(†Corresponding author; *Co-first author)

 

Punna Ramu†, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu†. (2017). Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. doi: 10.1038/ng.3845

 

Punna Ramu†, Williams Esuma, Robert Kawuki, Ismail Y Rabbi, Chiedozie Egesi, Jessen V Bredeson, Rebecca S Bart, Janu Verma, Edward S Buckler, Fei Lu†. (2016). Cassava HapMap: Managing genetic load in a clonal crop species. bioRxiv. doi: http://dx.doi.org/10.1101/077123

 

Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Shem-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan Springer, Edward Buckler, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler, Kevin L. Childs, Mark Mikel. (2016). Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. The Plant Cell. doi:10.1105/tpc.16.00353

 

Williams Esuma, Liezel Herselman, Maryke Tine Labuschagne, Punna Ramu, Fei Lu, Yona Baguma, Edward S. Buckler, Robert Sezi Kawuki. (2016). Genome-wide association mapping of provitamin A carotenoid content in cassava. Euphytica. DOI: 10.1007/s10681-016-1772-5

 

Li, Y.-x., Li, C., Bradbury, P. J., Liu, X., Lu, F., Romay, M. C., Glaubitz, J. C., Wu, X., Peng, B., Shi, Y., Song, Y., Zhang, D., Buckler, E. S., Zhang, Z., Li, Y. and Wang, T. (2016), Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant J. doi:10.1111/tpj.13174

 

Fei Lu†, Maria C Romay, Jeff C Glaubitz, Peter J Bradbury, Rob J Elshire, Tianyu Wang, Yu Li, Yongxiang Li, Kassa Semagn, Xuecai Zhang, Alvaro G. Hernandez, Mark A. Mikel, Ilya Soifer, Omer Barad, Edward S Buckler†. (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications. DOI:10.1038/ncomms7914

 

Guillaume P. Ramstein, Alexander E. Lipka, Fei Lu, Denise E. Costich, Jerome H. Cherney, Edward S. Buckler and Michael D. Casler. (2015) Genome-Wide Association Study Based on Multiple Imputation with Low-Depth Sequencing Data: Application to Biofuel Traits in Reed Canarygrass. G3: Genes | Genomes | Genetics. DOI: 10.1534/g3.115.017533

 

Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES. (2014) TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PLoS ONE 9(2): e90346.

 

Lipka AE, Lu F, Cherney JH, Buckler ES, Casler MD, and Costich DE (2014). “Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selecting approaches”. PLoS ONE 9(11), e112227.

 

Lu F, Lipka AE, Elshire RJ, Glaubitz JC, Cherney JH, Casler MD, Buckler ES, Costich DE. (2013) Switchgrass genomic diversity, ploidy and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics 9(1):e1003215.

 

Abhijit Sanyal*, Ammiraju S.S.Jetty*, Fei Lu*, Yeisoo Yu Teri Rambo, Jennifer Currie, Kristi Kollura, Hye-Ran Kim, Jinfeng Chen, Jianxin Ma, Phillip San Miguel, Mingsheng Chen, Rod A. Wing and Scott A. Jackson. (2010). Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in sorghum. MOL BIOL EVOL. DOI:10.1093/molbev/msq133

 

Jetty S.S. Ammiraju, Chuanzhu Fan, Yeisoo Yu, Xiang Song, Karen A. Cranston, Ana Clara Pontaroli, Fei Lu, Abhijit Sanyal, Ning Jiang, Teri Rambo, Jennifer Currie, Kristi Collura, Jayson Talag, Jeffrey L. Bennetzen, Mingsheng Chen, Scott Jackson, Rod A. Wing. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. The Plant Journal. DOI: 10.1111/j.1365-313X.2010.04251.x

 

Lu, F. *, Ammiraju, J. S. *, Sanyal, A. *, Zhang, S. *, Song, R., Chen, J. *, Li, G., Sui, Y., Song, X., Cheng, Z., de Oliveira, A. C., Bennetzen, J. L.,Jackson, S., Wing, R. A., and Chen, M. (2009). Comparative sequence analysis of the MONOCULM1 orthologous regions in fourteen Oryza genomes. Proc Natl Acad Sci USA. 106(6):2071-6.

 

Ammiraju, J. S. *, Lu, F *., Sanyal, A. *, Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Chen, J., Bennetzen, J. L., Chen, M., Jackson, S., and Wing, R. A. (2008). Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set. The Plant Cell 10.1105/tpc.1108.063727

 

Lukas A. Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyce van Eck, Robert Buels, Adri A. Mills, Naama Menda, Isaak Y. Tecle, Aureliano Bombarely, Stephen Stack, Suzanne M. Royer, Song-Bin Chang, Lindsay A. Shearer, Byung Dong Kim, Sung-Hwan Jo, Cheol-Goo Hur, Doil Choi, Chang-Bao Li, Jiuhai Zhao, Hongling Jiang, Yu Geng, Yuanyuan Dai, Huajie Fan, Jinfeng Chen, Fei Lu, et al. (2009). A Snapshot of the Emerging Tomato Genome Sequence. The Plant Genome. 10.3835/plantgenome2008.08.0005: 78-92

 

Li C-B, Zhao JH, Jiang HL, Geng Y, Dai YY, Fan HJ,  Zhang DF, Chen JF, Lu F, Shi JF, Sun SH, Chen JJ, Yan XH, Lu C, Chen MS, Cheng ZK, Ling HQ, Wang Y, Xue YB, Li C. (2008). A snapshot of the Chinese SOL Project. Journal of Genomics and Genetics. 35: 387-390

 

Chen JF, Lu F, Chen SS, Tao SH. Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region. Genome (2006) 49:413–419.

 

Super-fast variant caller for whole genome shotgun (WGS) sequencing data. It works for diploid species, including both inbreds and outcrossers.

 

Fei Lu, Jeff Glaubitz, Terry Casstevens, Qi Sun, Robert Bukowski, Katie Hyma, Ed Buckler. TASSEL 5.0 Pan-genome Atlas (PanA) pipeline. (2014).

PanA combines genetic mapping and machine learning to produces millions of genetic anchor for the genome of a species.

 

Fei Lu, Jeff Glaubitz, James Harriman, Terry Casstevens, Rob Elshire. TASSEL 3.0 Universal Network Enabled Analysis Kit (UNEAK) pipeline. (2012).

A reference genome free SNP calling pipeline.