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. ncbi 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. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications340 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. ncbi 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. 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
    ....
  6. 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
    ....
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. pmc Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:5654-66. 2003
    ..The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations...
  14. pmc OrfPredictor: predicting protein-coding regions in EST-derived sequences
    Xiang Jia Min
    Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada H4B 1R6
    Nucleic Acids Res 33:W677-80. 2005
    ..OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at https://fungalgenome.concordia.ca/tools/OrfPredictor.html...
  15. ncbi 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...
  16. 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...
  17. 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...
  18. ncbi Microsatellites within genes: structure, function, and evolution
    You Chun Li
    Institute of Evolution, University of Haifa, Haifa, Israel
    Mol Biol Evol 21:991-1007. 2004
    ..Here, we review SSR distributions within expressed sequence tags (ESTs) and genes including protein-coding, 3'-UTRs and 5'-UTRs, and introns; and discuss the consequences ..
  19. 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...
  20. pmc REPuter: the manifold applications of repeat analysis on a genomic scale
    S Kurtz
    Faculty of Technology, University of Bielefeld, PO Box 10 01 31, D 33501 Bielefeld, Germany
    Nucleic Acids Res 29:4633-42. 2001
    ....
  21. 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...
  22. 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...
  23. 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...
  24. ncbi 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
    ....
  25. 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...
  26. ncbi 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...
  27. 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.
  28. pmc AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Universitat Gottingen, Goldschmidtstrasse, 37077 Gottingen, Germany
    Genome Biol 7:S11.1-8. 2006
    ..AUGUSTUS was among the tools that were tested in this project...
  29. ncbi A physical map of the 1-gigabase bread wheat chromosome 3B
    Etienne Paux
    Institut National de la Recherche Agronomique, Université Blaise Pascal INRA UBP, UMR 1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Ferrand, France
    Science 322:101-4. 2008
    ..This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach...
  30. ncbi Identification of soybean microRNAs and their targets
    Baohong Zhang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    Planta 229:161-82. 2008
    ....
  31. 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...
  32. 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...
  33. 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...
  34. pmc Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
    Alekos Athanasiadis
    Department of Biological Sciences, Lehigh University Bethlehem, Pennsylvania, USA
    PLoS Biol 2:e391. 2004
    ..The analysis suggests that modification of repetitive elements is a predominant activity for RNA editing with significant implications for cellular gene expression...
  35. ncbi The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
  36. 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 ..
  37. 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...
  38. 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...
  39. 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...
  40. 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...
  41. 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...
  42. pmc In silico comparative analysis of SSR markers in plants
    Filipe C Victoria
    Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
    BMC Plant Biol 11:15. 2011
    ..New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes...
  43. 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...
  44. 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
    ....
  45. ncbi Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant
    Qin Qin Wang
    Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
    Genomics 96:369-76. 2010
    ..Overall, the deep-sequencing analyses demonstrate the high degree of transcriptional complexity in early developing fibers and represent a major improvement over the microarrays for analyzing transcriptional changes on a large scale...
  46. 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...
  47. 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...
  48. pmc Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV)
    Fujie Zhang
    State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
    BMC Genomics 11:303. 2010
    ..To investigate its transcriptome and determine the differences between viruliferous and naïve L. striatellus, we employed 454-FLX high-throughput pyrosequencing to generate EST databases of this insect...
  49. 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...
  50. 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
    ....
  51. pmc Creating a honey bee consensus gene set
    Christine G Elsik
    Department of Animal Science, Texas A and M University, TAMU, College Station, Texas 77843, USA
    Genome Biol 8:R13. 2007
    ..Second, we wished to provide a single official gene list that the research community could further utilize for consistent and comparable analyses and functional annotation...
  52. 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...
  53. ncbi The molecular ecologist's guide to expressed sequence tags
    Amy Bouck
    Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
    Mol Ecol 16:907-24. 2007
    Genomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene ..
  54. ncbi 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...
  55. ncbi 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 ..
  56. pmc Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
    Guillaume Blanc
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, 2, Ireland
    Plant Cell 16:1667-78. 2004
    ..However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered...
  57. 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
    ....
  58. 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...
  59. 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...
  60. 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...
  61. pmc A white spruce gene catalog for conifer genome analyses
    Philippe Rigault
    Gydle, Inc, Quebec, Canada G1T 1Z2
    Plant Physiol 157:14-28. 2011
    ..b>Expressed sequence tags, mate-pair cDNA clone analysis, and custom sequencing were integrated through an iterative process to ..
  62. ncbi 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, ..
  63. 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...
  64. 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
    ....
