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(Click for frequent words.) 65 ESTs 63 microsatellite markers 63 cDNA sequences 62 cDNA libraries 62 intergenic regions 61 cDNA library 61 contigs 61 chloroplast genome 61 quantitative trait loci 60 cDNAs 60 synteny 60 At#g# 60 maize genome 60 transcriptome sequencing 60 Glycine max 59 ribosomal DNA 59 #S rRNA 59 introgression 59 cDNA microarray 59 RefSeq 59 orthologs 59 cytochrome b 58 rRNA 58 transcriptomes 58 QTLs 58 A. thaliana 58 genomic sequence 58 sequence homology 57 BAC clones 57 nucleotide sequences 57 RFLP 57 differentially expressed genes 57 Arabidopsis genome 57 dinucleotide 57 soybean Glycine max 57 TILLING 57 ORFs 57 rDNA 57 quantitative RT PCR 57 Nucleotide 57 MALDI TOF MS 57 ChIP seq 57 genome annotation 56 #S rRNA gene 56 site directed mutagenesis 56 indel 56 5 hmC 56 ChIP chip 56 Phylogenetic analysis 56 mitochondrial gene 56 β galactosidase 56 polyploid 56 Polymorphism 56 Illumina HiSeq 56 metazoan 56 desaturase 56 ortholog 56 splice variants 56 transcriptomic 55 endophytic 55 female gametophyte 55 Phenotypic 55 yeast genome 55 kDa protein 55 immunoblotting 55 ribonucleotide 55 exonuclease 55 metagenome 55 operon 55 Genotypic 55 Cytochrome 55 qRT PCR 55 comparative genomic analysis 55 eukaryotic genomes 55 comparative genomic 55 flow cytometric 55 ChIP Seq 55 Sanger Sequencing 55 homologous sequences 55 miRBase 55 indels 55 centromeric 55 sequenced genomes 55 synthases 55 chromosome #q#.# [002] 55 cellulases 55 paralogs 54 #S rDNA 54 nucleotide sequence 54 linkage disequilibrium LD 54 PFGE 54 transmembrane domain 54 orthologous 54 directed mutagenesis 54 lysates 54 QTL mapping 54 Trichoderma 54 chromatin immunoprecipitation 54 somatic embryogenesis 54 mammalian organisms 54 phylogenetic analyzes 54 RNA sequences 54 phenotypic traits 54 Corynebacterium 54 substrate specificity 54 meganuclease 54 yeast Saccharomyces cerevisiae 54 homologues 54 constitutively expressed 54 quantitative PCR 54 bisulfite sequencing 54 cytosine methylation 54 intronic 54 lysine residues 54 Supplementary Table 53 Deinococcus 53 exon intron 53 tetraploid 53 Fig. 3A 53 Salmonella enterica 53 lysate 53 sequenced genome 53 KIAA# 53 Transcriptome 53 Fig. 2A 53 Brassica juncea 53 plant Arabidopsis thaliana 53 PCR amplification 53 bioinformatic analysis 53 diploid 53 KeyGene 53 differential gene expression 53 operons 53 mRNA encoding 53 oligonucleotide microarrays 53 Fig. 1A 53 plastid 53 Cry1Ab 53 transcriptional profiling 53 bovine genome 53 quantitative PCR qPCR 53 phenotypic variation 53 Haplotype 53 nucleic acid molecules 53 Bayesian inference 53 siRNAs targeting 53 Taq polymerase 53 intergenic 53 carboxy terminal 53 sensu lato 53 Zea mays 53 genes differentially expressed 53 chromatogram 53 Medicago truncatula 53 biochemical assays 53 D. melanogaster 53 UTRs 53 phylogenetically 53 RNA seq 53 RT qPCR 53 hexose 53 chromatin