The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

[1]  C. Kole,et al.  Arabidopsis Genome Initiative , 2016 .

[2]  Xinbin Dai,et al.  An RNA-Seq based gene expression atlas of the common bean , 2014, BMC Genomics.

[3]  G. R. Gray,et al.  Cold acclimation, de-acclimation and re-acclimation of spring canola, winter canola and winter wheat: The role of carbohydrates, cold-induced stress proteins and vernalization , 2014 .

[4]  Richard M. Clark,et al.  A plant-specific HUA2-LIKE (HULK) gene family in Arabidopsis thaliana is essential for development , 2014, The Plant journal : for cell and molecular biology.

[5]  E. Brummer,et al.  A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome , 2014, G3: Genes, Genomes, Genetics.

[6]  Richard D. Hayes,et al.  The genome of Eucalyptus grandis , 2014, Nature.

[7]  Rod A Wing,et al.  A reference genome for common bean and genome-wide analysis of dual domestications , 2014, Nature Genetics.

[8]  Mahmut Can Hiz,et al.  Transcriptome Analysis of Salt Tolerant Common Bean (Phaseolus vulgaris L.) under Saline Conditions , 2014, PloS one.

[9]  M. Monteros,et al.  Development of an Alfalfa SNP Array and Its Use to Evaluate Patterns of Population Structure and Linkage Disequilibrium , 2014, PloS one.

[10]  Caroline Smith,et al.  Increasing Phosphatidylinositol (4,5)-Bisphosphate Biosynthesis Affects Basal Signaling and Chloroplast Metabolism in Arabidopsis thaliana , 2014, Plants.

[11]  L. Sweetlove,et al.  Increased β-cyanoalanine nitrilase activity improves cyanide tolerance and assimilation in Arabidopsis. , 2014, Molecular plant.

[12]  R. Shoemaker,et al.  Replication protein A subunit 3 and the iron efficiency response in soybean. , 2014, Plant, cell & environment.

[13]  T. Ruttink,et al.  De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification , 2014, BMC Genomics.

[14]  Z. Nan,et al.  Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa , 2013, PloS one.

[15]  C. Jacquet,et al.  Nod factor perception protein carries weight in biotic interactions. , 2013, Trends in plant science.

[16]  Yong Wang.  Characterization of a novel Medicago sativaNAC transcription factor gene involved in response to drought stress , 2013, Molecular Biology Reports.

[17]  Federico De Masi,et al.  ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana , 2013, FEBS open bio.

[18]  O. Postnikova,et al.  Analysis of the alfalfa root transcriptome in response to salinity stress. , 2013, Plant & cell physiology.

[19]  En-Hua Xia,et al.  Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants1[W][OA] , 2013, Plant Physiology.

[20]  M. Wisniewski,et al.  Understanding plant cold hardiness: an opinion. , 2013, Physiologia plantarum.

[21]  Carroll P. Vance,et al.  An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants1[W][OA] , 2012, Plant Physiology.

[22]  G. May,et al.  Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing , 2012, BMC Genomics.

[23]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[24]  Philip N Benfey,et al.  Control of Arabidopsis root development. , 2012, Annual review of plant biology.

[25]  E. Brummer,et al.  Applied Genetics and Genomics in Alfalfa Breeding , 2012 .

[26]  Martin Vingron,et al.  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..

[27]  M. Holsters,et al.  Never too many? How legumes control nodule numbers. , 2012, Plant, cell & environment.

[28]  Jasbir Singh,et al.  The effects of phenotypic plasticity on photosynthetic performance in winter rye, winter wheat and Brassica napus. , 2012, Physiologia plantarum.

[29]  M. Strand,et al.  Deep Sequencing Identifies Viral and Wasp Genes with Potential Roles in Replication of Microplitis demolitor Bracovirus , 2012, Journal of Virology.

[30]  Jun Li,et al.  LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes , 2011, Nucleic Acids Res..

[31]  Y. Im,et al.  Phosphoinositide signaling. , 2012, Annual review of plant biology.

[32]  T. Harkins,et al.  The Cassava Genome: Current Progress, Future Directions , 2012, Tropical Plant Biology.

[33]  Yuhong Tang,et al.  System responses to long-term drought and re-watering of two contrasting alfalfa varieties. , 2011, The Plant journal : for cell and molecular biology.

[34]  A. Myburg,et al.  SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus , 2011, BMC Plant Biology.

