contig mapping

Summary

Summary: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.

Top Publications

  1. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999
  2. pmc ABySS: a parallel assembler for short read sequence data
    Jared T Simpson
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 19:1117-23. 2009
  3. 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
  4. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
  5. 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
  6. 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
  7. pmc Optimization of de novo transcriptome assembly from next-generation sequencing data
    Yann Surget-Groba
    Department of Zoology and Animal Biology, University of Geneva, 1211 Geneva 4, Switzerland
    Genome Res 20:1432-40. 2010
  8. 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
  9. 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
  10. 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

Research Grants

  1. TRYPANASOMA CRUZI GENOME-SBRI
    Kenneth Stuart; Fiscal Year: 2004
  2. GENOMIC ORGANIZATION OF PHOTOSYNTHETIC GENES
    William Widger; Fiscal Year: 1993
  3. Molecular Mechanisms of Social Behavior
    Anna V Kukekova; Fiscal Year: 2010
  4. Molecular genetics of tame behavior
    ANNA KUKEKOVA; Fiscal Year: 2005
  5. Genome-wide Dissection of the Retinal Determination Network
    Rui Chen; Fiscal Year: 2009
  6. Characterization of the flexible portions of fibrinogen
    Russell Doolittle; Fiscal Year: 2007
  7. Genetic model of retinal pigment epithelium degeneration
    Douglas Vollrath; Fiscal Year: 2005
  8. Molecular Genetics of Cervical Cancer Progression
    Murty Vundavalli; Fiscal Year: 2004
  9. A DNA SEQUENCE ASSEMBLY PROGRAM
    Xiaoqiu Huang; Fiscal Year: 2003
  10. COMPUTATIONAL ANALYSIS OF HUMAN 'AT-RISK' DNA MOTIFS
    JUDITH STENGER; Fiscal Year: 2003

Detail Information

Publications242 found, 100 shown here

  1. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999
    ..PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints...
  2. pmc ABySS: a parallel assembler for short read sequence data
    Jared T Simpson
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 19:1117-23. 2009
    ..Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes...
  3. 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
    ....
  4. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  5. 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...
  6. 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...
  7. pmc Optimization of de novo transcriptome assembly from next-generation sequencing data
    Yann Surget-Groba
    Department of Zoology and Animal Biology, University of Geneva, 1211 Geneva 4, Switzerland
    Genome Res 20:1432-40. 2010
    ..The new methods were used to assemble successfully the transcripts of the core set of genes regulating tooth development in vertebrates, while classic de novo assembly failed...
  8. 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...
  9. 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...
  10. 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...
  11. ncbi Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics
    John G Gibbons
    Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
    Mol Biol Evol 26:2731-44. 2009
    ....
  12. ncbi Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
    Sébastien Renaut
    Institut de Biologie Intégrative et des Systèmes, Universite Laval, QC, Canada
    Mol Ecol 19:115-31. 2010
    ..This indicates an elevated activity of transposable elements, which could potentially contribute to the reduced fitness of hybrids previously documented...
  13. pmc An Eulerian path approach to DNA fragment assembly
    P A Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA
    Proc Natl Acad Sci U S A 98:9748-53. 2001
    ..euler, in contrast to the celera assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool...
  14. pmc Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
    Frédéric Choulet
    Institut National de la Recherche Agronomique, Universite Blaise Pascal, Unité Mixte de Recherche 1095 Genetics Diversity and Ecophysiology of Cereals, F 63100 Clermont Ferrand, France
    Plant Cell 22:1686-701. 2010
    ....
  15. 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...
  16. pmc The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
    Ray Ming
    Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
    Nature 452:991-6. 2008
    ....
  17. pmc Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication
    Jeong Hwan Mun
    Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin ro, Gwonseon gu, Suwon 441 707, Korea
    Genome Biol 10:R111. 2009
    ..rapa, which is a strong challenge of structural and comparative crop genomics...
  18. ncbi Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives
    Debashis Rana
    Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    Plant J 40:725-33. 2004
    ..napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure...
