gene library

Summary

Summary: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.

Top Publications

  1. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
  2. pmc Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    Eli Meyer
    University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    BMC Genomics 10:219. 2009
  3. 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
  4. pmc Comprehensive comparative analysis of strand-specific RNA sequencing methods
    Joshua Z Levin
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 7:709-15. 2010
  5. pmc Comprehensive transposon mutant library of Pseudomonas aeruginosa
    Michael A Jacobs
    Department of Medicine, University of Washington Genome Center, Box 352145, Seattle, WA 98195 2145, USA
    Proc Natl Acad Sci U S A 100:14339-44. 2003
  6. pmc Transcriptome analysis of the brown planthopper Nilaparvata lugens
    Jian Xue
    Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, Institute of Insect Science, Zhejiang University, Hangzhou, China
    PLoS ONE 5:e14233. 2010
  7. ncbi Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
    Vitantonio Pantaleo
    Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
    Plant J 62:960-76. 2010
  8. pmc Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing
    Qing Xin Song
    State Key Laboratory of Plant Genomics, Genome Biology Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
    BMC Plant Biol 11:5. 2011
  9. pmc Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:291-5. 2009
  10. ncbi An extensive class of small RNAs in Caenorhabditis elegans
    R C Lee
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Science 294:862-4. 2001

Research Grants

Detail Information

Publications284 found, 100 shown here

  1. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
    ..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
  2. pmc Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    Eli Meyer
    University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    BMC Genomics 10:219. 2009
    ..We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora...
  3. 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...
  4. pmc Comprehensive comparative analysis of strand-specific RNA sequencing methods
    Joshua Z Levin
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
    Nat Methods 7:709-15. 2010
    ..Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms...
  5. pmc Comprehensive transposon mutant library of Pseudomonas aeruginosa
    Michael A Jacobs
    Department of Medicine, University of Washington Genome Center, Box 352145, Seattle, WA 98195 2145, USA
    Proc Natl Acad Sci U S A 100:14339-44. 2003
    ..The transposons used to generate the mutant collection have added features that should facilitate downstream studies of gene expression, protein localization, epistasis, and chromosome engineering...
  6. pmc Transcriptome analysis of the brown planthopper Nilaparvata lugens
    Jian Xue
    Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, Institute of Insect Science, Zhejiang University, Hangzhou, China
    PLoS ONE 5:e14233. 2010
    ..Genomic information for BPH is currently unavailable, and, therefore, transcriptome and expression profiling data for this species are needed as an important resource to better understand the biological mechanisms of BPH...
  7. ncbi Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
    Vitantonio Pantaleo
    Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
    Plant J 62:960-76. 2010
    ..Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs...
  8. pmc Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing
    Qing Xin Song
    State Key Laboratory of Plant Genomics, Genome Biology Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
    BMC Plant Biol 11:5. 2011
    ....
  9. pmc Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:291-5. 2009
    ..We illustrate this by generating and analyzing DNA sequences from extremely (G+C)-poor (Plasmodium falciparum), (G+C)-neutral (Escherichia coli) and (G+C)-rich (Bordetella pertussis) genomes...
  10. ncbi An extensive class of small RNAs in Caenorhabditis elegans
    R C Lee
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Science 294:862-4. 2001
    ..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse...
  11. pmc Simple cDNA normalization using kamchatka crab duplex-specific nuclease
    Pavel A Zhulidov
    Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho Maklaya 16 10, 117871 Moscow, Russia
    Nucleic Acids Res 32:e37. 2004
    ..We also employed DSN normalization to normalize cDNA from nervous tissues of the marine mollusc Aplysia californica (a popular model organism in neuroscience) to illustrate further the efficiency of the normalization technique...
  12. ncbi Transcriptome-wide identification of microRNA targets in rice
    Yong Fang Li
    Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
    Plant J 62:742-59. 2010
    ..A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants...
  13. ncbi Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
    Marcelo A German
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Nat Biotechnol 26:941-6. 2008
    ..This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs...
  14. pmc Targeted capture and massively parallel sequencing of 12 human exomes
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 461:272-6. 2009
    ..This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact...
  15. ncbi Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction
    Y Y Zhu
    CLONTECH Laboratories, Palo Alto, CA, USA
    Biotechniques 30:892-7. 2001
    ..cDNA libraries generated using this method will be useful for accelerating the collection of mRNA 5' end sequence information, which is currently very limited in GenBank...
  16. pmc Identification of Birds through DNA Barcodes
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, Ontario, Canada
    PLoS Biol 2:e312. 2004
    ..The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens...