immunoprecipitation ChIP 53 fig. S2 53 N glycans 53 substituents 53 cDNA sequencing 53 Single Nucleotide Polymorphism 53 dbSNP 53 TaqMan Gene Expression Assays 53 fig. S1 53 homologs 52 posttranslational modifications 52 Western blotting 52 kbp 52 Arabidopsis genes 52 proteomic analysis 52 proteomic analyzes 52 ribosomal protein 52 cDNA 52 ncRNA 52 Saccharomyces 52 Solexa sequencing 52 cationic lipid 52 EXZACT Precision Technology 52 fig. S6 52 vertebrate genomes 52 QPCR 52 Gene Ontology terms 52 mRNA transcripts 52 siRNA duplexes 52 transmembrane protein 52 phospholipase 52 nucleotide substitutions 52 Drosophila genome 52 deletion mutant 52 subcellular localization 52 cytotoxicity assays 52 ligand binding 52 Phytophthora sojae 52 methylated DNA 52 Streptomyces 52 disulfide bond 52 galactosidase 52 PCR assay 52 proteolytic cleavage 52 Fig. 2a 52 Illumina Solexa 52 Gene Expression Assays 52 S. Typhimurium 52 immunofluorescent 52 bases adenine 52 amino acid residue 52 sorghum varieties 52 cis regulatory 52 pyrosequencing 52 codon usage 52 tRNA synthetase 52 Proteobacteria 52 peroxidase 52 silico prediction 52 clonally 52 Cry1Ac 52 VNTR 52 N acetyltransferase 52 DNA demethylation 52 B. cereus 52 bioinformatic 52 nucleic acid sequence 52 rhizobia 52 histone H3 52 multiplex assay 52 hydroxyproline 52 phylogenies 52 RRM1 52 Fig. 1D 52 DGGE 52 epidermidis 52 missense mutations 52 acyclic 52 subfamily 52 F. graminearum 52 miRNA assays 52 modified nucleoside 52 homodimer 52 immunoglobulin genes 52 amino acid residues 52 haplogroups 52 cell lysate 52 6S RNA 52 aCGH 52 transgenesis 52 Vitis vinifera 52 PCR primers 52 genotyping arrays 52 Polymorphisms 52 IFN g 52 amino acid substitution 52 carboxyl terminal 52 mRNA sequences 52 oligonucleotide microarray 52 Alu elements 51 S. cerevisiae 51 guanosine 51 cDNA clones 51 E. faecalis 51 histone acetyltransferase 51 phosphoprotein 51 miRNA sequences 51 GenBank accession 51 CpG 51 cytoplasmic domain 51 amine oxidase 51 #S rRNA genes 51 tkRNAi 51 Bacillus subtilis 51 chromatin modification 51 Fig. 2B 51 Aspergillus niger 51 angiosperm 51 SNP Genotyping Assays 51 plastids 51 polyploidy 51 kD 51 radioligand 51 guanine G 51 transferase 51 cytidine 51 Roche GS FLX 51 nucleated cells 51 SDS PAGE 51 RNA polymerases 51 serovar 51 Caenorhabditis 51 isotype 51 Chinese Hamster Ovary 51 gDNA 51 protein biosynthesis 51 chromosome #q# [001] 51 assay detects 51 ciliated 51 virulence genes 51 endonuclease 51 enolase 51 nucleases 51 noncoding 51 insertions deletions 51 insecticidal protein 51 autosomal 51 RNase L 51 haplotype map 51 chimpanzee genomes 51 P2X 51 Microarray analysis 51 BeadChips 51 Haplogroup 51 histone modification 51 cellulase 51 microarray datasets 51 metagenomes 51 benzimidazole 51 forkhead 51 trinucleotide 51 Prevotella 51 alternatively spliced 51 splice junctions 51 Fc receptor 51 haemagglutinin 51 biotinylated 51 EGIR 51 Pichia pastoris 51 Brassica napus 51 Replikins 51 centromeres 51 Agrobacterium 51 bacterial genomes 51 iTRAQ 51 1beta 51 C. albicans 51 EGFP 51 matK 51 Figure 1A 51 S. pombe 51 missense 51 amplicon sequencing 51 lectin 51 Arabidopsis 51 GPx 51 glycolipid 51 eukaryotic organisms 51 beta lactamases 51 transcriptome 51 #p#.