Journal Publications

The lab's most recent journal articles are listed below in reverse chronological order. Some articles are available for download.

2001-2007

Kalyanaraman A, SJ Emrich, PS Schnable, S Aluru (2007) Assembling genomes on large-scale parallel computers. Journal of Parallel and Distributed Computing, in press.

Jackson BN, S Aluru, PS Schnable (2007) Consensus genetic maps as median orders from inconsistent sources. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.

Zhang X, S Medi, L Borsuk, DS Nettleton, B Buckner, D Janick-Buckner, J Beck, M Timmermans, PS Schnable and MJ Scanlon (2007) Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem. PLoS Genetics 3(6): e101, in press.

Li J, LC Harper, I Golubovskaya, CR Wang, DF Weber, RB Meeley, J McElverd, B Bowen, WZ Cande, PS Schnable (2007) Functional analysis of maize RAD51 in meiosis and DSBs repair. Genetics, 176(3):1469-1482, in press. (selected by editors as an "Issue Highlight")

Barbazuk WB, SJ Emrich, HD Chen, PS Schnable (2007) SNP discovery via 454 transcriptome sequencing. Plant Journal, in press.

Ohtsu K, M Smith, SJ Emrich, LA Borsuk, R Zhou, T Chen, X Zhang, M Timmermans, J Beck, B Buckner, D Janick-Buckner, D Nettleton, MJ Scanlon, PS Schnable (2007) Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant Journal, in press.

Buckner B, J Beck, KF Browning, AE Fritz, E Hoxha, LD Grantham, ZN Kamvar, AN Lough, O Nikolova, PS Schnable, MJ Scanlon, and 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. [Full Text PDF]

Li J, Hsia AP, PS Schnable (2007) Recent advances in plant recombination. Current Opinion in Plant Biology, 10(2): 131-135. [Epub ahead of print]. [Full Text PDF]

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, 5:19-24. [Full Text PDF]

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, 175:429-439. (Epub: 2006 Nov 16) Selected as an Editors' Choice by Science magazine (19 Jan 2007) and MaizeGDB (Dec 2006). [Full Text PDF]

Emrich SJ, WB Barbazuk, L Li, PS Schnable (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research, 17:69-73. (Epub: 2006 Nov 9). [Full Text PDF]

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). [Full Text PDF]

Fu Y, T-J 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, 174:1671-1683. (Epub: 2006 Sep 1). [Full Text PDF]

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, 174:101-112. (Epub: 2006 Jul 2). [Full Text PDF]

Yandeau-Nelson MD, Y Xia, J Li, MG Beuffer, PS Schnable (2006) Unequal sister chromatid and homolog recombination at a tandem duplication of the a1 locus in maize. Genetics, 173:2211-2226. (Epub: 2006 Jun 4). [Full Text PDF]

Skibbe D, X Wang, X Zhao, LA Borsuk, D Nettleton, PS Schnable (2006) Scanning cDNA microarrays at multiple intensities increases the number of statistically significant differences detected. Bioinformatics, 22:1863-1870. (Epub: 2006 May 26). [Full Text PDF]

Swanson-Wagner R, Y Jia, R DeCook, LA Borsuk, D 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, 103:6805-6810. (Epub: 2006 Apr 25). [Full Text PDF]

Maher PM, H-H Chou, E Hahn, T-J Wen, PS Schnable (2006) GRAMA: A genetic mapping tool for the analysis of temperature gradient capillary electrophoresis (TGCE) data. Theoretical Applied Genetics, 113:156-162. (Epub: 2006 Apr 20). [Full Text PDF]

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, 5:4885-4893. (an image from this manuscript was selected for inclusion on the cover). [Full Text PDF]

Yao H, PS Schnable (2005) Cis-effects on meiotic recombination across distinct a1-sh2 intervals in a common Zea genetic background. Genetics, 170:1929-44. [Full Text PDF]

Woll K, LA Borsuk, H Stransky, D 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, 139:1255-67. [Full Text PDF]

Fu Y, SJ Emrich, L Guo, T-J 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, 102:12282-7. [Full Text PDF]

Wen T-J, F Hochholdinger, M Sauer, W Bruce, PS Schnable (2005) The roothairless 1 gene of maize (Zea mays) encodes a homolog of sec3, which is involved in polar exocytosis. Plant Physiology, 138:1637-43. [Full Text PDF]

Dietrich CR, MADN Perera, M 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, 42:844-861. [Full Text PDF]

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, 21:2560-2. [Full Text PDF]

Hsia A-P, T-J Wen, HD Chen, Z Liu, MD Yandeau, YWei, 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: 218-225. [Full Text PDF]

Yao H, L Guo, Y Fu, LA Borsuk, T-J Wen, DS Skibbe, X Cui, BE Scheffler, J Cao, SJ Emrich, DS Ashlock, PS Schnable (2005) Evaluation of seven ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biology, 57:445-60. [Full Text PDF]