  17. pmc A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    Ramya Rajagopalan
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 20:3407-25. 2006
    ....
  18. pmc High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
    Gyorgy Szittya
    School of Biological Sciences, University of East Anglia, Norwich, UK
    BMC Genomics 9:593. 2008
    ..High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula)...
  19. pmc Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development
    Guru Jagadeeswaran
    Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
    BMC Genomics 11:52. 2010
    ..Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs...
  20. 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
    ....
  21. pmc Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
    José Blanca
    Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia COMAV UPV, Camino de Vera s n, 46022 Valencia, Spain
    BMC Genomics 12:104. 2011
    ..However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding...
  22. 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...
  23. pmc Whole exome capture in solution with 3 Gbp of data
    Matthew N Bainbridge
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Genome Biol 11:R62. 2010
    ....
  24. pmc Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing
    Markus Hafner
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
    Methods 44:3-12. 2008
    ..This protocol includes the use of new deep sequencing methods (454/Roche and Solexa) to facilitate the characterization of diverse sequence pools of small RNAs...
  25. pmc Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)
    Roy R Chaudhuri
    Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
    BMC Genomics 10:291. 2009
    ..An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth...
  26. pmc Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
    Patrick D Schloss
    Department of Plant Pathology, University of Wisconsin Madison, 1630 Linden Dr, Madison, WI 53706, USA
    Appl Environ Microbiol 71:1501-6. 2005
    ..We anticipate that an equivalent extent of sampling for soil would require sampling more than 10,000 sequences, almost 100 times the size of typical sequence collections obtained from soil...
  27. pmc Novel and nodulation-regulated microRNAs in soybean roots
    Senthil Subramanian
    Donald Danforth Plant Science Center, 975 N Warson Road, St Louis, MO 63132, USA
    BMC Genomics 9:160. 2008
    ..g. soybean) and rhizobia bacteria (e.g. Bradyrhizobium japonicum) results in root nodules where the majority of biological nitrogen fixation occurs. We sought to identify microRNAs (miRNAs) regulated during soybean-B. japonicum symbiosis...
  28. ncbi Metagenomics: genomic analysis of microbial communities
    Christian S Riesenfeld
    Department of Plant Pathology, University of Wisconsin Madison, Wisconsin 53706, USA
    Annu Rev Genet 38:525-52. 2004
    ..This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses...
  29. 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...
  30. pmc New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, P O Box 915, Cardiff CF10 3TL, United Kingdom
    Appl Environ Microbiol 72:5734-41. 2006
    ..Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/...
  31. pmc MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries
    Merav Bar
    Divisions of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Stem Cells 26:2496-505. 2008
    ..Disclosure of potential conflicts of interest is found at the end of this article...
  32. 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...
  33. pmc Comparison of next generation sequencing technologies for transcriptome characterization
    P Kerr Wall
    Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
    BMC Genomics 10:347. 2009
    ..19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis...
  34. pmc Tuning genetic control through promoter engineering
    Hal Alper
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 102:12678-83. 2005
    ....
  35. pmc BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals
    Ina Poser
    Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D 01307 Dresden, Germany
    Nat Methods 5:409-15. 2008
    ..The same high-throughput approach will be generally applicable to other model systems...
  36. pmc A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
    Sheila Fisher
    Genome Sequencing Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
    Genome Biol 12:R1. 2011
    ..Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol...
  37. 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
    ....
  38. pmc Identification and characterization of novel amphioxus microRNAs by Solexa sequencing
    Xi Chen
    Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Hankou Road, Nanjing, Jiangsu 210093, PR China
    Genome Biol 10:R78. 2009
    ..While the number of known human and murine miRNAs is continuously increasing, information regarding miRNAs from other species such as amphioxus remains limited...
  39. pmc Hidden layers of human small RNAs
    Hideya Kawaji
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    BMC Genomics 9:157. 2008
    ....
  40. pmc Transposase mediated construction of RNA-seq libraries
    Jason Gertz
    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
    Genome Res 22:134-41. 2012
    ..Our results show that high-quality RNA-seq libraries can be constructed efficiently and in an automatable fashion using transposition technology...
  41. pmc Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology
    Jiao Wu
    College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
    BMC Plant Biol 10:234. 2010
    ..cv. Zuoshan-1. Our goal is to identify genes that are involved in resistance to grape DM disease...
  42. pmc Mechanism of chimera formation during the Multiple Displacement Amplification reaction
    Roger S Lasken
    J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Biotechnol 7:19. 2007
    ..Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them...
  43. 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
    ..We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible...
