基本信息
姓名： Patrick Schnable
性别：男
系别：植物遗传育种学系
职称：长江学者
学位：博士
个人简历
个人简介
2009年十一月合作完成了玉米自交系B73的测序工作，并于《Science》发表相关研究结果。
2008年－今 中国农业大学植物遗传育种系长江学者讲座教授，博士生导师；
1988年－今 爱荷华州立大学（Iowa State University ）教授，植物基因组学研究中心主任，固碳作物研究中心主任；
1986年－1988年在德国马普研究所（Max-Planck-Institute）博士后;
1986年 于爱荷华州立大学（Iowa State University ）获得博士学位；
1981年 于康奈尔大学（Cornell University ）获得学士学位；
更多个人介绍内容请访问：http://schnablelab.plantgenomics.iastate.edu/personnel/schnable_patrick.php
联系方式
联系方式：
实验室网址：http://schnablelab.plantgenomics.iastate.edu/
电子信箱：schnable@iastate.edu
中国农业大学实验室地址：西校区农学楼412房间
研究方向
１、玉米遗传学和基因组学
２、玉米功能基因组学
３、比较基因组学
４、生物信息学
美国Iowa State University的Patrick Schnable教授是中国农业大学农学与生物技术学院植物遗传育种系长江学者客座教授，是玉米基因组学、功能基因组学和杂种优势遗传机理研究领域世界知名科学家。Patrick Schnable教授2011年在植物遗传育种系继续招收硕士研究生，在中国农业大学完成硕士阶段的学习和硕士研究论文工作，主要从事玉米基因组生物信息学相关研究，如通过全基因组序列分析，解析位点多态性与遗传重组的关系等。Patrick Schnable教授主要通过来北京工作和网络视频实验室会议等方式具体指导研究工作。具体要求：
1、符合中国农业大学2011年硕士研究生复试条件的第一志愿和调剂考生。
2、有较强的英语交流能力。
3、有良好的生物学基础，对生物信息学和基因组学分析有浓厚兴趣。
4、有较强的计算机使用能力，熟悉或能较快掌握生物信息学软件及其工作平台（如Linux等），具备编程或能较快学习计算机编程能力。
5、英文简历（Resume）和申请信（Personal statement )。
有意申请的考生请将简历和申请信发给Schnable教授（email: schnable@iastate.edu)，或直接到农学楼412房间与Schnable教授在农大已招在读硕士研究生李德林（delin.bio@gmail.com）或黄银连（yinlianhuang@gmail.com）联系。通过初选的考生将由Schnable教授本人近日直接复试。Schnable教授在Iowa State University的具体情况见http://www.schnablelab.plantgenomics.iastate.edu/
2011年3月1日
论文著作
学术论文：
2005 ~ 2010发表的论文：
详细信息及下载请访问：http://schnablelab.plantgenomics.iastate.edu/publications/
2010 (7 篇)
• Fu Y*, NM Springer*, K Ying*, CT Yeh, AL Iniguez, T Richmond, W Wu, WB Barbazuk, DS Nettleton, JA Jeddeloh, PS Schnable (2010) High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. PLoS One, 5(12): e14178.
• Feuillet C, JE Leach, J Rogers, PS Schnable, K Eversole (2010) Crop genome sequencing: lessons and rationales. Trends Plant Sci, 16(2): 77-88.
• Lai J*, R Li*, X Xu*, W Jin*, M Xu*, H Zhao, Z Xiang, W Song, K Ying, M Zhang, Y Jiao, P Ni, J Zhang, D Li, X Guo, K Ye, M Jian, B Wang, H Zheng, H Liang, X Zhang, S Wang, S Chen, J Li, Y Fu, NM Springer, H Yang, J Wang, J Dai, PS Schnable, J Wang (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet, 42(11): 1027-1030. (Epub 2010 Oct 24 ; An image from this manuscript was selected for inclusion on the cover)
• The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463(7282): 763-768.
