Journal Publications
Embargoed
- Schnable et al.
- Swanson-Wagner et al.
Coming soon
Chou HH, A Trisiriroj, S Park, YC Hsin, PC Ronald, PS Schnable (2009) Direct calibration of PICKY-designed microarrays. BMC Bioinformatics, in press.
Liu S, CR Dietrich, PS Schnable (2009) DLA-based strategies for cloning insertion mutants: cloning the gl4 locus of maize using Mu transposon tagged alleles. Genetics, in press.
Liu S, CT Yeh, T Ji, K Ying, H Wu, HM Tang, Y Fu, DS Nettleton, PS Schnable (2009) Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic markers for open chromatin across the maize genome. PLoS Genetics, in press.
Wei F, J Zhang, S Zhou, R He, ML Schaeffer, K Collura, D Kudrna, BP Faga, M Wissotski, W Golser, SM Rock, TA Graves, RS Fulton, E Coe, PS Schnable, DC Schwartz, D Ware, SW Clifton, RK Wilson, RA Wing (2009) The physical and genetic framework of the maize B73 genome. PLoS Genetics, in press.
Springer NM, K Ying, Y Fu, T Ji, CT Yeh, Y Jia, W Wu, T Richmond, J Kitzman, H Rosenbaum, AL Iniguez, WB Barbazuk, JA Jeddeloh, DS Nettleton, PS Schnable (2009) Maize inbreds exhibit high levels of CNV and presence/absence differences in genome content. PLoS Genetics, in press.
Wei F, JC Stein, C Liang, J Zhang, RS Fulton, RS Baucom, E De Paoli, S Zhou, L Yang, Y Han, S Pasternak, A Narechania, L Zhang, CT Yeh, K Ying, DH Nagel, K Collura, D Kudrna, J Currie, J Lin, H Kim, A Angelova, G Scara, M Wissotski, W Golser, L Courtney, SS Kruchowski, TA Graves, SM Rock, S Adams, L Fulton, C Fronick, W Courtney, M Kramer, L Spiegel, L Nascimento, A Kalyanaraman, C Chaparro, J Deragon, P SanMiguel, N Jiang, SR Wessler, PJ Green, C Soderlund, Y Yu, DC Schwartz, BC Meyers, JL Bennetzen, RA Martienssen, WR McCombie, « view remaining 6 authors » (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics, in press.
Jia Y, DR Lisch, K Ohtsu, MJ Scanlon, DS Nettleton, PS Schnable (2009) Loss of RNA-dependent RNA Polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes and 24-nt small RNAs. PLoS Genetics, in press.
Buggs RJ, S Chamala, W Wu, L Gao, GD May, PS Schnable, DE Soltis, PS Soltis, WB Barbazuk (2009) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX genotyping. Molecular Ecology, in press.
Soltis DE, RJ Buggs, WB Barbazuk, PS Schnable, PS Soltis (2009) On the origins of species: does evolution repeat itself in polyploid populations of independent origin?. Cold Spring Harbor Symposia on Quantitative Biology, in press.
2009
Brooks III L, J Strable, X Zhang, K Ohtsu, R Zhou, A Sarkar, S Hargreaves, RJ Elshire, D Eudy, T Pawlowska, D Ware, D Janick-Buckner, B Buckner, MC Timmermans, PS Schnable, DS Nettleton, MJ Scanlon (2009) Microdissection of shoot meristem functional domains. PLoS Genetics, 5(5): e1000476. (Epub: 2009 May 5)
Wei Y, M Lin, DJ Oliver, PS Schnable (2009) The Roles of aldehyde dehydrogenases (ALDHs) in the PDH Bypass of Arabidopsis. BMC Biochemistry, 10(7).
Nogueira FT, DH Chitwood, S Madi, K Ohtsu, PS Schnable, MJ Scanlon, MC Timmermans (2009) Regulation of small RNA accumulation in the maize shoot apex. PLoS Genetics, 5(1): e1000320.
Jackson BG, PS Schnable, S Aluru (2009) Parallel short sequence assembly of transcriptomes. BMC Bioinformatics, 10(Suppl 1): S14.
Shimizu R, J Ji, E Kelsey, K Ohtsu, PS Schnable, MJ Scanlon (2009) Tissue Specificity and Evolution of Meristematic WOX3 Function. Plant Physiology, 149(2): 841-850.
2008
Jung KH, C Dardick, LE Bartley, P Cao, J Phetsom, P Canlas, YS Seo, M Shultz, S Ouyang, Q Yuan, BC Frank, E Ly, L Zheng, Y Jia, AP Hsia, K An, HH Chou, D Roche, GC Lee, PS Schnable, G An, CR Buell, PC Ronald (2008) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. Plos One, 3(10).