  65. 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...
  66. 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...
  67. 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...
  68. 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.
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. pmc A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa
    Hong Kyu Choi
    Department of Plant Pathology, University of California, Davis, California 95616, USA
    Genetics 166:1463-502. 2004
    ..sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map...
  74. pmc Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes
    M Speek
    Center for Gene Technology, Tallinn Technical University, and National Institute of Chemical Physics and Biophysics, Tallinn EE12618, Estonia
    Mol Cell Biol 21:1973-85. 2001
    ..These results indicate that many L1Hs contain active ASPs which are capable of interfering with normal gene expression, and this type of transcriptional control may be widespread...
  75. 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...
  76. 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 ..
  77. pmc Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
    Hugues Richard
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    Nucleic Acids Res 38:e112. 2010
    ..The software is available as an open-source R-package called Solas at http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/...
  78. ncbi 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...
  79. 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 ..
  80. pmc iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
    Yi Zheng
    Department of Ornamental Horticulture, China Agricultural University, Beijing 100094, China
    BMC Bioinformatics 12:453. 2011
    b>Expressed Sequence Tags (ESTs) have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms...
  81. ncbi A draft sequence for the genome of the domesticated silkworm (Bombyx mori)
    Qingyou Xia
    Southwest Agricultural University, Chongqing Beibei, 400716, China
    Science 306:1937-40. 2004
    ..Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content...
  82. pmc A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)
    Doug J Hinchliffe
    USDA ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124, USA
    BMC Genomics 12:445. 2011
    ..In a near-isogenic state with a wild-type cotton line, Li2 is a model system with which to study fiber elongation...
  83. 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...
  84. pmc Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
    Pablo F Cavagnaro
    Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
    BMC Genomics 11:569. 2010
    ..Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber...
  85. ncbi Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro)
    Z M Gao
    International Center for Bamboo and Rattan, State Forestry Administration Key Open Laboratory on Bamboo and Rattan Science and Technology, Beijing, 100102, People s Republic of China
    Plant Cell Rep 30:2045-57. 2011
    ..These results will provide genome-wide knowledge about the molecular physiology of Ma bamboo young leaves and tools for advanced studies of molecular mechanism underlying leaf growth and development...
  86. ncbi Analysis of the transcriptome of the root lesion nematode Pratylenchus coffeae generated by 454 sequencing technology
    Annelies Haegeman
    Ghent University, Department of Molecular Biotechnology, Ghent, Belgium
    Mol Biochem Parasitol 178:7-14. 2011
    ..migratory nematodes by studying the transcriptome of the nematode Pratylenchus coffeae through generating expressed sequence tags (ESTs) on a 454 sequencing platform...
  87. 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
    ....
  88. 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...
  89. ncbi 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...
  90. 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...
  91. ncbi 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...
  92. 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...
  93. 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...
  94. 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...
  95. 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...
  96. 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...
  97. 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
    ....
  98. 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.
  99. 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...
  100. 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
    ....
  101. 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...

Research Grants62

  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. Functional Characterization of CCDC130 Gene
    Deepak Kumar; Fiscal Year: 2012
    ..a novel gene MGC10471/CCDC130, now referred as CCDC130 (NCBI nomenclature), from pancreatic cancer Expressed Sequence Tags (EST) libraries...
  4. Resources for Teleost Gene Duplicates and Human Disease
    JOHN HARVEY POSTLETHWAIT; Fiscal Year: 2011
    ..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...
  5. Resources for Teleost Gene Duplicates and Human Disease
    JOHN HARVEY POSTLETHWAIT; Fiscal Year: 2013
    ..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...
  6. Standardized Next Generation Transcriptome Profiling Tools for X. Tropicalis
    Zhihua Jiang; Fiscal Year: 2013
    ..1) and GenBank databases have over 36,000 mRNA sequences plus 1,271,480 ESTs (expressed sequence tags) available for further gene/transcript annotation and validation...
  7. Research Resources for Model Amphibians
    STEPHEN RANDAL VOSS; Fiscal Year: 2013
    ..be increased by integrating paired-end sequences from fosmids, protein-coding sequences deriving from expressed sequence tags, and markers defining linkage group 3 of the Ambystoma meiotic map...
  8. MicroRNAs and other non-coding RNAs in Colorectal Metastasis
    EDMUND S KOPETZ; Fiscal Year: 2010
    ..First, based on microarray experiments with genome-wide miRNA and expressed sequence tags (ESTs) profiling and on bioinformatics studies, we will develop a large database of miRNAs, ..
