expressed sequence tags
Summary: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Publications279 found, 100 shown here
- High-throughput functional annotation and data mining with the Blast2GO suiteStefan Götz
Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
Nucleic Acids Res 36:3420-35. 2008..Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data...
- Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencingJ Cristobal Vera
Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
Mol Ecol 17:1636-47. 2008..DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608,053 expressed sequence tags (mean length = 110 nucleotides), which assembled into 48,354 contigs (sets of overlapping DNA segments) ..
- Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTsBastien Chevreux
Department of Molecular Biophysics, German Cancer Research Centre Heidelberg, 69120 Heidelberg, Germany
Genome Res 14:1147-59. 2004....
- High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genomeEvandro Novaes
School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
BMC Genomics 9:312. 2008..However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation...
- The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)G A Tuskan
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Science 313:1596-604. 2006..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
- Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discoveryThomas L Parchman
Department of Botany, University of Wyoming, Laramie, WY 82071, USA
BMC Genomics 11:180. 2010..Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies...
- Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequencesWeizhong Li
Burnham Institute for Medical Research La Jolla, CA 92037, USA
Bioinformatics 22:1658-9. 2006..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
- Genic microsatellite markers in plants: features and applicationsRajeev K Varshney
Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
Trends Biotechnol 23:48-55. 2005..Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed...
- De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesisChao Sun
Institute of Medicinal Plant Development IMPLAD, Chinese Academy of Medical Sciences, Haidian District, Beijing, China
BMC Genomics 11:262. 2010..Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known about ginsenoside biosynthesis in American ginseng, especially the late steps of the pathway...
- TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasetsGeo Pertea
The Institute for Genomic Research, Rockville, MD 20850, USA
Bioinformatics 19:651-2. 2003TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with ..
- Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)T Thiel
Institute of Plant Genetics and Crop Plant Research (IPK, Corrensstrasse 3, D-06466 Gatersleben, Germany
Theor Appl Genet 106:411-22. 2003....
- De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technologyJacob E Crawford
Department of Entomology, Cornell University, Ithaca, New York, United States of America
PLoS ONE 5:e14202. 2010..funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform...
- Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencingWei Wang
Department of Biology and the State Key Lab for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, PR China
BMC Genomics 10:465. 2009..The most prominent anti-malarial drug artemisinin, a sesquiterpene lactone, is produced in glandular trichomes of Artemisia annua. However, only limited genomic information is currently available in this non-model plant species...
- Transcriptome sequencing and comparative analysis of cucumber flowers with different sex typesShaogui Guo
1National Engineering Research Center for Vegetables, Beijing 100097, China
BMC Genomics 11:384. 2010....
- Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis)Omprakash Mittapalli
Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
PLoS ONE 5:e13708. 2010..primarily in the Midwestern United States and Ontario, Canada. However, despite its high impact status little knowledge exists for A. planipennis at the molecular level...
- Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) MaximShaohua Zeng
Key Laboratory of Pant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
BMC Genomics 11:94. 2010..Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum.
- GENCODE: producing a reference annotation for ENCODEJennifer Harrow
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
- Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infectionAbdelali Barakat
The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
BMC Plant Biol 9:51. 2009....
- Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabaseElodie Fleury
UMR M100 Ifremer Université de Caen Basse Normandie Physiologie et Ecophysiologie des Mollusques Marins, Centre de Brest, B, P, 70, 29280 Plouzané IBFA, IFR ICORE 146, Esplanade de la Paix, 14032 Caen Cedex, France
BMC Genomics 10:341. 2009..cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database...
- In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal speciesRajeev K Varshney
Institute of Plant Genetics and Crop Plant Research (IPK, Corrensstrasse 3, D 06466 Gatersleben, Germany
Cell Mol Biol Lett 7:537-46. 2002..sequencing and genomics programmes in various cereal species at different laboratories, a large set of expressed sequence tags (ESTs) is being generated, which can be used to search for microsatellites...
- GMAP: a genomic mapping and alignment program for mRNA and EST sequencesThomas D Wu
Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
Bioinformatics 21:1859-75. 2005....