  44. pmc High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing
    Hideo Matsumura
    Iwate Biotechnology Research Center, Kitakami, Japan
    PLoS ONE 5:e12010. 2010
    ....
  45. pmc An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis
    Qi Tang
    Institute of Medicinal Plant, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
    BMC Genomics 12:343. 2011
    ..Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway...
  46. pmc Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels
    Hamid Rismani-Yazdi
    Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA
    BMC Genomics 12:148. 2011
    ..Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production...
  47. pmc Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus
    Thean Hock Tang
    Institute of Experimental Pathology, Von Esmarch Strasse 56, 48149 Munster, Germany
    Proc Natl Acad Sci U S A 99:7536-41. 2002
    ..Our study further supports the importance of snmRNAs in all three domains of life...
  48. ncbi A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
    Jason Moffat
    Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
    Cell 124:1283-98. 2006
    ..This work provides a widely applicable resource for loss-of-function screens, as well as a roadmap for its application to biological discovery...
  49. 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...
  50. ncbi Functional metagenomics for enzyme discovery: challenges to efficient screening
    Taku Uchiyama
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8566, Japan
    Curr Opin Biotechnol 20:616-22. 2009
    ..This review highlights recent studies on the screening of metagenomic libraries and discusses some possible solutions for overcoming the expression problem in function-based screening...
  51. ncbi Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
    Toshiaki Watanabe
    Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411 8540, Japan
    Nature 453:539-43. 2008
    ..Our results reveal a role for endogenous siRNAs in mammalian oocytes and show that organisms lacking RdRP activity can produce functional endogenous siRNAs from naturally occurring dsRNAs...
  52. ncbi Community genomics among stratified microbial assemblages in the ocean's interior
    Edward F DeLong
    Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 311:496-503. 2006
    ..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
  53. pmc A combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of microRNAs and their targets in cucumber
    Weihua Mao
    Department of Horticulture, Zhejiang University, Hangzhou, China
    PLoS ONE 7:e33040. 2012
    ..Our study provides an overview of miRNA expression profile and interaction between miRNA and target, which will help further understanding of the important roles of miRNAs in cucumber plants...
  54. pmc Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    Nadin Rohland
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Res 22:939-46. 2012
    ..We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study...
  55. ncbi Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C(3) and C(4) species
    Andrea Bräutigam
    Plant Biochemistry, Universitatsstrasse 1, Heinrich Heine University, D 40225 Dusseldorf, Germany
    J Exp Bot 62:3093-102. 2011
    ..The pathways and cellular processes tagged in the transcriptome assemblies reflect processes of a mature leaf. The databases are useful for extracting transcripts related to C(4) processes as full-length or nearly full-length sequences...
  56. pmc Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2162-8. 2004
    ..The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans...
  57. pmc A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate
    Larry A Gallagher
    Department of Genome Sciences, University of Washington, Campus Box 355065, 1705 NE Pacific Street, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 104:1009-14. 2007
    ..The library provides a resource for virtually complete identification of genes involved in virulence and other nonessential processes...
  58. ncbi Linear amplification for deep sequencing
    Wieteke A M Hoeijmakers
    Department of Molecular Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
    Nat Protoc 6:1026-36. 2011
    ..Moreover, in contrast to amplification-free methods, LADS can generate sequencing libraries from a few nanograms of DNA, which is essential for all applications in which the starting material is limited...
  59. ncbi Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus
    Thean Hock Tang
    Institute for Research in Molecular Medicine, University Sains Malaysia Health Campus, 16150 Kubang Kerian, Kelatan, Malaysia
    Mol Microbiol 55:469-81. 2005
    ..In conclusion, this is the first report of stably expressed antisense RNAs in an archaeal species and it raises the prospect that antisense-based mechanisms are also used widely in Archaea to regulate gene expression...
  60. pmc Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries
    Stacia K Wyman
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 4:e5311. 2009
    ..A critical step toward these goals is to establish a comprehensive view of miRNAs expressed in epithelial ovarian cancer tissues as well as in normal ovarian surface epithelial cells...
  61. pmc MicroRNAs of Bombyx mori identified by Solexa sequencing
    Shiping Liu
    The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
    BMC Genomics 11:148. 2010
    ....
  62. ncbi PILER: identification and classification of genomic repeats
    Robert C Edgar
    Bioinformatics 21:i152-8. 2005
    ..We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster...
  63. ncbi FACS-optimized mutants of the green fluorescent protein (GFP)
    B P Cormack
    Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305 5402, USA
    Gene 173:33-8. 1996
    ..coli, the folding of the mutant proteins is more efficient than folding of wt GFP. These two properties contribute to a greatly increased (100-fold) fluorescence intensity, making the mutants useful for a number of applications...