  19. pmc The physical and genetic framework of the maize B73 genome
    Fusheng Wei
    Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
    PLoS Genet 5:e1000715. 2009
    ..Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1)...
  20. pmc Fast algorithms for large-scale genome alignment and comparison
    Arthur L Delcher
    Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
    Nucleic Acids Res 30:2478-83. 2002
    ..The system code is being made freely available by the authors...
  21. ncbi A physical map of the chicken genome
    John W Wallis
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 432:761-4. 2004
    ..This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes...
  22. pmc Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
    Axel Künstner
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
    Mol Ecol 19:266-76. 2010
    ..Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms...
  23. ncbi A whole-genome assembly of Drosophila
    E W Myers
    Celera Genomics, Inc, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 287:2196-204. 2000
    ..99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community...
  24. pmc Local de novo assembly of RAD paired-end contigs using short sequencing reads
    Paul D Etter
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
    PLoS ONE 6:e18561. 2011
    ....
  25. pmc Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome
    Raja Ragupathy
    Cereal Research Centre, Agriculture and Agri Food Canada, Winnipeg, MB, Canada
    BMC Genomics 12:217. 2011
    ..We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome...
  26. pmc A first generation BAC-based physical map of the rainbow trout genome
    Yniv Palti
    National Center for Cool and Cold Water Aquaculture, ARS USDA, Kearneysville, WV 25430, USA
    BMC Genomics 10:462. 2009
    ..This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species...
  27. pmc Comparative analysis of catfish BAC end sequences with the zebrafish genome
    Hong Liu
    The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
    BMC Genomics 10:592. 2009
    ..This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish...
  28. pmc Hierarchical scaffolding with Bambus
    Mihai Pop
    The Institute for Genomic Research TIGR, Rockville, Maryland 20850, USA
    Genome Res 14:149-59. 2004
    ..Bambus is available as an open-source package from our Web site...
  29. pmc Sequence-based physical mapping of complex genomes by whole genome profiling
    Jan van Oeveren
    Keygene N V, Wageningen, The Netherlands
    Genome Res 21:618-25. 2011
    ..We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data...
  30. ncbi A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator)
    Falko Roeding
    Zoological Institute and Museum, University of Hamburg, D 20146 Hamburg, Germany
    Mol Phylogenet Evol 53:826-34. 2009
    ..In summary, we have shown that 454 pyrosequencing is a cost-effective method that provides sufficient data and coverage depth for gene detection and multigene-based phylogenetic analyses...
  31. pmc Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
    Christopher D Town
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Cell 18:1348-59. 2006
    ..We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes...
  32. pmc A draft physical map of a D-genome cotton species (Gossypium raimondii)
    Lifeng Lin
    Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA
    BMC Genomics 11:395. 2010
    ..Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing...
  33. pmc Genome physical mapping of polyploids: a BIBAC physical map of cultivated tetraploid cotton, Gossypium hirsutum L
    Meiping Zhang
    Department of Soil and Crop Sciences, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 7:e33644. 2012
    ....
  34. ncbi Genome-wide SNP detection in the great tit Parus major using high throughput sequencing
    Nikkie E M van Bers
    Animal Breeding and Genomics Centre, Wageningen University, The Netherlands
    Mol Ecol 19:89-99. 2010
    ..The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines...
  35. ncbi GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
    Alexey A Gritsenko
    The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, Delft
    Bioinformatics 28:1429-37. 2012
    ..They use this limited information to construct scaffolds, often preferring scaffold length over accuracy, when faced with the tradeoff...
  36. ncbi Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5
    J Y Park
    Department of Horticulture, Chungnam National University, Kung Dong 220, Yusong gu, Daejeon 305 764, South Korea
    Mol Genet Genomics 274:579-88. 2005
    ..pekinensis chromosomes. The homoeologous segments corresponding to chromosome 4 of Arabidopsis were located on chromosomes 2, 8 and 7, whereas those of chromosome 5 were present on chromosomes 6, 1 and 4 of B. rapa ssp. pekinensis...