- Phylogenomics reshuffles the eukaryotic supergroupsFabien Burki
Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland
PLoS ONE 2:e790. 2007..Yet, the composition of these large assemblages and their relationships remain controversial...
- An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)Albert Mascarell-Creus
Molecular Genetics Department, Centre for Research in Agricultural Genomics CRAG CSIC IRTA UAB, Barcelona 08034, Spain
BMC Genomics 10:467. 2009..However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression...
- Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit developmentFiammetta Alagna
CNR Institute of Plant Genetics, Via Madonna Alta 130, 06128 Perugia, Italy
BMC Genomics 10:399. 2009..454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits...
- Gene discovery and annotation using LCM-454 transcriptome sequencingScott J Emrich
Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50010, USA
Genome Res 17:69-73. 2007..We conclude that the coupling of LCM and 454 sequencing technologies facilitates the discovery of rare, possibly cell-type-specific transcripts...
- A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPsWellington Muchero
Departments of Nematology and Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
Proc Natl Acad Sci U S A 106:18159-64. 2009..These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes...
- Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencingMartin Trick
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
Plant Biotechnol J 7:334-46. 2009..of a polyploid crop, and the Solexa sequencing system was used to generate approximately 20 million expressed sequence tags (ESTs) from each of two cultivars: Tapidor and Ningyou 7...
- Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presenceAhmed Moustafa
Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
PLoS ONE 5:e9688. 2010..Here, we used massively parallel signature sequencing (MPSS) to understand global transcriptional regulation patterns in Alexandrium tamarense cultures that were grown under four different conditions...
- Synteny mapping between common bean and soybean reveals extensive blocks of shared lociPhillip E McClean
Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA
BMC Genomics 11:184. 2010..Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species...
- Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralizationCaroline Joubert
Ifremer Laboratoire de Biotechnologie et de Qualité de Perle, Centre Océanologique du Pacifique BP 7004, 98719 Taravao, French Polynesia
BMC Genomics 11:613. 2010..margaritifera, high-throughput Expressed Sequence Tag (EST) pyrosequencing was undertaken on the calcifying mantle, combined with a proteomic analysis of the shell...
- High-density integrated linkage map based on SSR markers in soybeanTae Young Hwang
National Agricultural Research Center for Hokkaido Region, Sapporo, Hokkaido 062 8555, Japan
DNA Res 16:213-25. 2009..8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding...
- Microarray analysis identifies candidate genes for key roles in coral developmentLauretta C Grasso
Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, Australia
BMC Genomics 9:540. 2008....
- Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barleyMauricio La Rota
Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA
BMC Genomics 6:23. 2005..sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.
- EST-SSRs as a resource for population genetic analysesJ R Ellis
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
Heredity (Edinb) 99:125-32. 2007..in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa...
- Quality assessment parameters for EST-derived SNPs from catfishShaolin Wang
The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
BMC Genomics 9:450. 2008..This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs...
- SNP discovery via 454 transcriptome sequencingW Brad Barbazuk
Donald Danforth Plant Science Center, St Louis, MO 63132, USA
Plant J 51:910-8. 2007..These results demonstrate that 454-based transcriptome sequencing is an excellent method for the high-throughput acquisition of gene-associated SNPs...
- An approach to transcriptome analysis of non-model organisms using short-read sequencesLesley J Collins
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Genome Inform 21:3-14. 2008..Our approach demonstrates that transcriptome analysis using high-throughput short-read sequencing need not be restricted to the genomes of model organisms...
- Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)Susan R McCouch
Plant Breeding Dept, Cornell University, Ithaca, NY 14853 1901, USA
DNA Res 9:199-207. 2002..In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb...
- "Stemness": transcriptional profiling of embryonic and adult stem cellsMiguel Ramalho-Santos
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute (HHMI, Harvard University, Cambridge, MA 02138, USA
Science 298:597-600. 2002..to differentiated cell types, stem cells express a significantly higher number of genes (represented by expressed sequence tags) whose functions are unknown...