  64. ncbi Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences
    Pablo F Cavagnaro
    Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
    Mol Genet Genomics 281:273-88. 2009
    ..Moreover, among eight dicot species used for comparison purposes, carrot BES had highest homology to protein-coding sequences from tomato. This deep-coverage library will aid carrot breeding and genetics...
  65. pmc Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing
    Minseon Cho
    Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA
    Proc Natl Acad Sci U S A 107:15373-8. 2010
    ..Given that many biocombinatorial libraries are encoded with nucleic acids, we extrapolate that our method may be extended to other types of libraries for a range of molecular functions...
  66. pmc Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
    Koh Aoki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Japan
    BMC Genomics 11:210. 2010
    ....
  67. pmc A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae
    D Ewen Cameron
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:8736-41. 2008
    ..cholerae flagellum appears to be derived from the cell's outer membrane, FlgT may play a direct role in flagellar sheath formation...
  68. pmc A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
    Niall J Lennon
    Genome Sequencing Platform, Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, MA 02141, USA
    Genome Biol 11:R15. 2010
    ..Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method...
  69. ncbi Uncultured soil bacteria are a reservoir of new antibiotic resistance genes
    Christian S Riesenfeld
    Department of Plant Pathology, University of Wisconsin Madison, Madison, WI 53706, USA
    Environ Microbiol 6:981-9. 2004
    ..The results indicate that soil bacteria are a reservoir of antibiotic resistance genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture-independent method...
  70. ncbi Construction of small RNA cDNA libraries for deep sequencing
    Cheng Lu
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Methods 43:110-7. 2007
    ..Here, we describe the methods used in our laboratory to construct small RNA cDNA libraries for high-throughput sequencing using technologies such as MPSS, 454 or SBS...
  71. ncbi Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal
    Zhao Sheng Zhou
    Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
    Plant Cell Environ 35:86-99. 2012
    ..Finally, 130 targets for 58 known (37 conserved and 21 non-conserved) miRNA families and 37 targets for 18 new M. truncatula-specific candidate miRNA families were identified by high-throughput degradome sequencing approach...
  72. pmc A simple method for directional transcriptome sequencing using Illumina technology
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 37:e148. 2009
    ..Hence, this simple method should prove a useful tool in aiding genome annotation and gene expression studies in both prokaryotes and eukaryotes...
  73. ncbi Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress
    Catalina Arenas-Huertero
    Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Av Universidad 2001, Cuernavaca, Morelos, Mexico
    Plant Mol Biol 70:385-401. 2009
    ..vulgaris. We propose that the novel miRNAs present in common bean and other legumes, are involved in regulation of legume-specific processes including adaptation to diverse external cues...
  74. pmc Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire
    Jacob Glanville
    Research Informatics, Rinat Pfizer Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
    Proc Natl Acad Sci U S A 106:20216-21. 2009
    ..5 x 10(10). The results provide insights into the role of IgM diversification, display library construction, and productive germline usages in antibody libraries and the humoral repertoire...
  75. pmc Enrichment of sequencing targets from the human genome by solution hybridization
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Genome Biol 10:R116. 2009
    ..9 Mb of sequence target. We demonstrate that the tiling probe frequency is important for generating sequence data with high uniform coverage of targets. We obtained 93% sensitivity to detect SNPs, with a calling accuracy greater than 99%...
  76. pmc Enrichment of a set of microRNAs during the cotton fiber development
    Pieter Bas Kwak
    Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, PR China
    BMC Genomics 10:457. 2009
    ..Small RNAs regulate many aspects of plant growth and development. However, whether small RNAs are involved in regulation of fiber cell development is unknown...
  77. ncbi Strategies for microsatellite isolation: a review
    L Zane
    Dipartimento di Biologia, Università di Padova Via Ugo Bassi 58 B, 35121, Padova, Italy
    Mol Ecol 11:1-16. 2002
    ..In addition, we propose a fast and easy protocol which is a combination of different published methods...
  78. pmc MicroRNA transcriptome profiles during swine skeletal muscle development
    Tara G McDaneld
    USDA ARS Meat Animal Research Center, Clay Center, NE, USA
    BMC Genomics 10:77. 2009
    ..To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult...
  79. 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 addition, little emphasis has been given to efforts aiming at an estimation of the overall transcriptional universe found in a multicellular organism at a specific developmental stage...