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, 169:917-929. [Full Text PDF]

Hochholdinger F, L Guo, PS Schnable (2004) Lateral roots affect the proteome of the primary root of maize (Zea mays L.). Plant Mol Biology, 56:397-412. [Full Text PDF]

Ashlock DA, SJ Emrich, KM Bryden, SM Corns, TJ Wen, PS Schnable (2004) A Comparison of Evolved Finite State Classifiers and Interpolated Markov Models for Improving PCR Primer Design, 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '04), pp. 190-197, ISBN 0-7803-8728-7. [Full Text PDF]

Fu Y, AP Hsia, L Guo, PS Schnable (2004) Types and frequencies of sequencing errors in methyl-filtered and high Cot maize genome survey sequences. Plant Physiology, 135:2040-2045. [Full Text PDF]

Chou HH, AP Hsia, D Mooney, PS Schnable (2004) PICKY: an oligo microarray design tool for large genomes. Bioinformatics, 20:2893-2902. [Full Text PDF]

Kirch HH, D Bartels, Y Wei, PS Schnable, AJ Wood (2004) The ALDH gene superfamily of Arabidopsis. Trends in Plant Science, 9:371-377. [Full Text PDF]

da Costa Silva O, R Lorbiecke, P Garg, L Müller, M Waßmann, P Lauert, M Scanlon, AP Hsia, PS Schnable, K Krupinska, U Wienand (2004) The Etched1 gene of Zea mays (L.) encodes a zinc ribbon protein that belongs to the transcriptionally active chromosome (TAC) of plastids and is similar to the transcription factor TFIIS. Plant Journal, 38:923-939. [Full Text PDF]

Emrich SJ, S Aluru, Y Fu, TJ Wen, M Narayanan, L Guo, DA Ashlock, PS Schnable (2004) A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics, 20:140-147. [Full Text PDF]

Schnable PS, M Nakazono, F Hochholdinger (2004) Global Expression Profiling Applied to Plant Development. Current Opinion in Plant Biology, 7:50-56. [Full Text PDF]

Hochholdinger F, L Guo, PS Schnable (2004) Cytoplasmic regulation of the accumulation of nuclear-encoded proteins in the mitochondrial proteome of maize. Plant Journal, 37:199-208. [Full Text PDF]

Qiu F, L Guo, TJ Wen, DA Ashlock, PS Schnable (2003) DNA sequence-based "bar-codes" for tracking the origins of ESTs from a maize cDNA library constructed using multiple mRNA sources. Plant Physiology, 133:475-481. [Full Text PDF]

Nakazono M, F Qiu, L Borsuk, PS Schnable (2003) Laser capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: Identification of genes differentially expressed in epidermal cells or vascular tissues of maize. Plant Cell, 15:583-596. [Full Text PDF]

Cui X, A-P Hsia, F Liu, D Ashlock, RP Wise, PS Schnable (2003) Alternative Transcription Initiation Sites and Polyadenylation Sites Are Recruited During Mu Suppression at the rf2a Locus of Maize. Genetics, 163:685-698. [Full Text PDF]

Liu F, PS Schnable (2002) Functional specialization of maize mitochondrial aldehyde dehydrogenases. Plant Physiology, 130:1657-1674. [Full Text PDF]

Skibbe D, F Liu, TJ Wen, MD Yandeau, XQ Cui, J Cao, CR Simmons, PS Schnable (2002) Characterization of the aldehyde dehydrogenase gene families of Zea mays and Arabidopsis. Plant Molecular Biology, 48:751-764. [Full Text PDF]

Yao H, Q Zhou, J Li, H Smith, M Yandeau, B Nikolau, PS Schnable (2002) Meiotic recombination across the 140-kb multigenic maize a1-sh2 interval. Proc Natl Acad Sci, 99:6157-6162. (A commentary on this manuscript solicited by the editors of PNAS and written by Cliff Weil was provided in 99:5763-5765). [Full Text PDF]

Xu X, CR Dietrich, R Lessire, BJ Nikolau, PS Schnable (2002) The endoplasmic reticulum-associated maize GL8 protein is one of the components of the acyl-CoA elongase complex involved in the production of cuticular waxes. Plant Physiology, 128:924-934. [Full Text PDF]

Dietrich C, F Cui, M Packila, J Li, D Ashlock, B Nikolau, PS Schnable (2002) Maize Mu Transposons Are Targeted to the 5' Untranslated Region of the gl8 Gene and Sequences Flanking Mu Target-Site Duplications Exhibit Nonrandom Nucleotide Composition Throughout the Genome. Genetics, 160:697-716. [Full Text PDF]

Liu F, X Cui, HT Horner, H Weiner, PS Schnable (2001) Mitochondrial aldehyde dehydrogenase activity is required for male fertility in maize (Zea mays L.). Plant Cell, 13:1063-1078. [Full Text PDF]

Updated: 2007-04-04