- Next generation transcriptomes for next generation genomes using est2assemblyAlexie Papanicolaou
Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
BMC Bioinformatics 10:447. 2009..This rapid growth in data has outstripped the ability of researchers working on non-model species to analyze and mine transcriptome data efficiently...
- Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencingJulio C Vega-Arreguín
Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Carretera Irapuato León, Irapuato, Gto, Mexico
BMC Genomics 10:299. 2009..In some cases, deep parallel sequencing of Expressed Sequence Tags (ESTs), although not yet optimized for the sequencing of cDNAs, has represented an efficient procedure ..
- A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traitsFeng Li
Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University, 1 1 Tsutsumidori Amamiyamachi, Aoba, Sendai, Miyagi 981 8555, Japan
DNA Res 16:311-23. 2009..Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits...
- The TIGR Rice Genome Annotation Resource: improvements and new featuresShu Ouyang
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 35:D883-7. 2007..Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads...
- Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatulaCarine Ameline-Torregrosa
Laboratoire des Interactions Plantes Microorganismes, UMR CNRS INRA 442 2594, 31326, Castanet Tolosan, France
Plant Physiol 146:5-21. 2008..This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome...
- Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based databaseFrédéric Beisson
Department of Plant Biology, Michigan State University, East Lansing 48824, USA
Plant Physiol 132:681-97. 2003....
- OrchidBase: a collection of sequences of the transcriptome derived from orchidsChih Hsiung Fu
Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
Plant Cell Physiol 52:238-43. 2011..Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-..
- A high-density transcript linkage map of barley derived from a single populationK Sato
Research Institute for Bioresources, Okayama University, Chuo, Kurashiki, Japan
Heredity (Edinb) 103:110-7. 2009..linkage map of barley was created using a single doubled haploid (DH) mapping population, only 3'-end expressed sequence tags (ESTs) and only PCR-based assays...
- Computational identification of novel microRNAs and targets in Brassica napusFu Liang Xie
Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
FEBS Lett 581:1464-74. 2007..We used previously known miRNAs from Arabidopsis, rice and other plant species against both expressed sequence tags (EST) and genomic survey sequence (GSS) databases to search for potential miRNAs in B. napus...
- Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpisDaniel A Hahn
Department of Entomology and Nematology, The University of Florida, Gainesville, FL 32611 0620, USA
BMC Genomics 10:234. 2009..To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription...
- A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)Rajeev K Varshney
International Crops Research Institute for the Semi Arid Tropics ICRISAT, Patancheru, Greater Hyderabad, AP, India
BMC Genomics 10:523. 2009..This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers.
- QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid speciesJifeng Tang
Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands
BMC Bioinformatics 7:438. 2006..for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures...
- Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defenceY Pauchet
School of Biosciences, University of Exeter, Cornwall Campus, Penryn, UK
Insect Mol Biol 19:61-75. 2010..Following a recent pyrosequencing study generating immune related expressed sequence tags (ESTs), here we use this new technology to define the M. sexta larval midgut transcriptome...
- Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reeseiPamela K Foreman
Genencor International, Inc, Palo Alto, California 94304, USA
J Biol Chem 278:31988-97. 2003..However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction...
- High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technologyDiego Lijavetzky
Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas CSIC, C Darwin 3, 28049 Madrid, Spain
BMC Genomics 8:424. 2007..b>Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative ..
- Conservation and divergence of plant microRNA genesBaohong Zhang
The Institute of Environmental and Human Health (TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409-1163, USA
Plant J 46:243-59. 2006..Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years...
- Identification of soybean microRNAs and their targetsBaohong Zhang
Department of Biology, East Carolina University, Greenville, NC 27858, USA
Planta 229:161-82. 2008....
- Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model speciesDiana Bellin
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
BMC Genomics 10:555. 2009..We describe here an innovative approach for this purpose and demonstrate its potential also for non-model species...
- Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plantsTheresa M Fulton
Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
Plant Cell 14:1457-67. 2002..This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution...
- MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequencesPaola Venier
Department of Biology, University of Padova, Via U Bassi 58 B, Padova, Italy
BMC Genomics 10:72. 2009....
- From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate Amphidinium carteraeTsvetan R Bachvaroff
Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland, United States of America
PLoS ONE 3:e2929. 2008..This combination of features appears to be unique among eukaryotes...
- Insights into corn genes derived from large-scale cDNA sequencingNickolai N Alexandrov
Ceres, Inc, 1535 Rancho Conejo Blvd, Thousand Oaks, CA 91320, USA
Plant Mol Biol 69:179-94. 2009..All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST)...
- Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray designJohn S Ramsey
Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
BMC Genomics 8:423. 2007..However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species...
- A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis)Steven G Ralph
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
BMC Genomics 9:484. 2008..Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome ..
- Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallidaJohn T Jones
Plant Pathology Programme, SCRI, Invergowrie, Dundee DD2 5DA, UK
Mol Plant Pathol 10:815-28. 2009In this article, we describe the analysis of over 9000 expressed sequence tags (ESTs) from cDNA libraries obtained from various life cycle stages of Globodera pallida. We have identified over 50 G...
- Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulationHongmei Luo
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haidian District, Beijing, China
BMC Plant Biol 10:209. 2010..We focused on gene discovery in the areas of bioactive compound biosynthesis and transcriptional regulation as well as genetic marker detection in these species...
- Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridisCécile Sabourault
Universite de Nice Sophia Antipolis, EA4228 ECOMERS, Nice, France
BMC Genomics 10:333. 2009....
- A high density barley microsatellite consensus map with 775 SSR lociR K Varshney
Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Corrensstrasse 3, 06466 Gatersleben, Germany
Theor Appl Genet 114:1091-103. 2007..This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley...
- 'Green revolution' genes encode mutant gibberellin response modulatorsJ Peng
John Innes Centre, Norwich Research Park, UK
Nature 400:256-61. 1999..Transgenic rice plants containing a mutant GAI allele give reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologues could be used to increase yield in a wide range of crop species...
- Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.)I Fernández-Silva
IRTA, Centre de Recerca en Agrigenòmica CSIC IRTA UAB CRAG, Carretera de Cabrils, Km 2, 08348, Cabrils, Barcelona, Spain
Theor Appl Genet 118:139-50. 2008..A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR...
- dCAS: a desktop application for cDNA sequence annotationYongjian Guo
Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology and Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
Bioinformatics 25:1195-6. 2009..Compared with other available tools, dCAS provides a more convenient and user-friendly solution to biologists for extracting biological meaning from sequence data...
- A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genesR Harel-Beja
Department of Vegetable Research, Agricultural Research Organization, Newe Ya ar Research Center, P O Box 1021, Ramat Yishay, 30095, Israel
Theor Appl Genet 121:511-33. 2010..The RI population described here provides a useful resource for further genomics and metabolomics studies in melon, as well as useful markers for breeding for fruit quality...
- LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria)Zongyuan Ma
National Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
BMC Genomics 7:11. 2006..We developed the first transcriptomic database of the locust (LocustDB), building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future...
- Characterization of the soybean genome using EST-derived microsatellite markersHiroshi Hisano
Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
DNA Res 14:271-81. 2007....
- MELOGEN: an EST database for melon functional genomicsDaniel Gonzalez-Ibeas
Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafologia y Biologia Aplicada del Segura CEBAS CSIC, Apdo, correos 164, 30100 Espinardo Murcia, Spain
BMC Genomics 8:306. 2007..up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions.
- Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadenseYu Yu
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
BMC Genomics 12:15. 2011..To construct a genome-wide, functional marker-based genetic linkage map in cotton, we isolated and mapped expressed sequence tag-simple sequence repeats (EST-SSRs) from cotton ESTs derived from the A1, D5, (AD)1, and (AD)2 genome...