  80. pmc Metagenomic analyses: past and future trends
    Carola Simon
    Abteilung Genomische und Angewandte Mikrobiologie, Institut fur Mikrobiologie und Genetik, Georg August Universitat, Grisebachstr 8, 37077 Gottingen, Germany
    Appl Environ Microbiol 77:1153-61. 2011
    ....
  81. ncbi HIV-1 proviral DNA excision using an evolved recombinase
    Indrani Sarkar
    Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D 01307 Dresden, Germany
    Science 316:1912-5. 2007
    ..Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses...
  82. pmc Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources
    Kazuhiro Sato
    Research Institute for Bioresources, Okayama University, Kurashiki, Japan
    DNA Res 16:81-9. 2009
    ..Sequence data from this article have been deposited with the DDBJ/EMBL/GenBank Data Libraries under accession nos AK248134-AK253139. The online database with annotation is available at http://www.shigen.nig.ac.jp/barley/...
  83. pmc Digital gene expression signatures for maize development
    Andrea L Eveland
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Plant Physiol 154:1024-39. 2010
    ..Results from this study provide a basis for the analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene...
  84. ncbi Reverse methanogenesis: testing the hypothesis with environmental genomics
    Steven J Hallam
    Monterey Bay Aquarium Research Institute, Moss Landing, CA 95064, USA
    Science 305:1457-62. 2004
    ..These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation...
  85. pmc Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum
    Lili Hao
    Laboratory of Parasitology, Institute of Pathogen Biology Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing 100730, PR China
    BMC Genomics 11:55. 2010
    ..The objective of this study is to investigate the transcriptional profile and potential function of the small non-coding RNAs in the development of S. japanicum...
  86. pmc Single-cell expression profiling of human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence
    Kim B Jensen
    Keratinocyte Laboratory, Cancer Research UK London Research Institute, 44 Lincoln s Inn Fields, London WC2A 3PX, UK
    Proc Natl Acad Sci U S A 103:11958-63. 2006
    ..Lrig1 acted in part by negatively regulating the Myc promoter. We propose that Lrig1 maintains epidermal stem cells in a quiescent nondividing state, and that Lrig1 down-regulation triggers proliferation...
  87. pmc Computational annotation of genes differentially expressed along olive fruit development
    Giulio Galla
    Scuola Superiore Sant Anna Pisa, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
    BMC Plant Biol 9:128. 2009
    ..This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software...
  88. ncbi Genome-scale transcriptome analysis of the desert poplar, Populus euphratica
    Qiang Qiu
    Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, Lanzhou University, Lanzhou 730000, China
    Tree Physiol 31:452-61. 2011
    ..euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species...
  89. 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
    ....
  90. pmc Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
    C Manichanh
    Unité d Ecologie et de Physiologie du Système Digestif, INRA UEPSD, 78350 Jouy en Josas, France
    Gut 55:205-11. 2006
    ..However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches...
  91. pmc A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication
    Man Lung Yeung
    Molecular Virology Section, Laboratory of Molecular Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892 0460, USA
    J Biol Chem 284:19463-73. 2009
    ..We discuss the similarities and differences between our shRNA findings for HIV-1 using a spreading infection assay in human Jurkat T-cells and results from other investigators who used siRNA-based screenings in HeLa or 293T cells...
  92. pmc Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences
    Javier Terol
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada, Náquera, Km 4, 5 Moncada, Valencia, E46113, Spain
    BMC Genomics 9:423. 2008
    ..000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement...
  93. pmc RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles
    Mathieu Rederstorff
    Division of Genomics and RNomics, Innsbruck Biocentre, Innsbruck Medical University, Innsbruck and Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
    Nucleic Acids Res 38:e113. 2010
    ..Additionally, a number of ncRNAs mapped to repetitive sequences. Thus, our RNP approach provides an efficient way to identify new functional small ncRNA candidates, involved in RNP formation...
  94. pmc The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  95. ncbi Functional conservation of an insect odorant receptor gene across 250 million years of evolution
    Walton D Jones
    Laboratory of Neurogenetics and Behavior, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Curr Biol 15:R119-21. 2005
    ..The medical and economic impact of these animals can be ascribed in part to the sensitivity and selectivity of their olfactory systems, essential for location of their preferred plant and animal hosts...
  96. pmc Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
    Oliver H Tam
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nature 453:534-8. 2008
    ..Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals...
  97. ncbi Comparative metagenomics of microbial communities
    Susannah Green Tringe
    Department of Energy DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 308:554-7. 2005
    ..The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments...