• Fu Y, NM Springer, D Gerhardt, K Ying, CT Yeh, W Wu, RA Swanson-Wagner, M D'Ascenzo, T Millard, L Freeberg, N Aoyama, J Kitzman, D Burgess, T Richmond, T Albert, WB Barbazuk, JA Jeddeloh, PS Schnable (2010) Repeat subtraction-mediated sequence capture from a complex genome. Plant J, 62(5): 898-909. (Epub: 4 Mar 2010; An image from this manuscript was selected for inclusion on the cover)
• Liu S, HD Chen, I Makarevitch, R Shirmer, SJ Emrich, CR Dietrich, WB Barbazuk, NM Springer, PS Schnable (2010) High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics, 184: 19-26.
• Buggs RJA, S Chamala, W Wu, L Gao, GD May, PS Schnable, DE Soltis, PS Soltis, WB Barbazuk (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology, 19(s1): 132-146.
2009 (16 篇)
• 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, 183: 1215-1225. (Selected as an Editors' Choice by MaizeGDB, 11/09)
• Schnable PS*, D Ware*, RS Fulton, et al (2009) The B73 maize genome: complexity, diversity and dynamics. Science, 326(5956): 1112-1115. (Highlighted by Faculty of 1000 Biology; An image from this manuscript was selected for inclusion on the cover)
• 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, 5(11): e1000737. (Selected as an Editors' Choice by MaizeGDB, 12/09)
• Wei F, JC Stein, .. PS Schnable,.. et al (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics, 5(11): e1000728. (Selected as an Editors' Choice by MaizeGDB, 12/09)
• Swanson-Wagner RA, R DeCook, Y Jia, T Bancroft, T Ji, X Zhao, DS Nettleton, PS Schnable (2009) Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science, 326(5956): 1118-1120. (Highlighted by Faculty of 1000 Biology)
• 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, 5(11): e1000734. (Selected as an Editors' Choice by MaizeGDB, 12/09)
• 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, 5(11): e1000715. (Selected as an Editors' Choice by MaizeGDB, 12/09)
• 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, 5(11): e1000733. (Selected as an Editors' Choice by MaizeGDB, 12/09)
• Chou HH, A Trisiriroj, S Park, YIC Hsing, PC Ronald, PS Schnable (2009) Direct calibration of PICKY-designed microarrays. BMC Bioinformatics, 10(34).
• Soltis DE, RJA 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.
• Scanlon MJ, K Ohtsu, MCP Timmermans, PS Schnable (2009) Laser microdissection-mediated isolation and in vitro transcriptional amplification of plant RNA. Curr Protoc Mol Biol, Unit 25A.3.
• 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, MCP Timmermans, PS Schnable, DS Nettleton, MJ Scanlon (2009) Microdissection of shoot meristem functional domains. PLoS Genetics, 5(5): e1000476. (Epub: 8 May 2009)
• 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 FTS, DH Chitwood, S Madi, K Ohtsu, PS Schnable, MJ Scanlon, MCP Timmermans (2009) Regulation of small RNA accumulation in the maize shoot apex. PLoS Genetics, 5(1): e1000320. (Selected as an Editors' Choice by MaizeGDB, 6/09)
• Shimizu R, J Ji, E Kelsey, K Ohtsu, PS Schnable, MJ Scanlon (2009) Tissue specificity and evolution of meristematic WOX3 function. Plant Physiol, 149(2): 841-850. (Highlighted by Faculty of 1000 Biology)
• Jackson BG, PS Schnable, S Aluru (2009) Parallel short sequence assembly of transcriptomes. BMC Bioinformatics, 10(Suppl 1): S14.
2008 (8 篇)
• Skibbe DS, X Wang, LA Borsuk, 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.
• Jung KH, CD 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 Rocke, 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): e3337.
• Strable J, LA Borsuk, DS Nettleton, PS Schnable, EE Irish (2008) Microarray analysis of vegetative phase change in maize. Plant J, 56(6): 1045-1057.
• Lu R, GC Lee, M Shultz, CD Dardick, KH Jung, J Phetsom, Y Jia, RH Rice, Z Goldberg, PS Schnable, PC Ronald, D Rocke (2008) Assessing probe-specific dye and slide biases in two-color microarray data. BMC Bioinformatics, 9(314).
