{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T13:52:57Z","timestamp":1770990777586,"version":"3.50.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S13","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2016,10]]},"DOI":"10.1186\/s12859-016-1227-y","type":"journal-article","created":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T13:12:17Z","timestamp":1475759537000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["PGen: large-scale genomic variations analysis workflow and browser in SoyKB"],"prefix":"10.1186","volume":"17","author":[{"given":"Yang","family":"Liu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saad M.","family":"Khan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juexin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mats","family":"Rynge","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanxun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuai","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiyuan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joao V.","family":"Maldonado dos Santos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Babu","family":"Valliyodan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prasad P.","family":"Calyam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nirav","family":"Merchant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry T.","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dong","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trupti","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,10,6]]},"reference":[{"issue":"4","key":"1227_CR1","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/nbt.3096","volume":"33","author":"Z Zhou","year":"2015","unstructured":"Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, Fang C, Shen Y, Liu T, Li C, Li Q, Wu M, Wang M, Wu Y, Dong Y, Wan W, Wang X, Ding Z, Gao Y, Xiang H, Zhu B, Lee SH, Wang W, Tian Z. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol. 2015;33(4):408\u201314.","journal-title":"Nat Biotechnol"},{"issue":"4","key":"1227_CR2","doi-asserted-by":"crossref","first-page":"e0124617","DOI":"10.1371\/journal.pone.0124617","volume":"10","author":"J Duitama","year":"2015","unstructured":"Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheer B, Farmer A, Torres E, Oard J, Tohme J. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One. 2015;10(4):e0124617.","journal-title":"PLoS One"},{"key":"1227_CR3","doi-asserted-by":"crossref","first-page":"23598","DOI":"10.1038\/srep23598","volume":"6","author":"B Valliyodan","year":"2016","unstructured":"Valliyodan B, Qiu D, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, Nguyen HT. Landscape of genomic diversity and trait discovery in soybean. Sci Rep. 2016;6:23598.","journal-title":"Sci Rep"},{"issue":"14","key":"1227_CR4","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with burrows wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"9","key":"1227_CR5","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: a MapReduce framework for analyzing next-generation dna sequencing data. Genome Res. 2010;20(9):1297\u2013303.","journal-title":"Genome Res"},{"issue":"3","key":"1227_CR6","first-page":"219","volume":"13","author":"E Deelman","year":"2005","unstructured":"Deelman E, Singh G, Su MH, Blythe J, Gil Y, Kesselman C, Mehta G, Vahi K, Berriman GB, Good J, Laity A. Pegasus: A framework for mapping complex scientific workflows onto distributed systems. Sci Program. 2005;13(3):219\u201337.","journal-title":"Sci Program"},{"key":"1227_CR7","doi-asserted-by":"crossref","unstructured":"Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Res. 2013. 905.","DOI":"10.1109\/BIBM.2013.6732755"},{"issue":"1","key":"1227_CR8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-13-199","volume":"13","author":"T Joshi","year":"2012","unstructured":"Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D. Soybean knowledge base (SoyKB): a web resource for soybean translational genomics. BMC Genomics. 2012;13(1):1.","journal-title":"BMC Genomics"},{"issue":"7278","key":"1227_CR9","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature08670","volume":"463","author":"J Schmutz","year":"2010","unstructured":"Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindguist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178\u201383.","journal-title":"Nature"},{"issue":"D1","key":"1227_CR10","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1093\/nar\/gkr944","volume":"40","author":"DM Goodstein","year":"2012","unstructured":"Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):1178\u201386.","journal-title":"Nucleic Acids Res"},{"key":"1227_CR11","unstructured":"Andrews S. Fastqc: A quality control tool for high throughput sequence data. Reference Source. 2010."},{"key":"1227_CR12","unstructured":"Picard tools. [ http:\/\/broadinstitute.github.io\/picard\/ ]."},{"key":"1227_CR13","first-page":"34","volume":"2","author":"SA Goff","year":"2011","unstructured":"Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, et al. The iplant collaborative: cyberinfrastructure for plant biology. Frontiers in plant science. 2011;2:34.","journal-title":"Frontiers in plant science"},{"issue":"2","key":"1227_CR14","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80\u201392.","journal-title":"Fly"},{"issue":"9","key":"1227_CR15","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1093\/nar\/gks003","volume":"40","author":"G Klambauer","year":"2012","unstructured":"Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, Hochreiter S. cn.MOPS: mixture of poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res. 2012;40(9):e69.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1227_CR16","doi-asserted-by":"crossref","first-page":"94150","DOI":"10.1371\/journal.pone.0094150","volume":"9","author":"T Langewisch","year":"2014","unstructured":"Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K. Major soybean maturity gene haplotypes revealed by Snpviz analysis of 72 sequenced soybean genomes. PLoS One. 2014;9(4):94150.","journal-title":"PLoS One"},{"issue":"5","key":"1227_CR17","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1109\/MCSE.2014.80","volume":"16","author":"J Towns","year":"2014","unstructured":"Towns J, Cockerill T, Dahan M, Foster I, Gaither K, Grimshaw A, Hazlewood V, Lathrop S, Lifka D, Peterson GD, Roskies R, Scott J, Willkins-Diehr N. XSEDE: accelerating scientific discovery. Computing in Science & Engineering. 2014;16(5):62\u201374.","journal-title":"Computing in Science & Engineering"},{"key":"1227_CR18","unstructured":"Texas advanced computing center (TACC). [ http:\/\/www.tacc.utexas.edu ]."},{"key":"1227_CR19","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.pmcj.2015.09.004","volume":"28","author":"P Calyam","year":"2015","unstructured":"Calyam P, Mishra A, Antequera RB, Chemodanov D, Berryman A, Zhu K, Abbott C, Skubic M. Synchronous big data analytics for personalized and remote physical therapy. Pervasive and Mobile Computing. 2015;28:3\u201320.","journal-title":"Pervasive and Mobile Computing"},{"issue":"1","key":"1227_CR20","doi-asserted-by":"crossref","first-page":"54985","DOI":"10.1371\/journal.pone.0054985","volume":"8","author":"Q Song","year":"2013","unstructured":"Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB. Development and evaluation of soysnp50k, a high-density genotyping array for soybean. PLoS One. 2013;8(1):54985.","journal-title":"PLoS One"},{"issue":"1","key":"1227_CR21","first-page":"1","volume":"6","author":"J Wang","year":"2015","unstructured":"Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen HT, Zhang J, Xu D. A bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. BMC Genomics. 2015;6(1):1.","journal-title":"BMC Genomics"},{"issue":"1","key":"1227_CR22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-016-2431-x","volume":"17","author":"JV Maldonado Dos Santos","year":"2016","unstructured":"Maldonado Dos Santos JV, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J, Vuong TD, de Oliveira MF, Marcelino-Guimar\u00e3es FC, Xu D, Nguyen HT. Evaluation of genetic variation among brazilian soybean cultivars through genome resequencing. BMC Genomics. 2016;17(1):1.","journal-title":"BMC Genomics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1227-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,14]],"date-time":"2019-09-14T09:37:29Z","timestamp":1568453849000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1227-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10]]},"references-count":22,"journal-issue":{"issue":"S13","published-print":{"date-parts":[[2016,10]]}},"alternative-id":["1227"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1227-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,10]]},"article-number":"337"}}