  98. ncbi Global patterns of diversity and community structure in marine bacterioplankton
    T Pommier
    Department of Natural Science, Kalmar University, SE 39182, Kalmar, Sweden
    Mol Ecol 16:867-80. 2007
    ..The general processes behind those patterns are likely to be comparable across taxa and major global biomes...
  99. ncbi Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries
    Jiayuan Quan
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    Nat Protoc 6:242-51. 2011
    ..CPEC is highly efficient, accurate and user friendly. Once the inserts and the linear vector have been prepared, the CPEC reaction can be completed in 10 min to 3 h, depending on the complexity of the gene libraries...
  100. pmc Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont
    Shinichi Sunagawa
    School of Natural Sciences, University of California, Merced, CA 95344, USA
    BMC Genomics 10:258. 2009
    ..a system that is gaining popularity as a model to study cellular, molecular, and genomic questions related to cnidarian-dinoflagellate symbioses...
  101. pmc Identification of small non-coding RNAs from mitochondria and chloroplasts
    Birgit Lung
    Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz Pregl Strasse 3, 6020 Innsbruck, Austria
    Nucleic Acids Res 34:3842-52. 2006
    ..The absence from our libraries of abundant small RNA species that are not encoded by the organellar genomes suggests that the import of RNAs into cell organelles is of very limited significance or does not occur at all...

Research Grants56

  1. OCULAR SURFACE STEM CELL GENES
    JOSE WOLOSIN; Fiscal Year: 2006
    ..Given our current very limited understanding of stem cells, acquisition of a gene library is an essential, high impact step in the long path to unravel the process underlying the functionality of these ..
  2. Expanding the Scope of Protein Evolution
    David R Liu; Fiscal Year: 2010
    ..including those described above) have adopted a format in which a discrete mutagenesis step generates a gene library, a discrete screen or selection step enriches the library for desired members, a discrete DMA or RNA isolation ..
  3. Human Proteome Arrays for Auto-Antibody Identification in Clinical Cancer Studies
    John H Kenten; Fiscal Year: 2011
    ..We will test normal and cancer patient sera against protein arrays generated using a gene library expressing human full-length proteins...
  4. SEEKING THE YEAST SPARKING STEROL
    Martin Bard; Fiscal Year: 1991
    ..A Candida gene library will be used to complement existing Saccharomyces erg mutations or the cloned Saccharomyces ERG genes will be ..
  5. GENE LIBRARY RESOURCE FOR THE SEA URCHIN S. PURPURATUS
    Eric H Davidson; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): This revised proposal seeks support for the Gene Library Resource for the purple sea urchin, Strongylocentrotus purpuratus...
  6. GENETICS OF H. AEGYPTIUS BRAZILIAN PURPURIC FEVER CLONE
    Luis Actis; Fiscal Year: 2000
    ..This will be achieved by constructing a gene library using the innovative subtraction genomic hybridization technique...
  7. THE STRUCTURAL BASIS OF RELAXIN ACTION
    Christian Schwabe; Fiscal Year: 1990
    ..to obtain partial sequence information concerning the relaxin receptor that would eventually aid in the construction of a nucleotide probe with which a relaxin receptor-coding sequence may be isolated from the appropriate gene library.
  8. Plague vaccine candidates by a functional genomic screen
    Kathryn Sykes; Fiscal Year: 2002
    ..pestis genome for protective antigens, ii) identify protocols for producing a complete Y. pestis gene library iii) define the optimal gene dose and design for this genome screen by testing Y...
  9. Single Cell Screen for Enzyme Expression and Activity
    Justin Stege; Fiscal Year: 2001
    Diversa leverages its proprietary technology in gene library generation and gene evolution to provide robust bio-catalytic solutions across a broad spectrum of chemical industries...
  10. Chemokine Receptor Chimeras by Synthetic Gene Library
    Michael Dustin; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  11. Target Validation using Gene Knockouts in Somatic Cells
    Robert Finney; Fiscal Year: 2002
    ..Specific aims proposed are 1) generation of a 2,000 gene library for gene knockouts, 2) creation of 10 gene knockout vectors, 3) inactivation of 10 genes in 2 human pancreatic ..
  12. PROFILING AUTOANTIGENS IN UVEITIS
    Wei Li; Fiscal Year: 2010
    ..These efforts will advance our understanding of the disease etiology and prognosis, and improve the diagnosis and therapy. ..
  13. Modulation of CD4+ T cells in autoimmune uveitis
    Wei Li; Fiscal Year: 2003
    ..These studies will not only yield new insights for the underlying causes and pathogenesis of autoimmune uveitis, but may also lead to a more selective immunotherapy for the disease. ..