  37. ncbi A BAC-based physical map of the channel catfish genome
    Peng Xu
    The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
    Genomics 90:380-8. 2007
    ..The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits...
  38. pmc A BAC-based physical map of Zhikong scallop (Chlamys farreri Jones et Preston)
    Xiaojun Zhang
    Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
    PLoS ONE 6:e27612. 2011
    ....
  39. pmc A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes
    Yang Zhang
    Department of Soil and Crop Sciences, Texas A and M University, College Station, TX 77843, USA
    BMC Genomics 12:447. 2011
    ..To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species...
  40. pmc Rapid and accurate pyrosequencing of angiosperm plastid genomes
    Michael J Moore
    Department of Botany, University of Florida, Gainesville, FL 32611, USA
    BMC Plant Biol 6:17. 2006
    ....
  41. pmc Short read fragment assembly of bacterial genomes
    Mark J Chaisson
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA
    Genome Res 18:324-30. 2008
    ....
  42. pmc Generation of a BAC-based physical map of the melon genome
    Víctor M González
    Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG CSIC IRTA UAB, Jordi Girona, 18 26, 08034 Barcelona, Spain
    BMC Genomics 11:339. 2010
    ..A BAC-based melon physical map will be a useful tool to help assemble and refine the draft genome data that is being produced...
  43. 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...
  44. pmc PCAP: a whole-genome assembly program
    Xiaoqiu Huang
    Department of Computer Science Iowa State University, Ames, Iowa 50011 1040, USA
    Genome Res 13:2164-70. 2003
    ..The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use...
  45. pmc Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map
    G R Lazo
    U S Department of Agriculture Agricultural Research Service USDA ARS, Western Regional Research Center, Albany, California 94710 1105, USA
    Genetics 168:585-93. 2004
    ..Results from this project have established the foundation for future developments in wheat genomics...
  46. pmc A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes
    Rajat Aggarwal
    Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 10:293. 2009
    ..A physical map is needed to improve the ability to perform both positional cloning and comparative genomic analyses with the fully sequenced genomes of other dipteran species...
  47. pmc Transcriptome analysis of Gerbera hybrida ray florets: putative genes associated with gibberellin metabolism and signal transduction
    Qi Kuang
    Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
    PLoS ONE 8:e57715. 2013
    ....
  48. pmc Sequence and structure of Brassica rapa chromosome A3
    Jeong Hwan Mun
    Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin ro, Gwonseon gu, Suwon 441 707, Korea
    Genome Biol 11:R94. 2010
    ..Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species...
  49. pmc Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans)
    Geoffrey M Attardo
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
    BMC Genomics 11:160. 2010
    ..3438 expressed sequence tags were sequenced and analyzed...
  50. pmc Graph accordance of next-generation sequence assemblies
    Guohui Yao
    The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Bioinformatics 28:13-6. 2012
    ..We describe an algorithm to take advantages of different assembly algorithms or sequencing platforms to improve the quality of next-generation sequence (NGS) assemblies...
  51. pmc Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
    Song Gao
    NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
    J Comput Biol 18:1681-91. 2011
    ..Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ )...
  52. pmc A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers
    Roland Schafleitner
    Germplasm Enhancement and Crop Improvement Division, International Potato Center, La Molina, Lima, Peru
    BMC Genomics 11:604. 2010
    ..We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species...
  53. pmc Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
    Richard Cronn
    Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR 97331, USA
    Nucleic Acids Res 36:e122. 2008
    ..056%, and conspicuous errors are evident from the assembly process. This efficient sequencing approach yields high-quality draft genomes and should have immediate applicability to genomes with comparable complexity...
  54. ncbi The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs
    T Raudsepp
    Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A and M University, College Station, TX 77843 4458, USA
    Cytogenet Genome Res 121:102-9. 2008
    ..Although striking differences like those observed between human and mouse may be rare, variations similar to those seen between horse and human may be prevalent among mammals...
