expressed sequence tags

Summary

Summary: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.

Top Publications

  1. pmc High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan Götz
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Nucleic Acids Res 36:3420-35. 2008
  2. pmc Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    Bastien Chevreux
    Department of Molecular Biophysics, German Cancer Research Centre Heidelberg, 69120 Heidelberg, Germany
    Genome Res 14:1147-59. 2004
  3. doi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J Cristobal Vera
    Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 17:1636-47. 2008
  4. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
  5. pmc Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    Thomas L Parchman
    Department of Botany, University of Wyoming, Laramie, WY 82071, USA
    BMC Genomics 11:180. 2010
  6. pmc High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
    Evandro Novaes
    School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
    BMC Genomics 9:312. 2008
  7. pmc Comparing de novo assemblers for 454 transcriptome data
    Sujai Kumar
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    BMC Genomics 11:571. 2010
  8. ncbi 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
  9. ncbi 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
  10. ncbi Conservation and divergence of plant microRNA genes
    Baohong 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

Detail Information

Publications313 found, 100 shown here

  1. pmc High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan 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...
  2. pmc Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
    Bastien Chevreux
    Department of Molecular Biophysics, German Cancer Research Centre Heidelberg, 69120 Heidelberg, Germany
    Genome Res 14:1147-59. 2004
    ....
  3. doi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J 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) ..
  4. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    TGICL 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 ..
  5. pmc Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    Thomas 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...
  6. pmc High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
    Evandro 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...
  7. pmc Comparing de novo assemblers for 454 transcriptome data
    Sujai Kumar
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    BMC Genomics 11:571. 2010
    ..We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis...
  8. ncbi 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...
  9. ncbi 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
    ....
  10. ncbi Conservation and divergence of plant microRNA genes
    Baohong 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...
  11. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong 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...
  12. pmc De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology
    Jacob 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...
  13. pmc De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity
    Massimo Iorizzo
    Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
    BMC Genomics 12:389. 2011
    ..The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms...
  14. pmc Transcriptomics of the bed bug (Cimex lectularius)
    Xiaodong Bai
    Department of Entomology, Ohio Agricultural and Research Development Center, The Ohio State University, Wooster, Ohio, United States of America
    PLoS ONE 6:e16336. 2011
    ..lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance...
  15. pmc Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers
    Wenliang Wei
    Key Laboratory of Oil Crops Biology of the Ministry of Agriculture, Sesame Germplasm and Genetic Breeding Laboratory, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences OCRI CAAS, Wuhan, 430062, China
    BMC Genomics 12:451. 2011
    ..High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development...
  16. doi Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
    Martin 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...
  17. doi Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    Mario Stanke
    Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Bioinformatics 24:637-44. 2008
    ..For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes...
  18. doi Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)
    Alexandra M Allen
    School of Biological Sciences, University of Bristol, Bristol, UK
    Plant Biotechnol J 9:1086-99. 2011
    ..To mine selected elite wheat germplasm for intervarietal single-nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next-generation sequencing of normalized wheat ..
  19. ncbi 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...
  20. doi Stem cell transcriptome profiling via massive-scale mRNA sequencing
    Nicole Cloonan
    Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Queensland, 4072, Australia
    Nat Methods 5:613-9. 2008
    ....
  21. ncbi GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
    ....
  22. doi Identification of soybean microRNAs and their targets
    Baohong Zhang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    Planta 229:161-82. 2008
    ....
  23. pmc Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
    Vardges Ter-Hovhannisyan
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Genome Res 18:1979-90. 2008
    ..By eliminating the effort necessary to build comprehensive training sets, the new algorithm can streamline and accelerate the process of annotation in a large number of fungal genome sequencing projects...
  24. pmc Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development
    Fiammetta 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...
  25. pmc Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
    L Duret
    Laboratoire de Biometrie, Génétique et Biologie des Populations, Unité Mixte de Recherche Centre National de la Recherche Scientifique 5558, Villeurbanne Cedex, France
    Proc Natl Acad Sci U S A 96:4482-7. 1999
    ..This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms...
  26. pmc Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
    Wei 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...
  27. doi Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
    K R Elmer
    Department of Biology, University of Konstanz, Germany
    Mol Ecol 19:197-211. 2010
    ..next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, ..
  28. pmc Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection
    Abdelali 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
    ....
  29. ncbi Identification and characterization of new plant microRNAs using EST analysis
    Bao Hong Zhang
    The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Cell Res 15:336-60. 2005
