Research Topics
Species | Robert WaterstonSummaryAffiliation: University of Washington Country: USA Publications
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Detail Information
Publications
Comparison and calibration of transcriptome data from RNA-Seq and tiling arraysAshish Agarwal
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
BMC Genomics 11:383. 2010..Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs...- Investigating hookworm genomes by comparative analysis of two Ancylostoma speciesMakedonka Mitreva
Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
BMC Genomics 6:58. 2005..Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum... - AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesisThomas J Boyle
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
BMC Bioinformatics 7:275. 2006.... - Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryoZafer Aydin
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
BMC Bioinformatics 11:84. 2010..e., editing) is performed manually using a graphical interface tool named AceTree, which is specifically developed for this task. For a single experiment, this manual annotation task takes several hours... - More on the sequencing of the human genomeRobert H Waterston
Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 100:3022-4; author reply 3025-6. 2003 
Initial sequencing and comparative analysis of the mouse genomeRobert H Waterston
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 420:520-62. 2002....- Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegansMakedonka Mitreva
Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
Genome Res 14:209-20. 2004..We also provide functional classifications of S. stercoralis clusters... - Generation and annotation of the DNA sequences of human chromosomes 2 and 4Ladeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA
Nature 434:724-31. 2005..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions... - The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTreeJohn Isaac Murray
Department of Genome Sciences, University of Washington Box 357730, Seattle, Washington 98195, USA
Nat Protoc 1:1468-76. 2006..The protocol requires about 1 h of user time spread over 2 days to generate the raw lineage, and an additional 2 or 4 h to edit the lineage to the 194- or 350-cell stage, respectively... - Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and syntenyLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
PLoS Biol 5:e167. 2007..The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently... - On the sequencing of the human genomeRobert H Waterston
Genome Sequencing Center, Washington University, Saint Louis, MO 63108, USA
Proc Natl Acad Sci U S A 99:3712-6. 2002..Our analysis does not imply that a WGS approach could not be successfully applied to assemble a draft sequence of a large mammalian genome, but merely that the Celera paper does not provide such evidence... - Nematode.net: a tool for navigating sequences from parasitic and free-living nematodesTodd Wylie
The Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
Nucleic Acids Res 32:D423-6. 2004..The long-term goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species... - Genomics in C. elegans: so many genes, such a little wormLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
Genome Res 15:1651-60. 2005..We now have a solid platform on which to build toward the lofty goal of a true molecular understanding of worm biology with all its implications including those for human health... - Novel transcription regulatory elements in Caenorhabditis elegans muscle genesDebraj GuhaThakurta
Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
Genome Res 14:2457-68. 2004..We find that these DNA motifs are also present in the muscle promoters of C. briggsae, indicating that they are functionally conserved in the nematodes... - The DNA sequence of human chromosome 7Ladeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 424:157-64. 2003..Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame... - Positioning a medical school for modern biomedical research: the department of genome sciences at the University of Washington School of MedicineStanley Fields
Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195 7730, USA
Acad Med 81:882-5. 2006..Lessons learned in crafting this department are also discussed, as well as how these might apply to other medical schools... - Completing the map of human genetic variationEvan E Eichler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nature 447:161-5. 2007 - Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegansZhongying Zhao
Department of Genome Sciences, Box 355065, University of Washington, 1705 NE Pacific St, Seattle, WA 98195 5065, USA
Dev Biol 314:93-9. 2008.... - New tools for investigating the comparative biology of Caenorhabditis briggsae and C. elegansZhongying Zhao
Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
Genetics 184:853-63. 2010..elegans. With the emerging sequence of nematode species more closely related to C. briggsae, these tools may open novel avenues of experimentation in C. briggsae itself... 