  9. Efficient and Sensitive Mining System for G-Protein Coupled Receptors
    Etsuko Moriyama; Fiscal Year: 2009
    ..Finally we will perform actual mining from diverse genomes including underutilized short Expressed Sequence Tags data (Aim 4)...
  10. 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 ..
  11. QTLS UNDERLYING MOLECULAR ACTION OF GENERAL ANESTHETICS
    Thomas Johnson; Fiscal Year: 2000
    ....
  12. GENE DISCOVERY FOR THE KENNY CAFFEY SYNDROME
    Bruce Gelb; Fiscal Year: 2000
    ..smaller-insert genomic clones (PACs and BACs) will be established to facilitate the mapping of STRs and expressed sequence tags (ESTs), as well as the identification of novel genes in the KCS critical region...
  13. 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 ..
  14. 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 ..
  15. 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 ..
  16. Identification of Metastasis-related Gene in Oral Cancer
    Zhuo Chen; Fiscal Year: 2004
    ..The preliminary experiments revealed the existence of several genes and expressed sequence tags whose expressions were significantly altered in the selected metastatic cell lines...
  17. 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 ..
  18. MOLECULAR GENETIC ALTERATIONS OF ENDOMETRIAL CARCINOMA
    LORA ELLENSON; Fiscal Year: 1999
    ..One will rely on routine searching of dbEST (database of Expressed Sequence Tags) with known mismatch repair genes and the other will involve a genetic screen in S...
  19. Tsetse-Trypanosome Interactions
    Serap Aksoy; Fiscal Year: 2009
    ..This exploratory application will study the large expressed sequence tags (ESTs) that have been generated from various tissues of tsetse including midgut, fat body, salivary ..
  20. 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 ..
  21. GLUCOCORTICOID REGULATION OF THYMOCYTE APOPTOSIS
    ROGER MIESFELD; Fiscal Year: 1999
    ..intermediate and late steps in the apoptotic pathway, 2) Characterize a collection of differentially expressed sequence tags (DESTs) previously isolated from dexamethasone-treated WEHI 7...
  22. INACTIVATION PROFILE OF X CHROMOSOME--A GENOMIC STUDY
    HUNTINGTON WILLARD; Fiscal Year: 2002
    ..Our previous work has examined the inactivation status of over 200 X-linked genes and expressed sequence tags (ESTs), has revealed the existence of at least four distinct types, classified according to their ..
  23. Mount Desert Island Biological Laboratory Internet Conn
    John Forrest; Fiscal Year: 2001
    ..bandwidth for rapid uploading of large sequences of DNA, up to 1200 base pairs per sample, including Expressed Sequence Tags, generated by the Marine DNA Sequencing Center...
  24. 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...
  25. DIFFERENTIAL GENE EXPRESSION IN SCLERODERMA FIBROBLASTS
    JOSEPH KORN; Fiscal Year: 2002
    ..We used differential display and hybridization to large arrays of expressed sequence tags to compare gene expression in scleroderma and healthy fibroblasts...
  26. INTEGRATED ZEBRAFISH GENOMIC RESOURCES
    Stephen Johnson; Fiscal Year: 2003
    ..of the zebrafish requires a variety of genetic and genomic resources not yet fully developed, including expressed sequence tags (ESTs), high density genetic and physical, and robust inbred mapping strains...
  27. Mechanisms of RGS Function in Vertebrate Development
    DIANE SLUSARSKI; Fiscal Year: 2005
    ..In zebrafish, the investigators have identified expressed sequence tags encoding all nine members of the R4 subfamily of RGS proteins as well as G-alpha proteins...
  28. NIDDK BIOTECHNOLOGY CENTER
    Towia Libermann; Fiscal Year: 2002
    ..maximally utilize the expression data sets to determine functional dependencies among the known genes and Expressed Sequence Tags (ESTs) and direct further biological validation of these putative dependencies...
  29. INTESTINAL T-REGULATORY-1 CELLS IN MUCOSAL HOMEOSTASIS
    CHARLES ELSON; Fiscal Year: 2006
    ..microarray analysis of highly differentiated and well characterized T cell lines to identify genes or expressed sequence tags distinctive to Tr1 cells vs. other T-cell subsets using...
  30. GENETIC MICROSYSTEMS GMS417 ARRAY SEQUENCER/418 ARRAYER
    Lorraine Flaherty; Fiscal Year: 2000
    ..These include analyzing arrays of mammalian expressed sequence tags (ESTs) to investigate the genetic basis of kidney disease, memory and cerebellar development, identifying ..