- Carbohydrate mobilization and gene regulatory profile in the pseudobulb of Oncidium orchid during the flowering processChih Yu Wang
Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
Planta 227:1063-77. 2008..These results demonstrated a novel functional profile of polysaccharide mobilization pathway as well as their relevant gene expression in the pseudobulb of Oncidium orchid during the flowering process...
- SNP discovery and linkage map construction in cultivated tomatoKenta Shirasawa
Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
DNA Res 17:381-91. 2010..In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato...
- Analysis of organ-specific, expressed genes in Oncidium orchid by subtractive expressed sequence tags libraryJun Tan
Institute of Plant Biology, National Taiwan University, 106, Taipei, Taiwan
Biotechnol Lett 27:1517-28. 2005..In total, 1080 subtractive expressed sequence tags (ESTs) were obtained. Analysis revealed approximately 636 unique gene parts, 120 clusters and 516 singles...
- Development and analysis of EST-SSRs for flax (Linum usitatissimum L.)Sylvie Cloutier
Cereal Research Centre, Agriculture and Agri Food Canada, Winnipeg, MB, Canada
Theor Appl Genet 119:53-63. 2009A set of 146,611 expressed sequence tags (ESTs) were generated from 10 flax cDNA libraries...
- Analysis of expressed sequence tags from a single wheat cultivar facilitates interpretation of tandem mass spectrometry data and discrimination of gamma gliadin proteins that may play different functional roles in flourSusan B Altenbach
USDA ARS Western Regional Research Center, U S Department of Agriculture Agricultural Research Service, 800 Buchanan Street, Albany, CA 94710, USA
BMC Plant Biol 10:7. 2010..The ability to differentiate among the gamma gliadins is important for studies of wheat flour quality because proteins with similar sequences can have different effects on functional properties...
- Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.)David L Joly
Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P, O, Box 10380, Stn, Sainte Foy, Quebec, QC, G1V 4C7, Canada
BMC Genomics 11:422. 2010..Recently, whole genome sequence data has allowed the prediction of secretomes, facilitating the identification of putative effectors...
- Genes expression analyses of sea-island cotton (Gossypium barbadense L.) during fiber developmentLi Li Tu
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
Plant Cell Rep 26:1309-20. 2007..The 887 high-quality expressed sequence tags obtained were assembled into 645 consensus sequences (582 singletons and 63 contigs), of which 455 were ..
- Mining an Ostrinia nubilalis midgut expressed sequence tag (EST) library for candidate genes and single nucleotide polymorphisms (SNPs)B S Coates
USDA ARS, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa 50011, USA
Insect Mol Biol 17:607-20. 2008..nubilalis larval midgut expressed sequence tags (ESTs). Full-length cDNA sequence of 12 putative serine proteinase genes and 3 partial O...
- Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeastsYu Liu
Robert Cedergren Centre, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
Mol Biol Evol 26:27-34. 2009....
- Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarrayKristy B Lidie
Marine Biotoxins Program, NOAA Center for Coastal Environmental and Biomolecular Research, SC 29412, USA
Mar Biotechnol (NY) 7:481-93. 2005..Large-scale sequencing yielded 7001 high-quality expressed sequence tags (ESTs), which clustered into 5280 unique gene groups...
- Parallel evolution of nacre building gene sets in molluscsDaniel J Jackson
School of Biological Sciences, University of Queensland, Brisbane, Australia
Mol Biol Evol 27:591-608. 2010..The expression of novel biomineralizing RLCD proteins in each of these two molluscs and, interestingly, sea urchins suggests that the evolution of such structural proteins has occurred independently multiple times in the Metazoa...
- A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysisIk Young Choi
Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
Genetics 176:685-96. 2007....
- Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cottonZ-G Han
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, 210095 Nanjing, China
Mol Genet Genomics 272:308-27. 2004..genomics to elucidate fiber development and breeding in cotton, we sampled microsatellite sequences from expressed sequence tags (ESTs) transcribed during fiber elongation in the A-genome species Gossypium arboreum to evaluate their ..