# [001] 51 Supplementary Fig 51 Homology 51 Zinc Finger 51 Arabidopsis thaliana 51 tetramers 51 subcellular compartments 51 amino acid substitutions 51 kilobase 51 Xanthomonas 51 cytokine receptor 50 mutational analysis 50 coding sequences 50 Infinium assay 50 Gene Ontology 50 subfamilies 50 Fig. 3d 50 Phylogenetic analyzes 50 PacBio RS 50 GPI anchored 50 cell lysates 50 miRview meso 50 gene expression assays 50 #q#.# [002] 50 glycan structures 50 morphological characteristics 50 untranslated regions 50 humanus 50 plant Arabidopsis 50 N. benthamiana 50 amino acid sequences 50 intermediate filaments 50 GFP fluorescence 50 PAX5 50 glycosylated 50 mitochondrial genomes 50 Histone H3 50 antimicrobial peptide 50 glycan microarray 50 protein quantitation 50 microsatellite loci 50 heterochromatic 50 transgenic traits 50 DNA Polymerase 50 Phenylalanine 50 Phaseolus vulgaris 50 budding yeast 50 Single Nucleotide Polymorphism SNP 50 oligonucleotide probes 50 thymine T 50 Photosystem 50 homologous genes 50 MDRNA proprietary 50 mammalian genomes 50 PBMCs 50 gene deletions 50 cDNA clone 50 phenotypic characteristics 50 genetic loci 50 shRNA libraries 50 FluForecast 50 Saccharomyces cerevisiae 50 multiplexing capability 50 phosphatidylinositol 50 amino terminal 50 glabrata 50 homologies 50 genomewide 50 retrotransposon 50 metazoans 50 Aspergillus nidulans 50 replicon 50 experimentally validated 50 molecular phylogenetic 50 homodimers 50 Drosophila melanogaster 50 Fig. 1b 50 transcriptomics 50 Aspergillus oryzae 50 CCR1 50 ribosomal proteins 50 HybSelect 50 single celled yeast 50 hypervariable 50 Schematic representation 50 DDB1 50 array CGH 50 PKC isoforms 50 Supplementary Figs 50 microbial genome 50 Microarray Analysis 50 Crystallographic 50 deacetylases 50 Transfection 50 ligand induced 50 homolog 50 microdroplet based 50 hybridizations 50 immunofluorescence microscopy 50 SH2 domain 50 Amborella 50 vesicle fusion 50 biotypes 50 pseudogenes 50 HLA DQ 50 metabolomic profiles 50 ultrastructure 50 Sanger sequencing 50 short hairpin RNAs 50 Supplemental Figure 50 Fig. 1E 50 homozygosity 50 pairwise 50 cyclase 50 Htt 50 Figure S4 50 chromosome #q# [002] 50 Sequence Capture 50 rRNA gene 50 RNA helicases 50 globin genes 50 methylation patterns 50 Amino acid 50 Geniom 50 coexpression 49 stilbene 49 MANF 49 reagent kit 49 chemometrics 49 siRNA reagents 49 microbial genomes 49 Bt toxins 49 proteomes 49 fig. S# 49 gene inactivation 49 FTIR spectrometer 49 piggyBac 49 CD1d 49 fungal genomes 49 amplicon 49 potently inhibits 49 decarboxylase 49 tropomyosin 49 ssDNA 49 DiLA2 49 Fig. 3a 49 Sequenced 49 