• 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 Hered, 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 J, 54(5): 888-898. (Selected as an Editors' Choice by MaizeGDB, 6/08)
• 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(1): 57-66. (Selected as an Editors' Choice by MaizeGDB, 2/08)
• Jackson BG, S Aluru, PS Schnable (2008) Consensus genetic maps as median orders from inconsistent sources. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(2): 161-171.
2007 (12 篇)
• Dembinsky D, K Woll, M Saleem, Y Liu, Y Fu, LA Borsuk, T Lamkemeyer, C Fladerer, J Madlung, WB Barbazuk, A Nordheim, DS Nettleton, PS Schnable, F Hochholdinger (2007) Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiol, 145(3): 575-588.
• Ohtsu K, MB Smith, SJ Emrich, LA Borsuk, R Zhou, T Chen, X Zhang, MCP 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 J, 52(3): 391-404. (Highlighted by Faculty of 1000 Biology)
• Barbazuk WB, SJ Emrich, HD Chen, L Li, PS Schnable (2007) SNP discovery via 454 transcriptome sequencing. Plant J, 51(5): 910-918. (Cited in Wikipedia: http://en.wikipedia.org/wiki/RNA-Seq)
• Zhang X, S Madi, LA Borsuk, DS Nettleton, B Buckner, D Janick-Buckner, J Beck, MCP 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. (Selected an Editors' Choice by MaizeGDB, 7/07)
• Li J, LC Harper, I Golubovskaya, CR Wang, D Weber, RB Meeley, J McElver, 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 of Genetics as an "Issue Highlight"; selected as an Editors'Choice by MaizeGDB, 8/07)
• Buckner B, J Beck, KF Browning, AE Fritz, L Grantham, E Hoxha, Z Kamvar, A 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.
• 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 Physiol, 48(1): 3-7. (Epub: 2006 Dec 5)
• 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. (Featured in Science(315:302) as in Editor's Choice: Highlights of the recent literature; selected as an Editors' Choice by MaizeGDB, 12/06)
• Emrich SJ*, WB Barbazuk*, L Li, PS Schnable (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res, 17(1): 69-73. (Epub: 2006 Nov 9)
• 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. (Special issue devoted to IPDPS best papers)
2006 (7 篇)
• 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)
• Kalyanaraman A, S Aluru, PS Schnable (2006) Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons. Comput Syst Bioinformatics Conf, 5: 167-178. (Conference Website)
• 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. Highlighted by Faculty of 1000 Biology)
• Yandeau-Nelson MD, Y 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 RA*, 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. PNAS, 103(18): 6805-6810. (Epub: 2006 Apr 25. Highlighted by Faculty of 1000 Biology)
• 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. Theor Appl Genet, 113(1): 156-162. (Epub: 2006 Apr 20)
2005 (13篇)
• Ashlock DA, RA Swanson-Wagner, PS Schnable (2005) Selection of genetically diverse recombinant inbreds with an ordered gene evolutionary algorithm. CIBCB'05: 237-242.
• 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)
• 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 Physiol, 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. PNAS, 102(34): 12282-12287.
• Jackson BG, S Aluru, PS Schnable (2005) Consensus genetic maps: a graph theoretic approach. Comput Syst Bioinformatics Conf: 35-43.
• 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 Physiol, 138(3): 1637-1643. (Epub: 2005 Jun 24; Selected as an Editors' Choice by MaizeGDB, 4/07)
• Hsia AP, TJ Wen, HD Chen, Z Liu, MD Yandeau-Nelson, 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. Theor Appl Genet, 111(2): 218-225.
• Ding J, K Viswanathan, D Berleant, ES Wurtele, DA Ashlock, JA Dickerson, A Fulmer, PS Schnable (2005) Using the biological taxonomy to access biological literature with PathBinderH. Bioinformatics, 21(10): 2560-2562.
• 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 J, 42(6): 844-861.
• 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.
• Yao H, L Guo, Y Fu, LA Borsuk, TJ Wen, DS Skibbe, X Cui, BE Scheffler, J Cao, SJ Emrich, DA Ashlock, PS Schnable (2005) Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biol, 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.
• Skibbe DS, PS Schnable (2005) Male sterility in maize. Maydica, 50: 367-376.