- Complementary DNA sequencing and identification of mRNAs from the venomous gland of Agkistrodon piscivorus leucostomaYing Jia
Natural Toxins Research Center, College of Arts and Sciences, Texas A and M University Kingsville, Kingsville, TX 78363, USA
Toxicon 51:1457-66. 2008..a cDNA library from the venom gland of Agkistrodon piscivorus leucostoma for the generation of expressed sequence tags (ESTs) database...
- Gene cataloging and expression profiling in human gastric cancer cells by expressed sequence tagsNam-Soon Kim
Laboratory of Human Genomics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, South Korea
Genomics 83:1024-45. 2004..This comprehensive molecular profiling of human gastric cancer should be useful for elucidating the genetic events associated with human gastric cancer...
- An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invictaJohn Wang
Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
Genome Biol 8:R9. 2007..From a normalized cDNA library we obtained 21,715 ESTs, which represent 11,864 putatively different transcripts with very diverse molecular functions. All ESTs were used to construct a cDNA microarray...
- Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profilingRosanne E Casu
CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia
Plant Mol Biol 54:503-17. 2004....
- Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperdaYouping Deng
Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
BMC Genomics 7:264. 2006..This study reports the results of an expressed sequence tag (EST) sequencing project in cells from the lepidopteran insect S. frugiperda, the fall armyworm...
- cDNA array analysis of Japanese quail lines divergently selected for four-week body weightI W Mott
Department of Genetics, University of Georgia, Athens, Georgia 30602-7223, USA
Poult Sci 83:1524-9. 2004..These limited findings suggest that anonymous cDNA array analysis is a productive means to identify differentially expressed genes in growth-selected poultry...
- Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413Juan Antonio Vizcaino
IBVF CIC Isla de la Cartuja, CSIC Universidad de Sevilla, Avda, Americo Vespucio s n, 41092, Sevilla, Spain
BMC Genomics 7:193. 2006..of this fungus, a functional genomics project called "TrichoEST" was developed to give insights into genes involved in biological control activities using an approach based on the generation of expressed sequence tags (ESTs).
- Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPsNathalie Pavy
Forest Genomics, Pavillon Charles Eugène Marchand, Universite Laval, Ste Foy, Quebec G1K 7P4, Canada
BMC Genomics 7:174. 2006..As a first step toward this goal, we aimed to develop a resource of candidate Single Nucleotide Polymorphisms (SNP) in white spruce (Picea glauca [Moench] Voss), a softwood tree of major economic importance...
- A survey of gene expression and diversity in the venom glands of the pitviper snake Bothrops insularis through the generation of expressed sequence tags (ESTs)Inacio de L M Junqueira-de-Azevedo
Centro de Biotecnologia, Instituto Butantan, Av Vital Brazil, 1500, Sao Paulo, SP 05503 900, Brazil
Gene 299:279-91. 2002..to RNA library from the venom glands of the Viperidae snake Bothrops insularis for the generation of expressed sequence tags (ESTs)...
- Subtractive hybridization reveals the expression of immunoglobulin-like transcript 7, Eph-B1, granzyme B, and 3 novel transcripts in human plasmacytoid dendritic cellsMarie Clotilde Rissoan
Laboratory for Immunological Research, Schering Plough, 27 chemin des Peupliers, BP11, 69571 Dardilly, France
Blood 100:3295-303. 2002..The identification of genes expressed in PDCs provides new insights into their function and origin...
- Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissueTae Hun Kim
Division of Animal Genomics and Bioinformatics, National Livestock Research Institute, Rural Development Administration, Omokchun dong 564, Suwon, Korea
BMC Genomics 7:36. 2006..A combination of quantitative trait locus mapping and microarray analysis is a useful approach to reduce the overall effort needed to identify genes associated with quantitative traits of interest...
- Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variantsGraeme Wistow
Section on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 2740, USA
Mol Vis 8:171-84. 2002..To explore the expression profile of the human lens and to provide a resource for microarray studies, expressed sequence tag (EST) analysis has been performed on cDNA libraries from adult lenses...
- Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epitheliumGraeme Wistow
Section on Molecular Structure and Function, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 2740, USA
Mol Vis 8:185-95. 2002..Expressed sequence tag (EST) analysis of human iris has been performed to explore the repertoire of genes expressed in this tissue...
- Shotgun Sequencing of the Trichomonas Vaginalis GenomeJane Carlton; Fiscal Year: 2003..In addition, we will generate 30,000 Expressed Sequence Tags (ESTs) to aid in gene identification...
- Metabolic Pathways and Defects in Fructose MetabolismDEAN TOLAN; Fiscal Year: 2009..The large database of expressed sequence tags (dbEST) will be analyzed for overlapping expression profiles of the GLUT5, GLUT2, ketohexokinase, ..
- Metabolic Pathways and Defects in Fructose MetabolismDEAN TOLAN; Fiscal Year: 2007..The large database of expressed sequence tags (dbEST) will be analyzed for overlapping expression profiles of the GLUT5, GLUT2, ketohexokinase, ..
- Genetic Heterogeneity and Protein Function in DBAColin Sieff; Fiscal Year: 2003..screen by cytogenetic techniques for deletions and translocations; (2) use cDNA arrays of the genes and expressed sequence tags (ESTs) in the critical region to define candidate genes by examining their pattern of expressed RNAs in ..
- The Tetrahymena Genome ProjectEduardo Orias; Fiscal Year: 2004..4,000 expressed sequence tags (ESTs) will constitute the backbone of the physical map...
- Identification of Metastasis-related Gene in Oral CancerZhuo Chen; Fiscal Year: 2003..The preliminary experiments revealed the existence of several genes and expressed sequence tags whose expressions were significantly altered in the selected metastatic cell lines...
- A GENOMIC APPROACH TO PARASITES FROM THE PHYLUM NEMATODAMakedonka Mitreva; Fiscal Year: 2007..University's Genome Sequencing Center (GSC) has generated and immediately made public over 210,000 expressed sequence tags (ESTs) from 25 nematode species, including representatives of all the major groups of human parasites ..
- CHROMATIN-TELOMERE STRUCTURE AND AT GENOMIC SENSITIVITYTEJ PANDITA; Fiscal Year: 2005..We found six expressed sequence tags aberrantly expressed in Atm null mice as compared to the normal control, and we will characterize them ..
- CHARACTERIZING THE ZEBRAFISH GENOMELeonard Zon; Fiscal Year: 2002..500 expressed sequence tags (ESTs) derived from cDNA libraries of various tissues and developmental stages will be mapped using this ..
- AUTOSOMAL DOMINANT FOCAL SEGMENTAL GLOMERULOSCLEROSISMichelle Winn; Fiscal Year: 2004..PACs and BACs will in turn be used to map expressed sequence tags (ESTs), microsatellites and genes in the MCR...
- EFFECTS OF GENE PATENTS ON GENETIC TESTING AND RESEARCHMildred Cho; Fiscal Year: 2002..Many gene sequences, including expressed sequence tags and single nucleotide polymorphisms are particularly useful for developing predictive or diagnostic tests ..
- Songbird Neurogenomics InitiativeDavid Clayton; Fiscal Year: 2005..a) a collection of cDNA clones representing the mRNAs in the zebra finch brain; b) a database of expressed sequence tags (ESTs) derived by high-throughput sequencing of the collection; c) a web-based publicly accessible server ..
- Resources for Teleost Gene Duplicates and Human DiseaseJOHN HARVEY POSTLETHWAIT; Fiscal Year: 2010..Aim 2 is to construct a resource of expressed sequence tags (ESTs) for gar and to develop bioinformatics that assign ESTs to thousands of markers on the linkage map...
- Comprehensive Assessment of Endocrine Active MixturesTimothy Zacharewski; Fiscal Year: 2003..cDNA clones or expressed sequence tags (ESTs) for the estrogen responsive genes will be used to construct a custom estrogen responsive cDNA/EST ..