  55. pmc Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    Sébastien Boisvert
    Département de Médecine Moléculaire, Universite Laval, Quebec, Canada
    J Comput Biol 17:1519-33. 2010
    ..sf.Net/). For online Supplementary Material , see www.liebertonline.com...
  56. pmc Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray
    Stephane Fenart
    Universite Lille Nord de France, Lille 1 UMR INRA 1281, SADV, F 59650 Villeneuve d Ascq cedex, France
    BMC Genomics 11:592. 2010
    ..In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax...
  57. ncbi Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7
    Z Xiong
    Division of Biological Sciences, Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
    Cytogenet Genome Res 129:190-8. 2010
    ..napus to demonstrate that this approach can facilitate studies of genome evolution by integrating the genetic, physical, and cytogenetic maps among closely related species of Brassica...
  58. pmc Genomic tools development for Aquilegia: construction of a BAC-based physical map
    Guang Chen Fang
    Department of Genetics and Biochemistry, Clemson University, SC 29634, USA
    BMC Genomics 11:621. 2010
    ..To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance...
  59. pmc Annotation of the Arabidopsis genome
    Jennifer R Wortman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 132:461-8. 2003
  60. pmc High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus
    Raul Bettencourt
    Department of Oceanography and Fisheries, University of the Azores, 9901 861 Horta, Portugal
    BMC Genomics 11:559. 2010
    ....
  61. pmc Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel
    Alessandro Coppe
    Biology Department, University of Padova, Italy
    BMC Genomics 11:635. 2010
    ..Yet, the species is poorly characterized at molecular level with little sequence information available in public databases...
  62. pmc De novo repeat classification and fragment assembly
    Pavel A Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
    Genome Res 14:1786-96. 2004
    ..Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes...
  63. pmc A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
    Xiaojun Zhang
    Department of Soil and Crop Sciences, Texas A and M University, College Station, Texas 77843 2474, USA
    BMC Genomics 11:501. 2010
    ..The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea...
  64. pmc Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies
    Shaolin Wang
    The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, 203 Swingle Hall, Auburn University, Auburn, AL 36849, USA
    Genome Biol 11:R8. 2010
    ..Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification...
  65. pmc Automated finishing with autofinish
    D Gordon
    Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195, USA
    Genome Res 11:614-25. 2001
    ..Autofinish has been used for finishing cDNA, genomic clones, and whole bacterial genomes (see http://www.phrap.org)...
  66. ncbi Integration of animal linkage and BAC contig maps using overgo hybridization
    M N Romanov
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Mich, USA
    Cytogenet Genome Res 102:277-81. 2003
    ..These data are publicly available, and they have been used in the assembly of a first generation BAC contig map of the chicken genome...
  67. pmc High-throughput sequence alignment using Graphics Processing Units
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    BMC Bioinformatics 8:474. 2007
    ....
  68. ncbi The Arabidopsis PBS1 resistance gene encodes a member of a novel protein kinase subfamily
    M R Swiderski
    Department of Biology, Indiana University, Bloomington, IN 47405 3700, USA
    Plant J 26:101-12. 2001
    ..These data suggest that PBS1 and Pto may fulfil different functions in the recognition of pathogen avirulence proteins. We discuss several possible models for the roles of PBS1 and RPS5 in AvrPphB recognition...
  69. pmc Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis
    Q Tao
    Department of Soil and Crop Sciences and Crop Biotechnology Center, Texas A and M University, College Station, TX 77843-2123, USA
    Genetics 158:1711-24. 2001
    ..This study indicates that genome-wide BAC-based physical maps can be developed quickly and economically for a variety of plant and animal species by restriction fingerprint analysis via DNA sequencing gel-based electrophoresis...
  70. ncbi OSLay: optimal syntenic layout of unfinished assemblies
    Daniel C Richter
    Center for Bioinformatics ZBIT, Institute for Computer Science, Tubingen University, 72076 Tubingen, Germany
    Bioinformatics 23:1573-9. 2007
    ..The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure...
