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1. Full Text ALLMAPS: Robust scaffold ordering based on multiple maps
by Tang, Haibao and Zhang, Xingtan and Miao, Chenyong and Zhang, Jisen and Ming, Ray and Schnable, James C and Schnable, Patrick S and Lyons, Eric and Lu, Jianguo
Genome Biology, ISSN 1474-7596, 01/2015, Volume 16, Issue 1, pp. 3 - 3
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes... 
SYNTENY | EVOLUTION | INTEGRATION | ASSEMBLIES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | CONSTRUCTION | GENETICS & HEREDITY | VALIDATION | ALGORITHMS | GENETIC-MAP | GENOME | Databases, Genetic | Chromosome Mapping | Genetic Markers | Algorithms | Animals | Chromosomes - genetics | Computer Simulation | Catfishes - genetics | Software | Genome | Genomics - methods | Medicago - genetics | Cluster Analysis | Genetic Linkage | Conflict resolution | Genomes | Gene mapping | Chromosomes | Bioinformatics | Index Medicus | Method
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2. Full Text Gene mapping via bulked segregant RNA-Seq (BSR-Seq)
by Liu, Sanzhen and Yeh, Cheng-Ting and Tang, Ho Man and Nettleton, Dan and Schnable, Patrick S
PLoS ONE, ISSN 1932-6203, 05/2012, Volume 7, Issue 5, pp. e36406 - e36406
Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to... 
ARABIDOPSIS-THALIANA | HUMAN GENOME | SNP DISCOVERY | BLIGHT | BIOSYNTHESIS | MULTIDISCIPLINARY SCIENCES | AFLP MARKERS | MAIZE | IDENTIFICATION | RESISTANCE GENE | CELL | Zea mays - genetics | Seeds - genetics | Chromosome Mapping | Gene Expression Profiling | Transcription Factors - genetics | Plant Proteins - genetics | Fatty Acids - genetics | Bayes Theorem | Cloning, Molecular | High-Throughput Nucleotide Sequencing | Polymorphism, Single Nucleotide | Mutation | Fatty Acids - biosynthesis | RNA sequencing | Genetic markers | Transposons | RNA | Gene mutations | Analysis | Genetic aspects | Genetic transcription | Fatty acids | GL3 gene | Transcription factors | Genomics | Genes | Identification | Biosynthesis | Mapping | Genomes | Maize | Single-nucleotide polymorphism | Genotype & phenotype | DNA methylation | Trends | Bioinformatics | Deoxyribonucleic acid--DNA | Cloning | Markers | Corn | Gene expression | Ribonucleic acid--RNA | Empirical analysis | Loci | Mutants | Alleles | Epigenetics | Gene mapping | Bayesian analysis | Binding sites | Apoptosis | Index Medicus | Deoxyribonucleic acid | Ribonucleic acid | DNA
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3. Full Text The B73 Maize Genome: Complexity, Diversity, and Dynamics
by Patrick S. Schnable and Doreen Ware and Robert S. Fulton and Joshua C. Stein and Fusheng Wei and Shiran Pasternak and Chengzhi Liang and Jianwei Zhang and Lucinda Fulton and Tina A. Graves and Patrick Minx and Amy Denise Reily and Laura Courtney and Scott S. Kruchowski and Chad Tomlinson and Cindy Strong and Kim Delehaunty and Catrina Fronick and Bill Courtney and Susan M. Rock and Eddie Belter and Feiyu Du and Kyung Kim and Rachel M. Abbott and Marc Cotton and Andy Levy and Pamela Marchetto and Kerri Ochoa and Stephanie M. Jackson and Barbara Gillam and Weizu Chen and Le Yan and Jamey Higginbotham