    ..A total of 18,694 plant expressed sequence tags (EST) were found in the GenBank EST databases by comparing all previously known Arabidopsis miRNAs to ..
  30. pmc Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches
    Mohamed Salem
    Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
    BMC Genomics 11:564. 2010
    ..Although a large number (258,973) of EST sequences are publicly available, the nature of rainbow trout duplicated genome hinders assembly and complicates annotation...
  31. pmc Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula
    Carine 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...
  32. ncbi Multiple sequence alignment using partial order graphs
    Christopher Lee
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 18:452-64. 2002
    ..Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts...
  33. ncbi Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
    B C Meyers
    Department of Vegetable Crops, University of California, Davis 95616, USA
    Plant J 20:317-32. 1999
    ..Sequence inferences suggest that these genes encode a novel class of nucleotide-binding proteins...
  34. pmc Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery
    Sukhjiwan Kaur
    Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Australia
    BMC Genomics 12:265. 2011
    ..There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality...
  35. ncbi Genic microsatellite markers in plants: features and applications
    Rajeev 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...
  36. pmc Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
    Shaogui Guo
    1National Engineering Research Center for Vegetables, Beijing 100097, China
    BMC Genomics 11:384. 2010
    ....
  37. pmc Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome
    Yuepeng Han
    Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, 430074, PR China
    J Exp Bot 62:5117-30. 2011
    ..These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple...
  38. pmc SNP discovery and linkage map construction in cultivated tomato
    Kenta 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...
  39. pmc Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim
    Shaohua 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.
  40. pmc GENCODE: producing a reference annotation for ENCODE
    Jennifer 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...
  41. pmc High-density integrated linkage map based on SSR markers in soybean
    Tae 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...
  42. pmc A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs
    Wellington 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...
  43. ncbi An approach to transcriptome analysis of non-model organisms using short-read sequences
    Lesley 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...
  44. pmc Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa
    Pavana J Hiremath
    International Crops Research Institute for the Semi Arid Tropics ICRISAT, Patancheru, India
    Plant Biotechnol J 9:922-31. 2011
    ..tentative unique sequences (TUSs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49,437 (47...
  45. pmc Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning
    Fabienne Bourgis
    Université de Bordeaux Ségalen, Laboratoire de Biogenese Membranaire, Bordeaux, France
    Proc Natl Acad Sci U S A 108:12527-32. 2011
    ....
  46. pmc Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak
    Saneyoshi Ueno
    INRA, UMR 1202 BIOGECO, 69 route d Arcachon, F 33612 Cestas, France
    BMC Genomics 11:650. 2010
    ....
  47. pmc 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...
  48. pmc Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase
    Elodie 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...
  49. ncbi In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species
    Rajeev 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...
  50. pmc A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis
    Ik Young Choi
    Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
    Genetics 176:685-96. 2007
    ....
  51. ncbi Computational identification of novel microRNAs and targets in Brassica napus
    Fu 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...
  52. pmc Phylogenomics reshuffles the eukaryotic supergroups
    Fabien 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...
  53. pmc A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome
    Yanbin Hong
    Guangdong Academy of Agricultural Sciences, Crops Research Institute, Guangzhou, PR China
    BMC Plant Biol 10:17. 2010
    ..was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank.
  54. pmc Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce
    Marie Claire Namroud
    Canada Research Chair in Forest and Environmental Genomics and Arborea, Forest Research Centre, Pavillon Charles Eugène Marchand, Universite Laval, Quebec, Quebec, CanadaP4
    Mol Ecol 17:3599-613. 2008
    ..The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels...
  55. ncbi Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei
    Pamela 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...
  56. pmc 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...
  57. pmc Gene discovery and annotation using LCM-454 transcriptome sequencing
    Scott 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...
  58. doi Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow
    Jochen B W Wolf
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plon, Germany
    Mol Ecol 19:162-75. 2010
    ..These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence...
  59. ncbi Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula
    Par K Ingvarsson
    Umea Plant Science Centre, Department of Ecology and Environmental Science, Umea University, Umea, Sweden
    Mol Biol Evol 24:836-44. 2007
    ..Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels ..
  60. pmc GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data
    Sook Jung
    Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164 6414, USA
    Nucleic Acids Res 36:D1034-40. 2008
    ..GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org...
  61. doi 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. 2009
    A set of 146,611 expressed sequence tags (ESTs) were generated from 10 flax cDNA libraries...
  62. pmc De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis
    Chao 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...
  63. pmc The odorant binding protein gene family from the genome of silkworm, Bombyx mori
    Da Ping Gong
    The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing, PR China
    BMC Genomics 10:332. 2009
    ..Insect chemoreception is mediated by two large and diverse gene superfamilies, chemoreceptors and odorant binding proteins (OBPs). OBPs are believed to transport hydrophobic odorants from the environment to the olfactory receptors...