[35]  A. Conesa,et al.  Differential expression in RNA-seq: a matter of depth. , 2011, Genome research.

[36]  Alvaro J. González,et al.  The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.

[37]  R. Longhi,et al.  Protection of Sinorhizobium against Host Cysteine-Rich Antimicrobial Peptides Is Critical for Symbiosis , 2011, PLoS biology.

[38]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[39]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[40]  C. Town,et al.  Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis , 2011, BMC Genomics.

[41]  N. Cogan,et al.  Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery , 2011, BMC Genomics.

[42]  S. Jackson,et al.  Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.) , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[43]  E. Bornberg-Bauer,et al.  Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing , 2011, BMC Genomics.

[44]  Christian Kappel,et al.  Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. , 2011, Journal of experimental botany.

[45]  Mingui Zhao,et al.  Comparative studies on tolerance of Medicago truncatula and Medicago falcata to freezing , 2011, Planta.

[46]  S. S. Yang,et al.  Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems , 2011, BMC Genomics.

[47]  Michele Magrane,et al.  UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.

[48]  D. Nettleton,et al.  The Soybean Rhg1 Locus for Resistance to the Soybean Cyst Nematode Heterodera glycines Regulates the Expression of a Large Number of Stress- and Defense-Related Genes in Degenerating Feeding Cells1[C][W][OA] , 2011, Plant Physiology.

[49]  Hong-Hwa Chen,et al.  Downregulation of putative UDP-glucose: flavonoid 3-O-glucosyltransferase gene alters flower coloring in Phalaenopsis , 2011, Plant Cell Reports.

[50]  Toshiro K. Ohsumi,et al.  Genome-wide identification of polycomb-associated RNAs by RIP-seq. , 2010, Molecular cell.

[51]  P. Christou,et al.  The regulation of carotenoid pigmentation in flowers. , 2010, Archives of biochemistry and biophysics.

[52]  P. Gresshoff,et al.  Asparagine as a major factor in the N-feedback regulation of N2 fixation in Medicago truncatula. , 2010, Physiologia plantarum.

[53]  Rex T. Nelson,et al.  RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome , 2010, BMC Plant Biology.

[54]  B. Sundberg,et al.  Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers. , 2010, The Plant journal : for cell and molecular biology.

[55]  H. Kouchi,et al.  How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground , 2010, Plant & cell physiology.

[56]  Lin Feng,et al.  Power of Deep Sequencing and Agilent Microarray for Gene Expression Profiling Study , 2010, Molecular biotechnology.

[57]  Trupti Joshi,et al.  An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. , 2010, The Plant journal : for cell and molecular biology.

[58]  T. Demura,et al.  VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation in Arabidopsis[W][OA] , 2010, Plant Cell.

[59]  Li Liu,et al.  A dynamic gene expression atlas covering the entire life cycle of rice. , 2010, The Plant journal : for cell and molecular biology.

[60]  Mikiko Abe,et al.  Plant Peptides Govern Terminal Differentiation of Bacteria in Symbiosis , 2010, Science.

[61]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[62]  S. S. Yang,et al.  Single‐Feature Polymorphism Discovery in the Transcriptome of Tetraploid Alfalfa , 2009 .

[63]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[64]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[65]  G. Weiller,et al.  A gene expression atlas of the model legume Medicago truncatula. , 2008, The Plant journal : for cell and molecular biology.

[66]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[67]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[68]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[69]  E. Stockinger,et al.  Comparative Genomic Sequence and Expression Analyses of Medicago truncatula and Alfalfa Subspecies falcata COLD-ACCLIMATION-SPECIFIC Genes1[W][OA] , 2008, Plant Physiology.

[70]  C. P. Vance.  Carbon and Nitrogen Metabolism in Legume Nodules , 2008 .

[71]  Hank C Wu,et al.  Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. , 2007, The Plant journal : for cell and molecular biology.

[72]  C. Sheaffer,et al.  Alfalfa Leaf Protein and Stem Cell Wall Polysaccharide Yields under Hay and Biomass Management Systems , 2007 .

[73]  Z. Chen,et al.  Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. , 2007, Annual review of plant biology.

[74]  T. A. Campbell,et al.  Genetic mapping of biomass production in tetraploid alfalfa , 2007 .

[75]  M. Dilworth.  Nitrogen-fixing leguminous symbioses , 2007 .

[76]  J. Bouton.  The economic benefits of forage improvement in the United States , 2007, Euphytica.