lentiviral 49 phospho 49 logistic regressions 49 ribonucleic acids 49 polynucleotide 49 QTL 49 A. gambiae 49 nucleotide variations 49 IgG1 49 microsomal 49 methyltransferase 49 fig. S3 49 Phylogenetic 49 linkage disequilibrium 49 Dictyostelium 49 tiny roundworm 49 immunoblot 49 isoleucine 49 telomeric 49 wildtype 49 Illumina Infinium 49 MedScan 49 haplotypes 49 sGC 49 comparative genomic hybridization 49 spore formation 49 transmembrane 49 conserved sequences 49 phylogenetic analysis 49 Mammalian Cells 49 C#BL/#J 49 C#BL 6 49 ant genomes 49 aggrecan 49 ZFP TFs 49 P. infestans 49 eukaryote 49 S. enterica 49 phosphorothioate 49 Comparative Genomic Hybridization 49 plasmid DNA vaccine 49 differentially expressed proteins 49 DNase 49 homeobox gene 49 physicochemical properties 49 siRNA knockdown 49 transcriptional activator 49 Spectral Genomics 49 kinase domain 49 transgenic mice expressing 49 HARN 49 miRNA expression 49 Affymetrix microarray technology 49 phenotyping 49 arabinogalactan 49 cRNA 49 serine threonine 49 recombinant antibodies 49 mRNA molecules 49 A. niger 49 Phytophthora species 49 accelerator mass spectrometry 49 HEK# cells 49 Y# [004] 49 archaeal 49 mitochondrial DNA mtDNA 49 DNA ligase 49 LabChip XT 49 inherited maternally 49 primate genomes 49 biosynthetic enzymes 49 Kreatech 49 organism genome 49 peptidome 49 Tribolium 49 chromosome #p# [001] 49 Figure 1C 49 SAXS 49 amino acid alanine 49 hydroxylase 49 homology modeling 49 symbiont 49 epistasis 49 trait locus 49 Genotypes 49 SNP Array #.# 49 defensin 49 Myeloperoxidase 49 morphologically 49 Lentiviral 49 proline 49 de novo sequencing 49 lipoxygenase 49 PCR Arrays 49 CpG island 49 transduced 49 T#M 49 endosymbiont 49 Alkaline Phosphatase 49 Bos taurus 49 multiplex PCR 49 chromosomal DNA 49 gene locus 49 chromatin structure 49 gene expression microarray 49 Pulsed Field 49 VeraCode 49 monophyletic 49 siRNA sequences 49 heritable traits 49 HER2 HER3 49 exon arrays 49 peptide receptor 49 Bacillus thuringiensis bacterium 49 gag pol 49 C#BL 6 mice 49 monomeric 49 NOD mouse 49 vacuolar 49 uracil 49 #S ribosomal RNA 49 massively parallel sequencing 49 COOH terminal 49 gel electrophoresis 49 covalently bound 49 positional cloning 49 array comparative genomic 49 ginsenosides 49 gene loci 49 trophoblast cells 49 coiled coil 49 Sub1 49 Eurofins MWG Operon 49 genomic sequences 49 genotypic 49 PDZ domains 49 TPMT 49 chloroplast 49 enzymatic pathway 49 multiprotein complex 49 ribosomal RNA rRNA 49 PTMs 49 degrading enzymes 49 chick embryo 49 pyrimidine 49 peptide sequences 49 genomic proteomic 49 TIMP 1 49 serine threonine kinase 49 Genome Database 49 proline rich 49 chloroplast DNA 49 Eukaryotic 49 zebrafish Danio rerio 48 Bt genes 48 glutamate transporter 48 SNP Genotyping 48 transcriptional repressor 48 Fig. 4a 48 DNA sequences 48 vitro cytotoxicity 48 rs# [004] 48 virosome technology 48 x ray crystallographic 48 