  64. pmc Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids
    Yu Yun Hsiao
    Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
    BMC Genomics 12:360. 2011
    ..We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome...
  65. pmc An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research
    Fabrice Legeai
    1IRISA, Equipe Symbiose, Campus Universitaire de Beaulieu, 35042 Rennes Cedex, France
    BMC Genomics 12:86. 2011
    ..Here, we describe an Expressed Sequence Tag (EST) project to characterize the antennal transcriptome of the noctuid pest model, Spodoptera littoralis, and to identify candidate genes involved in odour/pheromone detection...
  66. pmc Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology
    Rebekah E Oliver
    USDA ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA
    BMC Genomics 12:77. 2011
    ....
  67. pmc Gene expression analysis of flax seed development
    Prakash Venglat
    Plant Biotechnology Institute, NRC, 110 Gymnasium Place, Saskatoon, Saskatchewan, S7N 0W9, Canada
    BMC Plant Biol 11:74. 2011
    ..Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed...
  68. doi Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68
    Fu hao Lu
    Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340 802, Republic of Korea
    Mol Biol Rep 39:3327-35. 2012
    ..The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research...
  69. pmc Comparative gene expression analysis of susceptible and resistant near-isogenic lines in common wheat infected by Puccinia triticina
    Alagu Manickavelu
    Kihara Institute for Biological Research, Yokohama City University, Yokohama 244 0813, Japan
    DNA Res 17:211-22. 2010
    ..The molecular pathogenicity of leaf rust in wheat was studied and the EST data generated made a foundation for future studies...
  70. pmc Synteny mapping between common bean and soybean reveals extensive blocks of shared loci
    Phillip 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...
  71. pmc Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization
    Caroline 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...
  72. pmc A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome
    Marcio C Moretzsohn
    EMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF, Brazil
    BMC Plant Biol 9:40. 2009
    ..This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability...
  73. pmc 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 database
    Frédéric Beisson
    Department of Plant Biology, Michigan State University, East Lansing 48824, USA
    Plant Physiol 132:681-97. 2003
    ....
  74. ncbi EST-SSRs as a resource for population genetic analyses
    J 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...
  75. pmc Microarray analysis identifies candidate genes for key roles in coral development
    Lauretta C Grasso
    Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, Australia
    BMC Genomics 9:540. 2008
    ....
  76. pmc Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
    Mauricio 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.
  77. pmc High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus
    Raul Bettencourt
    Department of Oceanography and Fisheries, University of the Azores, 9901 861 Horta, Portugal
    BMC Genomics 11:559. 2010
    ....
  78. pmc Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence
    Ahmed 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...
  79. doi Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae
    J S Ramsey
    Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
    Insect Mol Biol 19:155-64. 2010
    ..However, given the incomplete M. persicae cDNA data set, the number of identified detoxification genes in this species is likely to be an underestimate...
  80. pmc SNP discovery via 454 transcriptome sequencing
    W 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...
  81. ncbi "Stemness": transcriptional profiling of embryonic and adult stem cells
    Miguel 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...
  82. pmc Quality assessment parameters for EST-derived SNPs from catfish
    Shaolin 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...
  83. pmc A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits
    Feng 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...
  84. pmc Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing
    Julio 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 ..
  85. pmc Next generation transcriptomes for next generation genomes using est2assembly
    Alexie 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...
  86. pmc The TIGR Rice Genome Annotation Resource: improvements and new features
    Shu 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...
  87. doi A high-density transcript linkage map of barley derived from a single population
    K 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...
  88. pmc Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis
    Daniel 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...
  89. doi OrchidBase: a collection of sequences of the transcriptome derived from orchids
    Chih 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-..
  90. pmc 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.
  91. doi Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence
    Y 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...
  92. pmc Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
    Theresa 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...
  93. pmc High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology
    Diego 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 ..
  94. pmc Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species
    Diana 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...
  95. pmc MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences
    Paola Venier
    Department of Biology, University of Padova, Via U Bassi 58 B, Padova, Italy
    BMC Genomics 10:72. 2009
    ....
  96. pmc QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species
    Jifeng 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...
  97. pmc From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate Amphidinium carterae
    Tsvetan 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...
  98. pmc Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design
    John 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...
  99. pmc Insights into corn genes derived from large-scale cDNA sequencing
    Nickolai 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)...
  100. pmc 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 ..
  101. doi Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida
    John T Jones
    Plant Pathology Programme, SCRI, Invergowrie, Dundee DD2 5DA, UK
    Mol Plant Pathol 10:815-28. 2009
    In 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...