  31. Coccidiodes immitis Genome Sequencing Project
    Malcolm Gardner; Fiscal Year: 2002
    ..genome sequence; 3) Mapping of groups of linked contigs to the four chromosomes; 4) Generation of 30,000 Expressed Sequence Tags (ESTs) and a C...
  32. The role of Obox in mammalian oogenesis
    Aleksandar Rajkovic; Fiscal Year: 2005
    ..We utilized in silico subtraction of expressed sequence tags (ESTs) derived from unfertilized egg library to discover a novel family of homeobox genes preferentially ..
  33. CROSS-REFERENCING GENES, GENETICS AND MAMMALIAN GENOMES
    Forrest Spencer; Fiscal Year: 1999
    ..The public database of Expressed Sequence Tags (dbEST) will serve as the source of novel human transcribed sequences that will be searched using model ..
  34. Harvard-Partners Genome Center
    Raju Kucherlapati; Fiscal Year: 2002
    ..We have identified several hundred BAC clones corresponding to mapped expressed sequence tags. These clones or other clones designated by the consortium will be the substrates for sequencing...
  35. ANALYSIS OF GENE EXPRESSION IN AGING DROSOPHILA
    Gregory Gibson; Fiscal Year: 1999
    ..5000 adult expressed sequence tags will be arrayed on glass slides and hybridized to pairs of messenger RNA preparations labeled with two ..
  36. Prediction of Conserved Alternative Splicing Events
    Christopher Burge; Fiscal Year: 2006
    ..conserved AS events, which have so far gone undetected by the standard approach of aligning cDNAs and expressed sequence tags (ESTs) to the genomic sequence...
  37. MOLECULAR ANALYSIS OF THE DEL(20Q) IN MYELOID LEUKEMIAS
    MICHELLE LE BEAU; Fiscal Year: 2003
    ..genes, we will prepare a transcript map of the commonly deleted segment by mapping known genes and expressed sequence tags within the region, and by searching for previously unidentified expressed sequences (Aim 2)...
  38. RETINA SPECIFIC TRANSCRIPT MAP OF THE HUMAN GENOME
    Kim Worley; Fiscal Year: 2001
    Description: (Adapted from the applicant's abstract): Since their conception, expressed sequence tags (ESTs) have increased in number and tissue variety, making them a valuable tool for regional gene cloning, as well as for the global ..
  39. GENE EXPRESSION IN SINGLE, IDENTIFIED CNS CELLS
    Constance Cepko; Fiscal Year: 2001
    ..Similarly, methods exist that might allow the determination of the presence of known genes and expressed sequence tags (ESTs) in such probe preparations...
  40. Prestin in Drosophila sensory systems
    JANICE FRITZ; Fiscal Year: 2004
    ..2) Since there are no mutations, P-element insertions, or expressed sequence tags reported in the dpres gene, targeted homologueous recombination will be used to create a loss of function ..
  41. GENETIC BASIS OF AUTOSOMAL DOMINANT HYPODONTIA
    Pragna Patel; Fiscal Year: 2001
    ..To identity the hypodontia gene, "strong" candidates will be selected from all known genes and expressed sequence tags (ESTs) that map within the candidate interval...
  42. NEW METHODS FOR PRODUCING CHROMOSOME SPECIFIC LIBRARIES
    Michael Lovett; Fiscal Year: 1999
    ..The second issue that this application addresses is the development and mapping of new Expressed Sequence Tags (ESTs)...
  43. IDENTIFYING MAJOR SUSCEPTIBILITY GENES OF IBD
    JUDY CHO; Fiscal Year: 2003
    ..b) Characterizing, through random sequencing, single nucleotide polymorphisms (SNPs) and expressed sequence tags in the region. c) Typing SNPs in Chaldeans and outbred, multiply affected families throughout the region...
  44. GENETICS,MOLECULAR BIOLANDPHARMACOLOGICS--EPILEPSY GENES
    Louis Ptacek; Fiscal Year: 2002
    ..outline in SPECIFIC AIM 2 will provide the foundation for the identification of candidate cDNAs and expressed sequence tags (ESTs) which will ultimately lead to the cloning of the mass1 gene...
  45. CLONING OF A GENE FOR DOMINANT STARGARDT'S DISEASE
    Kang Zhang; Fiscal Year: 2001
    ..Second, search for mutations in the candidate genes and Expressed Sequence Tags (ESTs) in pedigrees linked to STGD3 will be conducted...
  46. Color-coded transposor-mediated rat mutagenesis
    Richard Behringer; Fiscal Year: 2007
    ..ensembl.org/Rattus_norvegjcus) and more than 50,000 expressed sequence tags (ESTs). The rat model system is now primed for functional genomic studies...