  71. pmc Whole-genome shotgun optical mapping of Rhodospirillum rubrum
    Susan Reslewic
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
    Appl Environ Microbiol 71:5511-22. 2005
    ..With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a "molecular cytogenetics" approach to solving problems in genomic analysis...
  72. pmc Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey
    Hindrik H D Kerstens
    Animal Breeding and Genomics Center, Wageningen University, Marijkeweg 40, Wageningen, 6709 PG, The Netherlands
    BMC Genomics 10:479. 2009
    ..To illustrate the potential of this technique, we present the results obtained with a randomly sheared, enzymatically generated, 2-3 kbp genome fraction of six pooled Meleagris gallopavo (turkey) individuals...
  73. pmc A detailed physical map of the horse Y chromosome
    Terje Raudsepp
    Department of Veterinary Anatomy and Public Health, Texas A and M University, College Station, 77843, USA
    Proc Natl Acad Sci U S A 101:9321-6. 2004
    ..The foundation laid through the map will be critical in obtaining complete sequence of the euchromatic region of the horse Y chromosome, with an aim to identify Y specific factors governing male infertility and phenotypic sex variation...
  74. pmc Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa
    Jinsong Xu
    National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
    BMC Genomics 11:594. 2010
    ..An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola)...
  75. ncbi Genomic and genetic definition of a functional human centromere
    M G Schueler
    Department of Genetics, Case Western Reserve University School of Medicine and Center for Human Genetics, and, Research Institute, University Hospitals of Cleveland, Cleveland, OH 44106, USA
    Science 294:109-15. 2001
    ....
  76. pmc Contigs built with fingerprints, markers, and FPC V4.7
    C Soderlund
    Clemson University Genomic Institute, Clemson, South Carolina 29634 5808, USA
    Genome Res 10:1772-87. 2000
    ..This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation...
  77. pmc SNP discovery in swine by reduced representation and high throughput pyrosequencing
    Ralph T Wiedmann
    USDA, ARS, US Meat Animal Research Center, State Spur 18D, NE 68933 0166, USA
    BMC Genet 9:81. 2008
    ....
  78. ncbi Construction and analysis of a human-chimpanzee comparative clone map
    Asao Fujiyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Science 295:131-4. 2002
    ..We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes...
  79. pmc Pooled genomic indexing of rhesus macaque
    Aleksandar Milosavljevic
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 15:292-301. 2005
    ..A further innovation, short-tag pooled genomic indexing (ST-PGI), was also introduced to further improve the economy of mapping by sequencing multiple, short, mapable tags within a single sequencing reaction...
  80. ncbi A bacterial artificial chromosome based physical map of the Ustilago maydis genome
    Khalid Meksem
    Plants and Microbes Genomic and Genetics Laboratory, Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, IL 62901 4415, USA
    Genome 48:207-16. 2005
    ..BAC clones are available for repeat and unique gene cluster analysis including tDNA-mediated transformation. Program FingerPrint Contigs maps aligned with each chromosome can be viewed at http://www.siu.edu/~meksem/ustilago_maydis/...
  81. ncbi A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence
    Yaning Li
    Department of Soil and Crop Sciences, Texas A and M University, College Station, TX 77843 2474, USA
    Genome 50:278-88. 2007
    ..Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding...
  82. pmc Evaluation of short read metagenomic assembly
    Anveshi Charuvaka
    Computer Science Department, George Mason University, Fairfax, Virginia, USA
    BMC Genomics 12:S8. 2011
    ..We present an evaluation of assembly of simulated short-read metagenomic samples using a state-of-art de Bruijn graph based assembler...
  83. ncbi Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization
    Stephen E Diener
    Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200 Raleigh, NC 27606, USA
    Fungal Genet Biol 41:1077-87. 2004
    ..BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results...
  84. 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...
  85. pmc Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella
    Dietmar Schwarz
    Department of Entomology, University of Illinois, 320 Morrill Hall, 505 S, Goodwin Ave, Urbana, Illinois 61801, USA
    BMC Genomics 10:633. 2009
    ..To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies...