and Marco Cardenas and Jason Waligorski and Elizabeth Applebaum and Lindsey Phelps and Jason Falcone and Krishna Kanchi and Thynn Thane and Adam Scimone and Nay Thane and Jessica Henke and Tom Wang and Jessica Ruppert and Neha Shah and Kelsi Rotter and Jennifer Hodges and Elizabeth Ingenthron and Matt Cordes and Sara Kohlberg and Jennifer Sgro and Brandon Delgado and Kelly Mead and Asif Chinwalla and Shawn Leonard and Kevin Crouse and Kristi Collura and Dave Kudrna and Jennifer Currie and Ruifeng He and Angelina Angelova and Shanmugam Rajasekar and Teri Mueller and Rene Lomeli and Gabriel Scara and Ara Ko and Krista Delaney and Marina Wissotski and Georgina Lopez and David Campos and Michele Braidotti and Elizabeth Ashley and Wolfgang Golser and HyeRan Kim and Seunghee Lee and Jinke Lin and Zeljko Dujmic and Woojin Kim and Jayson Talag and Andrea Zuccolo and Chuanzhu Fan and Aswathy Sebastian and Melissa Kramer and Lori Spiegel and Lidia Nascimento and Theresa Zutavern and Beth Miller and Claude Ambroise and Stephanie Muller and Will Spooner and Apurva Narechania and Liya Ren and Sharon Wei and Sunita Kumari and Ben Faga and Michael J. Levy and Linda McMahan and Peter Van Buren and Matthew W. Vaughn and ...
Science, ISSN 0036-8075, 11/2009, Volume 326, Issue 5956, pp. 1112 - 1115
We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000... 
Genes | Genomics | Centromeres | Corn | Sorghum | Reports | Genomes | Plants | Chromosomes | Research universities | Rice | PLANT | ARABIDOPSIS-THALIANA | METHYLATION | EVOLUTION | ZEA-MAYS | GENETICS | MULTIDISCIPLINARY SCIENCES | GENES | TRANSPOSABLE ELEMENTS | RETROTRANSPOSONS | DIVERGENCE | Zea mays - genetics | Genes, Plant | Retroelements | Molecular Sequence Data | Chromosome Mapping | Genome, Plant | RNA, Plant - genetics | Sequence Analysis, DNA | DNA Transposable Elements | DNA Copy Number Variations | Genetic Variation | DNA Methylation | Centromere - genetics | Recombination, Genetic | Base Sequence | Ploidies | Inbreeding | Crops, Agricultural - genetics | MicroRNAs - genetics | Chromosomes, Plant - genetics | DNA, Plant - genetics | Genetic aspects | Research | Nucleotide sequencing | Methods | Evolutionary biology | Genetic recombination | Biological diversity | Index Medicus | Populations and Evolution | Biodiversity | Cellular Biology | DNA, Plant | Life Sciences | Computer Science | Biomolecules | Genetics | Crops, Agricultural | Vegetal Biology | Bioinformatics | Plants genetics | RNA, Plant | Zea mays | Quantitative Methods | Biochemistry, Molecular Biology | Chromosomes, Plant | Systematics, Phylogenetics and taxonomy | Plant breeding | Centromere | MicroRNAs | Molecular biology | Molecular Networks
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4. Full Text A high-throughput, field-based phenotyping technology for tall biomass crops
by Salas Fernandez, Maria G and Bao, Yin and Tang, Lie and Schnable, Patrick S
Plant Physiology, ISSN 0032-0889, 08/2017, Volume 174, Issue 4, pp. 2008 - 2022
Recent advances in omics technologies have not been accompanied by equally efficient, cost-effective, and accurate phenotyping methods required to dissect the... 