  14. Investigating the nature of prestin-associated proteins
    Jing Zheng; Fiscal Year: 2007
    ..This knowledge may make it possible to manipulate OHC function for therapeutic purposes. ..
  15. Metabolism of Carcinogens and Drugs by Human P450s
    F Guengerich; Fiscal Year: 2005
    ..Successful completion of these collective studies should provide better understanding of the ways in which human P450s catalyze oxidation of carcinogens and drugs and the significance of variations in these enzymes. ..
  16. Microevolution of conserved developmental genes
    PAUL HOHENLOHE; Fiscal Year: 2007
    ..Conversely, lack of variation and a negative selection result would suggest that other loci or regulatory pathways are involved in vertebral development. [unreadable] [unreadable] [unreadable]..
  17. Intrnational Clubfoot Symposium
    Jose Morcuende; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  18. 400 MHz NMR Spectrometer for CSU Chemistry Facility
    Robert Williams; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  19. Synthesis and Mechanism of DNA Cross-linking of FR900482
    Robert Williams; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  20. Genetic Mapping of Familial Idiopathic Scoliosis
    Jose Morcuende; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  21. In vivo regulation of M. tuberculosis cell wall lipids
    Lee W Riley; Fiscal Year: 2010
    ..tuberculosis and granulomas may contribute to our understanding of the mechanism of persistence of M. tuberculosis that could lead to new tests to differentiate active TB from latent TB infection. ..
  22. MULTIVALENT VACCINE FOR LYMPHATIC FILARIASIS
    Ramaswamy Kalyanasundaram; Fiscal Year: 2010
    ..The proposed studies are based on solid preliminary data and are hypotheses driven. Results from these studies, we believe will advance our knowledge towards developing a defined vaccine against lymphatic filariasis in the human. ..
  23. MOLECULAR MECHANISMS IN DIABETIC EMBRYOPATHY
    CLAUDIA T KAPPEN; Fiscal Year: 2010
    ..These experiments will generate new and comprehensive insights into the function of pancreatic transcription factors and their pathogenic potential in metabolic disease and fetal development. ..
  24. MENTORED QUANTITATIVE RESEARCH CAREER DEVELOPMENT AWARD
    Gregory Grant; Fiscal Year: 2005
    ..4) To complete a six-month lab rotation, the exact details of which are still to be worked out. This has been informally arranged with Dr. Vivian Cheung (Children's Hospital of Philadelphia). ..
  25. Genome-wide discovery of beta cell gene control elements
    Claudia Kappen; Fiscal Year: 2004
    ..Together, our studies will show how speck gene expression is achieved in beta cells and provide a framework to integrate gene transcription and beta cell biology. ..
  26. ANTIOXIDANT GENES OF MYCOBACERIUM TUBERCULOSIS
    Lee Riley; Fiscal Year: 2001
    ....
  27. MOLECULAR BIOLOGY OF INFECTION WITH M TUBERCULOSIS
    Lee Riley; Fiscal Year: 2002
    ..In addition, these studies may identify several potential targets for new chemotherapeutic agents or vaccine candidates. ..
  28. NEGATIVE REGULATION OF GENE EXPRESSION BY VITAMIN D
    NICHOLAS KOSZEWSKI; Fiscal Year: 2002
    ..abstract_text> ..
  29. FUNCTION AND REGULATION OF THE E COLI AIDB GENES
    Michael Volkert; Fiscal Year: 2002
    ..During the proposed funding period, I propose to characterize this factor further by genetic and biochemical means and to compare its induction mechanism with that of meAda. ..
  30. ANNEXIN PHOSPHORYLATION: CAUSES AND CONSEQUENCES
    CARL CREUTZ; Fiscal Year: 2004
    ....
  31. FUNCTION OF THE RETINOBLASTOMA PROTEIN
    Edward Harlow; Fiscal Year: 2002
    ..We have finished the initial characterization of these differences and in the next round of this grant will investigate the functional differences between pRB p107 and p130 in adipogenesis and in other defined differentiation systems. ..
  32. Nuclease-Resistant Aptamers for Anthrax Opsonization
    John Bruno; Fiscal Year: 2004
    ..Such shielded aptamers could even be used in inhalers to enhance alveolar macrophage phagocytosis. ..
  33. Nuclease-Resistant Aptamers to Botox and Anthrax Toxins
    John Bruno; Fiscal Year: 2004
    ..Such reagents could also be used in environmental biosensors or diagnostic test kits for detection of BOTOX and anthrax toxins in body fluids or environmental samples. ..
  34. Mechanism of MMP gene induction in osteoarthritis
    BIMAL RAY; Fiscal Year: 2004
    ..abstract_text> ..