  86. ncbi A Blumeria graminisf.sp. hordei BAC library--contig building and microsynteny studies
    Carsten Pedersen
    Plant Research Department, Risø National Laboratory, P O Box 49, 4000 Roskilde, Denmark
    Curr Genet 42:103-13. 2002
    ..The library provides an invaluable tool for the isolation of avirulence genes from B. graminis and for the study of gene synteny between this fungus and other fungi...
  87. pmc Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species
    Ming Cheng Luo
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    BMC Genomics 11:122. 2010
    ....
  88. ncbi Metagenomic analysis of coastal RNA virus communities
    Alexander I Culley
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Science 312:1795-8. 2006
    ..Our results show that the oceans are a reservoir of previously unknown RNA viruses...
  89. pmc A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
    Yong Q Gu
    1Genomics and Gene Discovery Research Unit, USDA ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
    BMC Genomics 10:496. 2009
    ..A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence...
  90. ncbi EST analysis and annotation of transcripts derived from a trichome-specific cDNA library from Salvia fruticosa
    Fani M Chatzopoulou
    Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
    Plant Cell Rep 29:523-34. 2010
    ....
  91. ncbi The reference genetic linkage map for the multinational Brassica rapa genome sequencing project
    Su Ryun Choi
    Department of Horticulture, Genome Research Center, Chungnam National University, Kung Dong 220, Yusong gu, Daejeon 305 764, South Korea
    Theor Appl Genet 115:777-92. 2007
    ..rapa and other cultivated Brassica species...
  92. pmc PAVE: program for assembling and viewing ESTs
    Carol Soderlund
    BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
    BMC Genomics 10:400. 2009
    ..The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs...
  93. ncbi Assembly reconciliation
    Aleksey V Zimin
    IPST, University of Maryland, College Park, Agencourt Bioscience Inc, Beverly, MA
    Bioinformatics 24:42-5. 2008
    ..The collaborators then pick the draft assembly that they judge to be the best and the information contained in the other assemblies is usually not used...
  94. pmc First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach
    Cinzia Cantacessi
    Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria, Australia
    Infect Genet Evol 10:1199-207. 2010
    ....
  95. pmc A BAC-based physical map of the Nile tilapia genome
    Takayuki Katagiri
    Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
    BMC Genomics 6:89. 2005
    ..Physical maps linking collections of BAC clones are a critical resource for both positional cloning and assembly of whole genome sequences...
  96. ncbi Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases
    Y Ding
    Beckman Institute, Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
    Genomics 74:142-54. 2001
    ..We have compared data obtained from this method to predicted HICF patterns of 10 fully sequenced BACs. We have further applied HICF to 555 BAC clones to assemble contigs spanning 16p11.2 to 16p13.1 of human chromosome 16...
  97. pmc Chromosome breakage in the Prader-Willi and Angelman syndromes involves recombination between large, transcribed repeats at proximal and distal breakpoints
    J M Amos-Landgraf
    Department of Genetics, Case Western Reserve University School of Medicine, and Center for Human Genetics, University Hospitals of Cleveland, Cleveland, OH 44106 4955, USA
    Am J Hum Genet 65:370-86. 1999
    ..Furthermore, we propose that active transcription of these repeats in male and female germ cells may facilitate the homologous recombination process...
  98. pmc AutoFACT: an automatic functional annotation and classification tool
    Liisa B Koski
    Robert Cedergren Center for Bioinformatics and Genomics, Universite de Montreal, Montreal, Quebec, Canada
    BMC Bioinformatics 6:151. 2005
    ..Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets...
  99. pmc Mouse BAC ends quality assessment and sequence analyses
    S Zhao
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 11:1736-45. 2001
    ..1% mBESs contain STSs. About 0.2% mBESs match human finished sequences and > 70% of these sequences have EST hits. The analyses indicate that our high-quality mouse BAC end sequences will be a valuable resource to the community...
  100. ncbi Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags
    Yasunari Ogihara
    Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Maioka cho 641 12, Yokohama 244 0813, Japan
    Plant J 33:1001-11. 2003
    ..This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants...