PLATFORM | QUANTITATIVE TRAIT LOCI | ARABIDOPSIS-THALIANA | IMAGING-SYSTEM | PHENOMICS | ARCHITECTURE | DROUGHT RESPONSES | SORGHUM-BICOLOR | PLANT-GROWTH | GENOME-WIDE ASSOCIATION | PLANT SCIENCES | Genome-Wide Association Study | Reproducibility of Results | Sorghum - anatomy & histology | Crops, Agricultural - anatomy & histology | Imaging, Three-Dimensional - methods | Biomass | Robotics | Phenotype | Algorithms | Plant Stems - anatomy & histology | Analysis of Variance | Polymorphism, Single Nucleotide - genetics | Sorghum - genetics | Physiological aspects | Botanical research | Genetic aspects | Energy crops | Research | Index Medicus
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5. Full Text Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content
by Springer, Nathan M and Ying, Kai and Fu, Yan and Ji, Tieming and Yeh, Cheng-Ting and Jia, Yi and Wu, Wei and Richmond, Todd and Kitzman, Jacob and Rosenbaum, Heidi and Iniguez, A. Leonardo and Barbazuk, W. Brad and Jeddeloh, Jeffrey A and Nettleton, Dan and Schnable, Patrick S
PLoS Genetics, ISSN 1553-7390, 11/2009, Volume 5, Issue 11, pp. e1000734 - e1000734
Following the domestication of maize over the past,10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype... 
ARTIFICIAL SELECTION | LINKAGE DISEQUILIBRIUM | FUNCTIONAL IMPACT | GENETICS & HEREDITY | GENE-EXPRESSION | ZEA-MAYS L | STRUCTURAL VARIATION | F-1 HYBRID | ARRAY CGH | LOCUS | CIRCULAR BINARY SEGMENTATION | Genetic Variation | Haplotypes | Sequence Deletion | Zea mays - genetics | Genes, Plant | Base Sequence | Genotype | Crops, Agricultural - genetics | Gene Dosage | Genome, Plant | Cytogenetics | Corn | Exhibitions | Research | Single nucleotide polymorphisms | DNA | Index Medicus | Inbreeding | Genetic diversity | Genomics | Genes | Deoxyribonucleic acid
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6. Full Text SNP discovery via 454 transcriptome sequencing
by Barbazuk, W. Brad and Emrich, Scott J and Chen, Hsin D and Li, Li and Schnable, Patrick S
The Plant Journal, ISSN 0960-7412, 09/2007, Volume 51, Issue 5, pp. 910 - 918
A massively parallel pyro‐sequencing technology commercialized by 454 Life Sciences Corporation was used to sequence the transcriptomes of shoot apical... 
SNPs | 454 sequencing | markers | ESTs | maize | Maize | Markers | MAIZE GENOME | DOMESTICATION | PATTERNS | HORDEUM-VULGARE L | PLANT SCIENCES | ARTIFICIAL SELECTION | EVOLUTION | GENES | MAYS L | EXPRESSION | SINGLE NUCLEOTIDE POLYMORPHISMS | Zea mays - genetics | Base Sequence | Meristem - metabolism | Molecular Sequence Data | Polymorphism, Single Nucleotide | Software | Genome, Plant | Zea mays - metabolism | Sequence Analysis, DNA - methods | Expressed Sequence Tags | Corn | Gene expression | Botany | Polymorphism | Index Medicus | Original
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7. Full Text A High-Throughput, Field-Based Phenotyping Technology for Tall Biomass Crops1[OPEN]
by Salas Fernandez, Maria G and Bao, Yin and Tang, Lie and Schnable, Patrick S
Plant Physiology, ISSN 0032-0889, 8/2017, Volume 174, Issue 4, pp. 2008 - 2022
A ground-based platform enables high-throughput, image-based data and analysis to characterize plant architecture of a tall biomass crop species. Recent... 
Breakthrough Technologies
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8. Full Text Field-based robotic phenotyping of sorghum plant architecture using stereo vision
: BAO et al
by Bao, Yin and Tang, Lie and Breitzman, Matthew W and Salas Fernandez, Maria G and Schnable, Patrick S
Journal of Field Robotics, ISSN 1556-4959, 03/2019, Volume 36, Issue 2, pp. 397 - 415
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9. Full Text Field-based architectural traits characterisation of maize plant using time-of-flight 3D imaging
by Bao, Yin and Tang, Lie and Srinivasan, Srikant and Schnable, Patrick S
Biosystems Engineering, ISSN 1537-5110, 02/2019, Volume 178, pp. 86 - 101
Maize ( L.) is one of the most economically important cereal crops. Though time-consuming and labour-intensive, manually measuring phenotypic traits in the... 