transcriptionally active 48 cM 48 Upregulation 48 H#K# [002] 48 Histone 48 mammalian genome 48 DNA methyltransferases 48 Fig. 1B 48 Xenopus tropicalis 48 HepG2 cells 48 PCR amplified 48 Fig. 2b 48 NanoChip R 48 rice Oryza sativa 48 homology 48 Epitope 48 DNA Methylation 48 transgene expression 48 transfected cells 48 evolutionary conserved 48 C#T [002] 48 previously undescribed 48 CRISPR 48 diamondback moth 48 COL#A# 48 amplicons 48 dependent protein kinase 48 hybridomas 48 Bioinformatic 48 Fig. 3b 48 T. brucei 48 isogenic 48 fig. S4 48 Genome Sequencer FLX System 48 FUS1 48 Nucleic Acids 48 immunostaining 48 Single Nucleotide Polymorphisms SNPs 48 photosystem II 48 phylogenetics 48 splice variant 48 prion strains 48 quasispecies 48 DNA glycosylase 48 Chlamydomonas 48 Apolipoprotein 48 DNA deoxyribonucleic acid 48 immunohistochemical 48 multidomain 48 proteolytic 48 prolyl 48 cDNA synthesis 48 ribonuclease 48 Ribosomal 48 X. laevis 48 metalloprotease 48 NF1 gene 48 SurePrint 48 acid phosphatase 48 M1 muscarinic 48 DNA nanoarrays 48 MPSS 48 Chromera 48 ploidy 48 Xenopus laevis 48 lactase persistence 48 S RNase 48 mammalian proteins 48 5 hydroxymethylcytosine 48 X ray absorption spectroscopy 48 variant rs# 48 heterodimers 48 Cre recombinase 48 MTHFR gene 48 Vps# 48 zebrafish genome 48 Catenin 48 BeadChip 48 replikin 48 immunoreactive 48 BMP2 48 encodes protein 48 phylogeographic 48 Western Blotting 48 miRview mets 48 extracellular domain 48 pyrophosphate 48 reagent kits 48 evolutionarily conserved 48 genome amplification 48 rRNA genes 48 Anticalin ® 48 SOCS3 48 viral nucleic acids 48 BMAL1 48 Microtubule 48 RNA extraction 48 FMR1 48 figs. 48 beta actin 48 chlorophylls 48 Cyclin 48 Green Fluorescent Protein 48 kilobases 48 serum antibodies 48 pharmacophore 48 dioxygenase 48 amyloidogenic 48 supertree 48 metabolome 48 Neandertal DNA 48 mammalian fatty acid 48 hybridoma cells 48 MetaCore TM 48 metabolomic 48 BACcel 48 genes encoding 48 chromosome #q#.# [001] 48 GeneCards R 48 trypanosome 48 Affymetrix GeneChip 48 MaxCyte STX 48 green alga 48 MYBPC3 48 epitope 48 cytochrome c oxidase 48 Gallus gallus 48 polynucleotides 48 Fig. 1c 48 Anopheles gambiae 48 Conserved 48 cyanobacterial 48 genotyping assays 48 bioassays 48 Agilent SureSelect 48 KLF4 48 HumanHap# BeadChip 48 tyrosine phosphorylation 48 homozygote 48 condensin 48 HLA DQ2 48 Cytoplasmic 48 MALDI-TOF/TOF 48 Paleobiology Database 48 protein ligand 48 ICPL 48 polyadenylation 48 glycosylation profile 48 arabidopsis 48 translationally 48 PCR RFLP 48 indirect immunofluorescence 48 Sequence Database 48 short hairpin RNA 48 haploid 48 RNA splicing 48 MTT assay 48 cytochrome 48 synthetase 48 tissue microarrays 48 mitochondrial genome 48 worm C. elegans 48 Sequencing Systems 48 isomerase 48 microarray gene expression 48 biomolecular interactions 48 Hematopoietic 48 soluble proteins 48 Secretase 48 miRNAs miR 48 bioinformatic tools 48 