  101. ncbi Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes
    Amy K Samuels
    University of Kentucky, Department of Biology, Lexington, KY 40506, USA
    Gene 349:43-53. 2005
    ..Our results show the benefit of using complete genome mitochondrial information in studies of recently and rapidly diverged taxa...

Research Grants15

  1. TRYPANASOMA CRUZI GENOME-SBRI
    Kenneth Stuart; Fiscal Year: 2004
    ..This phase, which will be completed in the first year, will generate data and materials for karyotype and contig mapping, complement data in the existing T. cruzi EST database, and identify many of the genes in T. cruzi...
  2. GENOMIC ORGANIZATION OF PHOTOSYNTHETIC GENES
    William Widger; Fiscal Year: 1993
    ..This map will allow us to understand how the Agmenellum genome controls photosynthesis. Tbe contig mapping experiments takes advantage of a technique used to group lambda clones from a overlapping clone library into ..
  3. Molecular Mechanisms of Social Behavior
    Anna V Kukekova; Fiscal Year: 2010
    ....
  4. Molecular genetics of tame behavior
    ANNA KUKEKOVA; Fiscal Year: 2005
    ..A set of candidate genes implicated in human and/or rodent behavior will be evaluated for co segregation with tame and wild type behavioural phenotypes using existing and three-generation experimental fox pedigrees. ..
  5. Genome-wide Dissection of the Retinal Determination Network
    Rui Chen; Fiscal Year: 2009
    ..Since both ey and many of its downstream genes are highly conserved in humans and many developmental parallels exist between Drosophila and mammalian retina, this work will directly impact our understanding of human retinal development. ..
  6. Characterization of the flexible portions of fibrinogen
    Russell Doolittle; Fiscal Year: 2007
    ..These studies are aimed at determining the degree of specificity involved in the assembly of fibrin units and protofibrils as well as the relative locations of the regions involved. ..
  7. Genetic model of retinal pigment epithelium degeneration
    Douglas Vollrath; Fiscal Year: 2005
    ....
  8. Molecular Genetics of Cervical Cancer Progression
    Murty Vundavalli; Fiscal Year: 2004
    ..The data generated from these studies will be used to determine the clinical significance and to develop a genetic prognostic model for identifying high-risk CINs that progress into invasive cancer. ..
  9. A DNA SEQUENCE ASSEMBLY PROGRAM
    Xiaoqiu Huang; Fiscal Year: 2003
    ..The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers. ..
  10. COMPUTATIONAL ANALYSIS OF HUMAN 'AT-RISK' DNA MOTIFS
    JUDITH STENGER; Fiscal Year: 2003
    ..3) To set up an interactive on-line database and program server so that the scientific community can use the information and apply it to drive experimental research. ..
  11. Sun Microsystems Sun Fire 6800 Server Supercomputer
    JUDITH STENGER; Fiscal Year: 2003
    ..This HPC will provide the database storage capacity and querying speed plus the computational processing capability needed to analyze our clinical, genotypic, and bioinformatics data. ..
  12. STRUCTURAL STUDIES ON FIBRINOGEN AND FIBRIN
    Russell Doolittle; Fiscal Year: 2003
    ..Combined with the full structures of the native molecules at high resolution, these results should dispel much of the mystery of fibrin formation. ..
  13. Trypanosome gene expression in tsetse
    Serap Aksoy; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  14. INTERACTION OF TSETSE--ITS SYMBIONTS AND TRYPANOSOMES
    Serap Aksoy; Fiscal Year: 2001
    ..The basic knowledge obtained will strengthen our understanding of tsetse biology and will also provide information relevant to other important disease vectors which harbor similar symbionts (e.g., ticks, fleas, reduviid bugs etc.). ..
  15. Adaptive evolution of pathogenesis towards symbiosis
    Serap Aksoy; Fiscal Year: 2009
    ..The role of functions typically associated with pathogenic microorganisms will be pursued in these beneficial microbes. ..