Strable J, L Borsuk, DS Nettleton, PS Schnable, EE Irish (2008) Microarray analysis of vegetative phase change in maize. Plant Journal, 56(6): 1045-1057.
Skibbe DS, X Wang, LA Boursuk, DA Ashlock, DS Nettleton, PS Schnable (2008) Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. occurs via programmed cell death. Journal of Genetics and Genomics, 35(10): 603-616.
Buckner B, KA Swaggart, CC Wong, HA Smith, KM Aurand, MJ Scanlon, PS Schnable, D Janick-Buckner (2008) Expression and nucleotide diversity of the maize RIK gene. J Heredity, 99(4): 407-416. (Epub: 2008 Feb 28)
Hochholdinger F, TJ Wen, R Zimmermann, P Chimit-Marolle, O da Costa e Silva, W Bruce, KR Lamkey, U Wienand, PS Schnable (2008) The maize (Zea mays L.) roothairless3 gene encodes a putative GPI-anchored, monocot-specific, COBRA-like protein that significantly affects grain yield. Plant Journal, 54(5): 888-898.
Li J, TJ Wen, PS Schnable (2008) The role of RAD51 in the repair of MuDR-induced Double-Strand Breaks in Maize (Zea mays L.). Genetics, 178: 57-66.
Jackson BN, S Aluru, PS Schnable (2008) Consensus genetic maps as median orders from inconsistent sources. ACM/IEEE Transactions Computational Biology and Bioinformatics, 5(2): 161-171.
2007
Dembinsky D, K Woll, M Saleem, Y Liu, Y Fu, LA Borsuk, T Lamkemeyer, C Fladerer, J Madlung, B Barbazuk, A Nordheim, DS Nettleton, PS Schnable, F Hochholdinger (2007) Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiology, 145: 575-588.
Kalyanaraman A, SJ Emrich, PS Schnable, S Aluru (2007) Assembling genomes on large-scale parallel computers. Journal of Parallel and Distributed Computing, 67: 1240-1255.
Zhang X, S Medi, LA Borsuk, DS Nettleton, B Buckner, D Janick-Buckner, J Beck, M Timmermans, PS Schnable, MJ Scanlon (2007) Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. PLoS Genetics, 3(6): 1040-1052.
Li J, LC Harper, I Golubovskaya, CR Wang, D Weber, RB Meeley, J McElverd, B Bowen, WZ Cande, PS Schnable (2007) Functional analysis of maize RAD51 in meiosis and double-strand break repair. Genetics, 176(3): 1469-1482. (selected by editors as an "Issue Highlight")
Barbazuk WB, SJ Emrich, HD Chen, L Li, PS Schnable (2007) SNP discovery via 454 transcriptome sequencing. Plant Journal, 51(5): 910-918.
Ohtsu K, MB Smith, SJ Emrich, LA Borsuk, R Zhou, T Chen, X Zhang, M Timmermans, J Beck, B Buckner, D Janick-Buckner, DS Nettleton, MJ Scanlon, PS Schnable (2007) Global gene expression analysis of the shoot apical meristem of maize (Zea Mays L.). Plant Journal, 52(3): 391-404. (Selected as one of the papers by Faculty 1000 in 2008)
Buckner B, J Beck, KF Browning, AE Fritz, E Hoxha, LD Grantham, ZN Kamvar, AN Lough, O Nikolova, PS Schnable, MJ Scanlon, D Janick-Buckner (2007) Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database. Genetics, 176(2): 741-747.
Li J, AP Hsia, PS Schnable (2007) Recent advances in plant recombination. Current Opinion in Plant Biology, 10(2): 131-135. (Epub: 2007 Feb 8)
Travers SE, MD Smith, J Bai, SH Hulbert, JE Leach, PS Schnable, AK Knapp, GA Milliken, PA Fay, A Saleh, KA Garrett (2007) Ecological genomics: making the leap from model systems in the lab to native populations in the field. Front Ecol Environ, 5(1): 19-24.