[77]  T. Demura,et al.  SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis[W] , 2006, The Plant Cell Online.

[78]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[79]  M. Piotrowski,et al.  Cyanide Metabolism in Higher Plants: Cyanoalanine Hydratase is a NIT4 Homolog , 2006, Plant Molecular Biology.

[80]  Tetsuro Mimura,et al.  Transcription switches for protoxylem and metaxylem vessel formation. , 2005, Genes & development.

[81]  J. Craig,et al.  The Xylem and Phloem Transcriptomes from Secondary Tissues of the Arabidopsis Root-Hypocotyl1[w] , 2005, Plant Physiology.

[82]  Stefan R. Henz,et al.  A gene expression map of Arabidopsis thaliana development , 2005, Nature Genetics.

[83]  Kathryn A. VandenBosch,et al.  Computational Identification and Characterization of Novel Genes from Legumes1[w] , 2004, Plant Physiology.

[84]  P. Lerouge,et al.  Purification and Characterization of Enzymes Exhibiting β-d-Xylosidase Activities in Stem Tissues of Arabidopsis1 , 2004, Plant Physiology.

[85]  N. Young,et al.  Legume genomes: more than peas in a pod. , 2003, Current opinion in plant biology.

[86]  R. Verma,et al.  The biosynthesis of L-arabinose in plants: molecular cloning and characterization of a Golgi-localized UDP-D-xylose 4-epimerase encoded by the MUR4 gene of Arabidopsis. , 2003, The Plant cell.

[87]  Mark W. Budwig,et al.  A Matter of Depth , 2003 .

[88]  Hansang Jung,et al.  Alfalfa Stem Tissues , 2002 .

[89]  F. M. Engels,et al.  Alfalfa Stem Tissues: Cell Wall Deposition, Composition, and Degradability , 2002 .

[90]  B. Winkel-Shirley,et al.  Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. , 2001, Plant physiology.

[91]  W. Lukowitz,et al.  Arabidopsis cyt1 mutants are deficient in a mannose-1-phosphate guanylyltransferase and point to a requirement of N-linked glycosylation for cellulose biosynthesis , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[92]  W. Wolkers,et al.  Isolation and characterization of a D-7 LEA protein from pollen that stabilizes glasses in vitro. , 2001, Biochimica et biophysica acta.

[93]  R. Dixon,et al.  Downregulation of Caffeic Acid 3-O-Methyltransferase and Caffeoyl CoA 3-O-Methyltransferase in Transgenic Alfalfa: Impacts on Lignin Structure and Implications for the Biosynthesis of G and S Lignin , 2001, Plant Cell.

[94]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[95]  C. Chapple,et al.  Modified lignin in tobacco and poplar plants over-expressing the Arabidopsis gene encoding ferulate 5-hydroxylase. , 2000, The Plant journal : for cell and molecular biology.

[96]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[97]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[98]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[99]  V. Hurry,et al.  Effects of a Short-Term Shift to Low Temperature and of Long-Term Cold Hardening on Photosynthesis and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase and Sucrose Phosphate Synthase Activity in Leaves of Winter Rye (Secale cereale L.) , 1994, Plant physiology.

[100]  V. Hurry,et al.  Low-Temperature Effects on Photosynthesis and Correlation with Freezing Tolerance in Spring and Winter Cultivars of Wheat and Rye , 1993, Plant physiology.

[101]  G. Marzluf,et al.  Isolation of nit-4, the minor nitrogen regulatory gene which mediates nitrate induction in Neurospora crassa , 1989, Journal of bacteriology.

[102]  A. A. Hanson,et al.  Alfalfa and Alfalfa Improvement , 1988 .

[103]  G. Bauchan,et al.  The genus Medicago and the origin of the Medicago sativa complex , 1988 .

[104]  C. Vance,et al.  Root Nodule Enzymes of Ammonia Assimilation in Alfalfa (Medicago sativa L.) : DEVELOPMENTAL PATTERNS AND RESPONSE TO APPLIED NITROGEN. , 1981, Plant physiology.

[105]  R. Cooper,et al.  Flower Pigments in Diploid Alfalfa 1 , 1964 .

[106]  D. R. Hoagland,et al.  The Water-Culture Method for Growing Plants Without Soil , 2018 .

[107]  R Fisher,et al.  Design of Experiments , 1936 .

[108]  C. Bonferroni.  Il calcolo delle assicurazioni su gruppi di teste , 1935 .