Research Grants69

  1. Shotgun Sequencing of the Trichomonas Vaginalis Genome
    Jane Carlton; Fiscal Year: 2003
    ..In addition, we will generate 30,000 Expressed Sequence Tags (ESTs) to aid in gene identification...
  2. Metabolic Pathways and Defects in Fructose Metabolism
    DEAN TOLAN; Fiscal Year: 2009
    ..The large database of expressed sequence tags (dbEST) will be analyzed for overlapping expression profiles of the GLUT5, GLUT2, ketohexokinase, ..
  3. Metabolic Pathways and Defects in Fructose Metabolism
    DEAN TOLAN; Fiscal Year: 2007
    ..The large database of expressed sequence tags (dbEST) will be analyzed for overlapping expression profiles of the GLUT5, GLUT2, ketohexokinase, ..
  4. Genetic Heterogeneity and Protein Function in DBA
    Colin 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 ..
  5. The Tetrahymena Genome Project
    Eduardo Orias; Fiscal Year: 2004
    ..4,000 expressed sequence tags (ESTs) will constitute the backbone of the physical map...
  6. A GENOMIC APPROACH TO PARASITES FROM THE PHYLUM NEMATODA
    Makedonka 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 ..
  7. CHROMATIN-TELOMERE STRUCTURE AND AT GENOMIC SENSITIVITY
    TEJ 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 ..
  8. CHARACTERIZING THE ZEBRAFISH GENOME
    Leonard Zon; Fiscal Year: 2002
    ..500 expressed sequence tags (ESTs) derived from cDNA libraries of various tissues and developmental stages will be mapped using this ..
  9. AUTOSOMAL DOMINANT FOCAL SEGMENTAL GLOMERULOSCLEROSIS
    Michelle Winn; Fiscal Year: 2004
    ..PACs and BACs will in turn be used to map expressed sequence tags (ESTs), microsatellites and genes in the MCR...
  10. Identification of Metastasis-related Gene in Oral Cancer
    Zhuo 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...
  11. EFFECTS OF GENE PATENTS ON GENETIC TESTING AND RESEARCH
    Mildred Cho; Fiscal Year: 2002
    ..Many gene sequences, including expressed sequence tags and single nucleotide polymorphisms are particularly useful for developing predictive or diagnostic tests ..
  12. Resources for Teleost Gene Duplicates and Human Disease
    JOHN 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...
  13. Songbird Neurogenomics Initiative
    David 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 ..
  14. Comprehensive Assessment of Endocrine Active Mixtures
    Timothy 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 ..