Maize | Plant phenotyping | Point cloud processing | Time-of-Flight | Skeletonisation | POPULATION | MANIPULATION | HIGH-THROUGHPUT | ALGORITHM | SHAPE | AGRICULTURAL ENGINEERING | IMAGES | AGRICULTURE, MULTIDISCIPLINARY
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10. Full Text Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm
by Amanda J. Waters and Irina Makarevitch and Steve R. Eichten and Ruth A. Swanson-Wagner and Cheng-Ting Yeh and Wayne Xu and Patrick S. Schnable and Matthew W. Vaughn and Mary Gehring and Nathan M. Springer
The Plant Cell, ISSN 1040-4651, 12/2011, Volume 23, Issue 12, pp. 4221 - 4233
Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo... 
Genes | DNA | Alleles | Corn | Endosperm | Methylation | Gene expression | Embryos | Hybridity | LARGE-SCALE BIOLOGY ARTICLES | Plant cells | ALLELE | FIE | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEED DEVELOPMENT | ARABIDOPSIS ENDOSPERM | IMPRINTED GENES | HYPOMETHYLATION | PLANT SCIENCES | CELL BIOLOGY | EVOLUTION | MEDEA | DEMETHYLATION | POLYCOMB-GROUP GENE | Zea mays - chemistry | Genomic Imprinting | Zea mays - genetics | Arabidopsis - chemistry | Genes, Plant | Gene Expression Profiling - methods | Oryza - chemistry | Genetic Loci | Endosperm - chemistry | Endosperm - genetics | Pollination | Polymorphism, Genetic | Arabidopsis - genetics | Inheritance Patterns | DNA Methylation | Sequence Analysis, RNA | Chromosomes, Plant - chemistry | Oryza - genetics | Gene Expression Regulation, Plant | Conserved Sequence | Chromosomes, Plant - genetics | Embryonic development | Plant genetics | Physiological aspects | Genetic aspects | Research | Index Medicus | Magnetoencephalography | Imprinting | DNA methylation | Gene polymorphism | Large-Scale Biology
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11. Full Text Parallel domestication of the Shattering1 genes in cereals
by Lin, Zhongwei and Li, Xianran and Shannon, Laura M and Yeh, Cheng-Ting and Wang, Ming L and Bai, Guihua and Peng, Zhao and Li, Jiarui and Trick, Harold N and Clemente, Thomas E and Doebley, John and Schnable, Patrick S and Tuinstra, Mitchell R and Tesso, Tesfaye T and White, Frank and Yu, Jianming
Nature Genetics, ISSN 1061-4036, 06/2012, Volume 44, Issue 6, pp. 720 - 724
A key step during crop domestication is the loss of seed shattering. Here, we show that seed shattering in sorghum is controlled by a single gene, Shattering1... 