  35. Identification of Imprinted Genes in Brain Development
    MICHAEL O NEILL; Fiscal Year: 2004
    ..abstract_text> ..
  36. Development and evaluation of subunit vaccine CmeC against Campylobacter jejuni
    Jun Lin; Fiscal Year: 2008
    ..S. The proposed research will provide novel information on the development of effective vaccine against C. jejuni to protect public health. [unreadable] [unreadable] [unreadable]..
  37. FOLATE AND HOX GENES IN CRANIOFACIAL DEVELOPMENT
    Claudia Kappen; Fiscal Year: 2003
    ..Knowledge about the interactions of genes with environmental factors will be important for designing therapeutic strategies and preventive measures against craniofacial defects. ..
  38. HOST IMMUNOMODULATION BY PARASITES
    Ramaswamy Kalyanasundaram; Fiscal Year: 2004
    ..Overall, the findings from these studies we believe might help improve per-cutaneous vaccination against this disease using defined candidate vaccine antigens against schistosomiasis. ..
  39. CALCIUM DEPENDENT MEMBRANE BINDING PROTEINS
    CARL CREUTZ; Fiscal Year: 2002
    ....
  40. Improved DNA Polymerases for Genomic Sequencing
    Thomas Schoenfeld; Fiscal Year: 2008
    ..One has been studied in detail and, as expected, it has characteristics that are expected to improve sequencing. [unreadable] [unreadable] [unreadable]..
  41. Epidemiology of an uropathogenic E coli clonal group
    Lee Riley; Fiscal Year: 2003
    ..coli can be spread by contaminated ingestible vehicles, and use the data generated from this project to design long-term studies to better characterize risk factors associated with CgA infection. ..
  42. Orgin of multidrug resistant uropathogenic E. coli
    Lee Riley; Fiscal Year: 2008
    ..This knowledge should lead to the implementation of improved control of drug-resistant infectious diseases. ..
  43. Therapeutic vaccine against tuberculosis
    Lee Riley; Fiscal Year: 2006
    ..Therapeutic vaccines against TB is a major priority in TB control, and we have an opportunity to identify such products by a novel approach using a simple, inexpensive, and reproducible animal model. ..
  44. Novel & Selective Small Molecular Inhibitors of Human Peptide Deformylase
    Hakim Djaballah; Fiscal Year: 2006
    ..Indeed, the likelihood that a compound interferes with both assays, and therefore behaves as a false positive in both assays, is vastly reduced compared to a strategy solely based on one technique. ..
  45. HUMAN OXIDATION RESISTANCE GENES
    Michael Volkert; Fiscal Year: 2007
    ..abstract_text> ..
  46. Middle Ear Epithelial Response to Cytokine Stimulation
    Joseph Kerschner; Fiscal Year: 2005
    ....
  47. LC/MDS TOF Spectrometer for Instrument Facility at CSU
    Robert Williams; Fiscal Year: 2006
    ..Finally, many of these measurements will be made in an open access environment. [unreadable] [unreadable]..
  48. Decidual macrophages in primate pregnancy
    Igor Slukvin; Fiscal Year: 2007
    ..abstract_text> ..
  49. GENETICS OF CANCER AND INHERITED DISEASES
    Edward Harlow; Fiscal Year: 2003
    ..These faculty are linked by their interest in cancer genetics, cancer biology human clinical genetics, and genetics of model organisms. ..
  50. A Genetic Approach to Virulence in C. albicans
    Suzanne Noble; Fiscal Year: 2007
    ..Results from this work should enhance our understanding of fungal pathogenesis and identify novel targets for antifungal therapy. [unreadable] [unreadable]..
  51. Immunobiological Role of Fertilization Antigen(FA-1)
    RAJESH NAZ; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  52. MECHANISM OF SERUM AMYLOID A PROTEIN SYNTHESIS
    BIMAL RAY; Fiscal Year: 2005
    ..Results of these studies will improve understanding of the basic mechanisms of cellular response to inflammation and help in the development of a therapeutic regimen to control harmful effects of chronic inflammation. ..
  53. MECHANISM OF SERUM AMYLOID A PROTEIN SYNTHESIS
    BIMAL RAY; Fiscal Year: 2003
    ..abstract_text> ..
  54. Genetic dissection of skeletal patterning
    Claudia Kappen; Fiscal Year: 2006
    ..The identification of modifier loci that act on skeletal patterning will reveal new molecular mechanisms in skeletal development and has important implications for the evolution of vertebrate body plans. ..