Specific roles for the GATA transcription factors end-1 and end-3 during C. elegans E-lineage developmentMax E Boeck
Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, WA 98195, USA
Dev Biol 358:345-55. 2011....- Automated analysis of embryonic gene expression with cellular resolution in C. elegansJohn Isaac Murray
Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
Nat Methods 5:703-9. 2008..Systematic application of this system could reveal the gene activity of each cell throughout development... - Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stagesMakedonka Mitreva
Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, Box 8501, 4444 Forest Park Boulevard, St Louis, MO 63108, USA
Mol Biochem Parasitol 137:277-91. 2004..The genes discovered, when put into context of functional classification, stage of expression, and biology of the parasite, should substantially enhance experimental potential for research on this parasite... - Automated cell lineage tracing in Caenorhabditis elegansZhirong Bao
Department of Genome Sciences, University of Washington, WA 98195, USA
Proc Natl Acad Sci U S A 103:2707-12. 2006..We envision that this automation will make it practical to systematically decipher the developmental genes and pathways encoded in the genome of C. elegans... - Analysis and functional classification of transcripts from the nematode Meloidogyne incognitaJames P McCarter
Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St, Louis, MO 63108, USA
Genome Biol 4:R26. 2003..As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita... - Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencingMichael C Wendl
Washington University School of Medicine, St Louis, Missouri 63108, USA
Genome Res 12:1943-9. 2002.... - Massively parallel sequencing of the polyadenylated transcriptome of C. elegansLadeana W Hillier
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195 5065, USA
Genome Res 19:657-66. 2009..Although most sequences align with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of >10 kb localized to somatic nuclei... - Control of cell cycle timing during C. elegans embryogenesisZhirong Bao
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
Dev Biol 318:65-72. 2008..elegans embryogenesis as a model to dissect the interaction between differentiation and proliferation, and an effective approach combining genetic and statistical analysis at single-cell resolution... - Finding functional features in Saccharomyces genomes by phylogenetic footprintingPaul Cliften
Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
Science 301:71-6. 2003.... - The male-specific region of the human Y chromosome is a mosaic of discrete sequence classesHelen Skaletsky
Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 423:825-37. 2003..9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes... - Abundant gene conversion between arms of palindromes in human and ape Y chromosomesSteve Rozen
Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 423:873-6. 2003..We conclude that during recent evolution, an average of approximately 600 nucleotides per newborn male have undergone Y-Y gene conversion, which has had an important role in the evolution of multi-copy testis gene families in the MSY... - A physical map of the mouse genomeSimon G Gregory
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Nature 418:743-50. 2002..The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy... - The genome sequence of Caenorhabditis briggsae: a platform for comparative genomicsLincoln D Stein
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
PLoS Biol 1:E45. 2003..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes... - A transcriptomic analysis of the phylum NematodaJohn Parkinson
Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
Nat Genet 36:1259-67. 2004..Nematode-specific families are particularly interesting as drug and vaccine targets... - Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene databaseLi Li
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 13:443-54. 2003..These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets... - The DNA sequence of the human X chromosomeMark T Ross
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 434:325-37. 2005..Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence... - An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides rattiFiona J Thompson
School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
Mol Biochem Parasitol 142:32-46. 2005..Many of the parasitic-specific genes are, as yet, uncharacterised: one of these represents 25% of all ESTs obtained from the parasitic stage... - Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle developmentTetsunari Fukushige
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
Genes Dev 20:3395-406. 2006.... - mls-2 and vab-3 Control glia development, hlh-17/Olig expression and glia-dependent neurite extension in C. elegansSatoshi Yoshimura
The Rockefeller University, Laboratory of Developmental Genetics, 1230 York Avenue, New York, NY 10065, USA
Development 135:2263-75. 2008..Our results suggest possible similarities between CEPsh glia development and oligodendrocyte development in vertebrates, and demonstrate that C. elegans provides a unique environment for studying glial functions in vivo... - A proposal to sequence the amphioxus genome submitted to the Joint Genome Institute of the US Department of EnergyJeremy J Gibson-Brown
Department of Biology, Washington University, St. Louis, Missouri 63130, USA
J Exp Zoolog B Mol Dev Evol 300:5-22. 2003 - Software for automated analysis of DNA fingerprinting gelsDaniel R Fuhrmann
Department of Electrical Engineering, Washington University, St. Louis, Missouri 63130, USA
Genome Res 13:940-53. 2003..Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects... - Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosomeStefan Kirsch
Institute of Human Genetics, University of Heidelberg, INF 366, 69120 Heidelberg, Germany
Genome Res 15:195-204. 2005....
Research Grants
- ENHANCING THE VALUE OF THE C ELEGANS GENOME SEQUENCERobert Waterston; Fiscal Year: 2003..elegans genome dictates the development, behavior, and other biology of this small but complex animal. In turn, the principles learned here should help to unlock the information stored in other animal genomes, including human. ..
- Automated single cell expression analysis in C. elegansRobert Waterston; Fiscal Year: 2007..Knowledge of gene expression patterns in C. elegans would not only provide insights into the role of these genes in development, but would suggest roles of homologous genes in health and disease in other animals, including humans. ..
- Global Identification of transcribed elements in the C. elegans genomeRobert Waterston; Fiscal Year: 2007..The experience gained with this modest genome should be of value in interpreting more complex genomes, such as human. ..
- Automated single cell expression analysis in C. elegansRobert Waterston; Fiscal Year: 2009..elegans would not only provide insights into the role of these genes in development, but would suggest roles of homologous genes in health and disease in other animals, including humans. ..
- Automated single cell expression analysis in C. elegansRobert H Waterston; Fiscal Year: 2010..We expect the atlas we create as well as the methods we develop will speed those insights. ..