ORIGIN | EVOLUTION | RICE ORYZA-SATIVA | WILD-RICE | GENETICS & HEREDITY | MARKERS | DIVERSITY | MAIZE | SORGHUM-BICOLOR | ASSOCIATION | GENOME | Zea mays - genetics | Edible Grain - genetics | Oryza - genetics | Genes, Plant | Base Sequence | Protein Isoforms | Molecular Sequence Data | Chromosome Mapping | Mutation | Sorghum - genetics | Gene mutations | Genetic transcription | Research | Haplotypes | Confidence intervals | Genes | Genomics | Crops | Cloning | Colleges & universities | Genetics | Agriculture | Genomes | Index Medicus
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12. Full Text Genome sequencing and analysis of the model grass Brachypodium distachyon
by Vogel, John P and Garvin, David F and Mockler, Todd C and Schmutz, Jeremy and Rokhsar, Dan and Bevan, Michael W and Barry, Kerrie and Lucas, Susan and Harmon-Smith, Miranda and Lail, Kathleen and Tice, Hope and Grimwood, Jane and McKenzie, Neil and Huo, Naxin and Gu, Yong Q and Lazo, Gerard R and Anderson, Olin D and You, Frank M and Luo, Ming-Cheng and Dvorak, Jan and Wright, Jonathan and Febrer, Melanie and Idziak, Dominika and Hasterok, Robert and Lindquist, Erika and Wang, Mei and Fox, Samuel E and Priest, Henry D and Filichkin, Sergei A and Givan, Scott A and Bryant, Douglas W and Chang, Jeff H and Wu, Haiyan and Wu, Wei and Hsia, An-Ping and Schnable, Patrick S and Kalyanaraman, Anantharaman and Barbazuk, Brad and Michael, Todd P and Hazen, Samuel P and Bragg, Jennifer N and Laudencia-Chingcuanco, Debbie and Weng, Yiqun and Haberer, Georg and Spannagl, Manuel and Mayer, Klaus and Rattei, Thomas and Mitros, Therese and Lee, Sang-Jik and Rose, Jocelyn K. C and Mueller, Lukas A and York, Thomas L and Wicker, Thomas and Buchmann, Jan P and Tanskanen, Jaakko and Schulman, Alan H and Gundlach, Heidrun and Beven, Michael and Costa De Oliveira, Antonio and Da C. Maia, Luciano and Belknap, William and Jiang, Ning and Lai, Jinsheng and Zhu, Liucun and Ma, Jianxin and Sun, Cheng and Pritham, Ellen and Salse, Jerome and Murat, Florent and Abrouk, Michael and Bruggmann, Remy and Messing, Joachim and Fahlgren, Noah and Sullivan, Christopher M and Carrington, James C and Chapman, Elisabeth J and May, Greg D and Zhai, Jixian and Ganssmann, Matthias and Gurazada, Sai Guna Ranjan and German, Marcelo and Meyers, Blake C and Green, Pamela J and Tyler, Ludmila and Wu, Jiajie and Thomson, James and Chen, Shan and Scheller, Henrik V and Harholt, Jesper and Ulvskov, Peter and Kimbrel, Jeffrey A and Bartley, Laura E and Cao, Peijian and Jung, Ki-Hong and Sharma, Manoj K and Vega-Sanchez, Miguel and Ronald, Pamela and Dardick, Christopher D and De Bodt, Stefanie and Verelst, Wim and ... and Int Brachypodium Initiative and International Brachypodium Initiative and The International Brachypodium Initiative and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
Nature, ISSN 0028-0836, 02/2010, Volume 463, Issue 7282, pp. 763 - 768
Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of... 
TRITICEAE | EVOLUTION | INTRASPECIES DIVERSITY | MULTIDISCIPLINARY SCIENCES | RETROTRANSPOSONS | ARABIDOPSIS | DIVERGENCE | AGROBACTERIUM-MEDIATED TRANSFORMATION | WHEAT | MAP | RICE | Synteny - genetics | Genome, Plant - genetics | Genomics | Molecular Sequence Data | Poaceae - genetics | RNA, Plant - analysis | RNA, Plant - genetics | Sequence Analysis, DNA | Poaceae - classification | Gene Fusion - genetics | Oryza - genetics | Genes, Plant - genetics | DNA Transposable Elements - genetics | Crops, Agricultural - genetics | Sorghum - genetics | Transcription, Genetic - genetics | Chromosomes, Plant - genetics | Evolution, Molecular | Analysis | Wetland flora | Genomes | Genetic aspects | Research | Grasses | Chromosomes | Genetics | Artificial chromosomes | Data bases | Rice | Index Medicus | Life Sciences | Cellular Biology
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