 DO - 10.1109/MCSE.2007.58 ID - Oliphant2007 ER - TY - JOUR AU - Matplotlib, H. J. D. PY - 2007 DA - 2007// TI - A 2D graphics environment JO - Comput Sci Eng VL - 9 ID - Matplotlib2007 ER - TY - STD TI - Fang C, Ma Y, Wu S, Liu Z, Wang Z, Yang R, et al. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biol. 2017;18:161. ID - ref23 ER - TY - JOUR AU - Lee, C. AU - Choi, M. -. S. AU - Kim, H. -. T. AU - Yun, H. -. T. AU - Lee, B. AU - Chung, Y. -. S. PY - 2015 DA - 2015// TI - Soybean [Glycine max (L.) Merrill]: importance as a crop and pedigree reconstruction of Korean varieties JO - Plant Breed Biotechnol VL - 3 UR - https://doi.org/10.9787/PBB.2015.3.3.179 DO - 10.9787/PBB.2015.3.3.179 ID - Lee2015 ER - TY - JOUR AU - Torkamaneh, D. AU - Belzile, F. PY - 2015 DA - 2015// TI - Scanning and filling: ultra-dense SNP genotyping combining genotyping-by-sequencing SNP Array and whole-genome resequencing data JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0131533 DO - 10.1371/journal.pone.0131533 ID - Torkamaneh2015 ER -