taxa 48 intron 48 striated muscle 48 Homozygous 48 rs# rs# 47 transcriptome analysis 47 transmembrane proteins 47 g mL 47 meganucleases 47 MDR1 47 ,#,# [002] 47 anti miRs 47 DNA methyltransferase 47 protein tyrosine phosphatase 47 promoter methylation 47 SmartChip TM Real 47 gene sequences 47 sequence tags ESTs 47 amino acid sequence 47 Aspergillus flavus 47 Ziplex 47 Tem PCR 47 GeneChip ® 47 http:/www.ncbi.nlm.nih.gov/pubmed/# 47 ERK1 2 47 subnetworks 47 heterozygotes 47 E1A 47 lymphoid cells 47 Annexin V 47 Xceed Molecular 47 Fig. 1d 47 landraces 47 P. gingivalis 47 prokaryotic 47 Mycoplasma genitalium 47 genomically 47 glutamine synthetase 47 lacZ 47 outer membrane proteins 47 multiplexed assay 47 transcriptional activity 47 nematode species 47 clonal 47 histone acetylation 47 TUNEL 47 CIDR 47 immunoregulatory 47 segmental duplications 47 genetically modified herbicide tolerant 47 effector proteins 47 TMPRSS2 ERG 47 mRNA expression 47 anti CD# antibodies 47 immunoprecipitation 47 #S proteasome 47 paraffin embedded tissue 47 ERK signaling 47 SNP genotyping 47 Axiom Genotyping Solution 47 Replikins Ltd. 47 Quantitative RT PCR 47 centromere 47 CHO K1 47 transferrin receptor 47 transcriptional profiles 47 PDZ domain 47 p# MAPK 47 transmembrane domains 47 PDGF B 47 cellTRAY 47 phylogenetic 47 virus AAV 47 Affymetrix GeneChip ® 47 mRNA Seq 47 ribonucleic acid RNA 47 DLC1 47 fruitfly Drosophila 47 protein translocation 47 bacterial chromosome 47 maternally inherited 47 RNA binding 47 brucei 47 EMBL scientists 47 L. pneumophila 47 chromatin remodeling complex 47 Resequencing 47 whole genome genotyping 47 variogram 47 SNP arrays 47 cathepsin B 47 transcriptome profiling 47 TMPRSS2 ERG fusion 47 nucleotide bases 47 Eukaryotes 47 unmutated 47 subtilis 47 phytate 47 International HapMap Project 47 ABL1 47 EF Tu 47 Xenopus 47 GenBank database 47 nitrogenase 47 H#K# [001] 47 Next Generation Sequencing NGS 47 MALAT1 47 eukaryotic algae 47 adduct 47 cytokeratin 47 annotation 47 fucose 47 sphingolipid 47 Mutation Analysis 47 disulfide 47 M. anisopliae 47 transcriptional regulation 47 unmethylated 47 Illumina sequencing 47 GeneSifter 47 RecA 47 extracellular proteins 47 μ opioid receptor 47 Polymerase 47 synthetic peptides 47 β1 47 Ice COLD PCR 47 PON1 gene 47 genomic DNA 47 nodulation 47 allelic 47 cytokine receptors 47 1alpha 47 chordates 47 #S subunit 47 Immunohistochemical staining 47 supernatants 47 fucoidan 47 extracellular domains 47 situ hybridisation 47 protein phosphorylation 47 genomic loci 47 diploid genome 47 distinct lineages 47 E#/E# [001] 47 Cytogenetic 47 clades 47 genomic variation 47 t# c# CLA 47 capsular polysaccharide 47 recombinantly 47 telomere DNA 47 nucleolar 47 Argonaute 47 F actin 47 antiparallel 47 replicase 47 immunofluorescence 47 thymidine kinase 47 NS5B 47 bioactivity 47 noncoding RNAs 47 peptide fragments 47 eIF2 47 nCounter Analysis System 47 coding exons