Emrich SJ, L Li, TJ Wen, MD Yandeau-Nelson, Y Fu, L Guo, HH Chou, S Aluru, DA Ashlock, PS Schnable (2007) Nearly identical paralogs (NIPs) and implications for maize genome evolution. Genetics, 175(1): 429-439. (Epub: 2006 Nov 16) (Selected as an Editors' Choice by Science magazine (19 Jan 2007) and MaizeGDB (Dec 2006))
Emrich SJ, WB Barbazuk, L Li, PS Schnable (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research, 17(1): 69-73. (Epub: 2006 Nov 9)
Ohtsu K, H Takahashi, PS Schnable, M Nakazono (2007) Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. Plant & Cell Physiology, 48(1): 3-7. (Epub: 2006 Dec 5)
2006
Fu Y, TJ Wen, YI Ronin, HD Chen, L Guo, DI Mester, Y Yang, M Lee, AB Korol, DA Ashlock, PS Schnable (2006) Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics, 174(3): 1671-1683. (Epub: 2006 Sep 1)
Yandeau-Nelson MD, BJ Nikolau, PS Schnable (2006) Effects of trans-acting genetic modifiers on the rates and distribution of meiotic recombination across the a1-sh2 interval of maize. Genetics, 174(1): 101-112. (Epub: 2006 Jul 2. Selected as one of the papers by Faculty 1000 in 2008)
Yandeau-Nelson MD, YJ Xia, J Li, MG Neuffer, PS Schnable (2006) Unequal sister chromatid and homolog recombination at a tandem duplication of the a1 locus in maize. Genetics, 173(4): 2211-2226. (Epub: 2006 Jun 4)
Skibbe DS, X Wang, X Zhao, LA Borsuk, DS Nettleton, PS Schnable (2006) Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes. Bioinformatics, 22(15): 1863-1870. (Epub: 2006 May 26)
Swanson-Wagner R, Y Jia, R DeCook, LA Borsuk, DS Nettleton, PS Schnable (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proceedings National Academy Science, 103(18): 6805-6810. (Epub: 2006 Apr 25. Selected as one of the papers by Faculty 1000 in 2008)
Maher PM, HH Chou, E Hahn, TJ Wen, PS Schnable (2006) GRAMA: A genetic mapping tool for the analysis of temperature gradient capillary electrophoresis (TGCE) data. Theoretical Applied Genetics, 113(1): 156-162. (Epub: 2006 Apr 20)
2005
Skibbe DS, PS Schnable (2005) Male sterility in maize. Maydica, 50: 367-376.
Hochholdinger F, K Woll, L Guo, PS Schnable (2005) The accumulation of abundant soluble proteins changes early in the development of the primary roots of maize (Zea mays L.). Proteomics, 5(18): 4885-4893. (an image from this manuscript was selected for inclusion on the cover)
Yao H, PS Schnable (2005) Cis-effects on meiotic recombination across distinct a1-sh2 intervals in a common Zea genetic background. Genetics, 170(4): 1929-1944.
Woll K, LA Borsuk, H Stransky, DS Nettleton, PS Schnable, F Hochholdinger (2005) Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize (Zea Mays L.) lateral and seminal root initiation mutant rum1. Plant Physiology, 139(3): 1255-1267.
Fu Y, SJ Emrich, L Guo, TJ Wen, S Aluru, DA Ashlock, PS Schnable (2005) Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proceedings National Academy Science, 102(34): 12282-12287.
Wen TJ, F Hochholdinger, M Sauer, W Bruce, PS Schnable (2005) The roothairless1 gene of maize (Zea mays) encodes a homolog of sec3, which is involved in polar exocytosis. Plant Physiology, 138(3): 1637-1643.
Dietrich CR, MA Perera, MD Yandeau-Nelson, RB Meeley, BJ Nikolau, PS Schnable (2005) Characterization of two gl8 paralogs reveals that the 3-ketoacyl reductase component of fatty acid elongase is essential for maize (Zea mays L.) development. Plant Journal, 42(6): 844-861.
Ding J, K Viswanathan, D Berleant, E Wurtele, D Ashlock, J Dickerson, A Fulmer, PS Schnable (2005) PathBinderH: a tool for sentence-focused, plant taxonomy-sensitive access to the biological literature. Bioinformatics, 21(10): 2560-2562.
Hsia AP, TJ Wen, HD Chen, Z Liu, MD Yandeau, Y Wei, L Guo, PS Schnable (2005) Temperature Gradient Capillary Electrophoresis (TGCE) - A tool for the high throughput discovery and mapping of SNPs and IDPs. Theoretical Applied Genetics, 111(2): 218-225.
Yao H, L Guo, Y Fu, LA Borsuk, TJ Wen, DS Skibbe, XQ Cui, BE Scheffler, J Cao, SJ Emrich, DA Ashlock, PS Schnable (2005) Evaluation of seven ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biology, 57(3): 445-460.
Yandeau-Nelson MD, Q Zhou, H Yao, X Xu, BJ Nikolau, PS Schnable (2005) MuDR transposase increases the frequency of meiotic crossovers in the vicinity of a Mu insertion in the maize a1 gene. Genetics, 169(2): 917-929.