  47. MOLECULAR GENETICS OF RETT SYNDROME
    Eric Hoffman; Fiscal Year: 2001
    ..Detailed physical mapping to define physical rearrangements in Xq28 will serve as a basis for testing candidate expressed sequence tags (ESTs) from within the critical region and for eventual gene and protein characterization.
  48. Omentin, A Novel Adipocytokine From Omental Fat Tissue
    Da Wei Gong; Fiscal Year: 2006
    ..to discover novel visceral adipose genes and to better understand fat cell biology, we sequenced 10,411 expressed sequence tags (ESTs) from a human omental fat library...
  49. SECOND GENERATION EST CLUSTER AND ANALYSIS TOOLS
    Todd Smith; Fiscal Year: 1999
    ..Systematic categorization of Expressed Sequence Tags (ESTs) by clustering and annotation play important roles in understanding normal homeostasis and disease ..
  50. The Significance of MARCO Expression by Tumor-Pulsed Dendritic Cells
    JAMES J MULE; Fiscal Year: 2010
    ..DC and TP-DC, using Affymetrix MG- U74Av2 oligonucleotide arrays, which contain ~12,000 genes and ESTs (expressed sequence tags)...
  51. DIFFERENTIAL GENE EXPRESSION BY T CELLS AND THYMOCYTES
    David Lewis; Fiscal Year: 1999
    ..studies will use a specialized gene microarray assay for approximately 11,000 named genes or anonymous expressed sequence tags (ESTs) expressed by human lymphoid cells...
  52. MOLECULAR STUDIES OF ESOPHAGEAL ADENOCARCINOMA
    David Beer; Fiscal Year: 2009
    ..Potential candidates may include known genes, uncharacterized expressed sequence tags, or genes isolated from genomic clones that map within the minimal region...
  53. Regulation of Actin Assembly and Cell Motility by IQGAPs
    GEORGE BLOOM; Fiscal Year: 2009
    ..which is known to exist at the protein level, and IQGAP3, which has been inferred from genomic DNA and expressed sequence tags (ESTs)...
  54. Method to identify the expression profile of antisense gene transcripts
    Paul Siebert; Fiscal Year: 2006
    ..Most of the knowledge of antisense transcripts is derived from in silico analysis of expressed sequence tags and full length transcripts...
  55. MAPPING GENES AND PROMOTERS IN EUCARYOTIC GENOMES
    ALEXANDER KONEV; Fiscal Year: 2003
    ..To date, mapping genes in genomic DNA sequence relies on the sequence data from expressed sequence tags (ESTs). This EST data is highly redundant due to repetitive sequencing of the abundant mRNA species...
  56. MOLECULAR DISSECTION OF ANGIOGENESIS THROUGH GENE DISCOV
    Gilbert Jay; Fiscal Year: 2001
    ..OTI). In this Phase I component, OTI proposes to generate expressed sequence tags (EST's) for 500 genes which are either turned on or turned off at successive stages of blood vessel ..
  57. EST ANALYSIS OF GENE EXPRESSION IN HUMAN ADIPOSE TISSUE
    Da Wei Gong; Fiscal Year: 2001
    ..the Investigator's Abstract): This R21 proposal proposes to systematically sequence 10,000 human adipose expressed sequence tags (ESTs) to 1) obtain a global view of normal adipocyte gene expression, 2) discover novel fat specific or ..
  58. Androgen Signaling in Neoplastic Prostate Growth
    Peter Nelson; Fiscal Year: 2006
    ..abstract_text> ..
  59. SERINE PROTEASES IN PROSTATE CANCER METASTASIS
    Peter Nelson; Fiscal Year: 2002
    ..4) Characterize the role of prostate and TMPRSS2 in prostate cancer bone metastasis using in vitro and in vivo systems. ..
  60. TRANSCRIPTOME ANALYSIS IN NORMAL AND NEOPLASTIC PROSTATE
    Peter Nelson; Fiscal Year: 2002
    ..The accomplishment of these aims will provide a genomics-based resource that defines cell type specific gene expression profiles associated with stages of normal development and neoplastic prostate growth. ..
  61. GENETICS OF PROSTATE CANCER SUSCEPTIBILITY
    Peter Nelson; Fiscal Year: 2005
    ..The resulting data will provide information about the type and distribution of mutations in high-risk families as well as provide useful information for understanding genetic heterogeneity of prostate cancer. ..
  62. Genome Mapping Resources for the Budgerigar
    Edward Smith; Fiscal Year: 2002
    ..abstract_text> ..