Monica Riley

Summary

Affiliation: Marine Biological Laboratory
Country: USA

Publications

  1. pmc Extending knowledge of Escherichia coli metabolism by modeling and experiment
    Eberhard O Voit
    Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Genome Biol 4:235. 2003
  2. pmc Genomics of an extreme psychrophile, Psychromonas ingrahamii
    Monica Riley
    Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    BMC Genomics 9:210. 2008
  3. ncbi request reprint Searchlight on domains
    Monica Riley
    Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Structure 15:1-2. 2007
  4. pmc Escherichia coli K-12: a cooperatively developed annotation snapshot--2005
    Monica Riley
    Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Nucleic Acids Res 34:1-9. 2006
  5. pmc Genes and proteins of Escherichia coli K-12 (GenProtEC)
    M Riley
    Marine Biology Laboratory, Woods Hole, MA 02540, USA
    Nucleic Acids Res 25:51-2. 1997
  6. pmc A functional update of the Escherichia coli K-12 genome
    M H Serres
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Genome Biol 2:RESEARCH0035. 2001
  7. pmc Genes and proteins of Escherichia coli K-12
    M Riley
    Marine Biology Laboratory, Woods Hole, MA 02540, USA
    Nucleic Acids Res 26:54. 1998
  8. ncbi request reprint Systems for categorizing functions of gene products
    M Riley
    Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Curr Opin Struct Biol 8:388-92. 1998
  9. ncbi request reprint Interim report on genomics of Escherichia coli
    M Riley
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
    Annu Rev Microbiol 54:341-411. 2000
  10. ncbi request reprint Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome
    Margrethe H Serres
    Marine Biological Laboratory, Woods Hole, Massachusetts 02543 1015, USA
    OMICS 8:306-21. 2004

Research Grants

  1. E. coli Annotation Workshop
    Monica Riley; Fiscal Year: 2005

Detail Information

Publications21

  1. pmc Extending knowledge of Escherichia coli metabolism by modeling and experiment
    Eberhard O Voit
    Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Genome Biol 4:235. 2003
    ..Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors...
  2. pmc Genomics of an extreme psychrophile, Psychromonas ingrahamii
    Monica Riley
    Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    BMC Genomics 9:210. 2008
    ..Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles...
  3. ncbi request reprint Searchlight on domains
    Monica Riley
    Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Structure 15:1-2. 2007
    ..Domain function is relevant to molecular evolution and to annotation of proteins known only by sequence...
  4. pmc Escherichia coli K-12: a cooperatively developed annotation snapshot--2005
    Monica Riley
    Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Nucleic Acids Res 34:1-9. 2006
    ..Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles...
  5. pmc Genes and proteins of Escherichia coli K-12 (GenProtEC)
    M Riley
    Marine Biology Laboratory, Woods Hole, MA 02540, USA
    Nucleic Acids Res 25:51-2. 1997
    ..coliproteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html ...
  6. pmc A functional update of the Escherichia coli K-12 genome
    M H Serres
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Genome Biol 2:RESEARCH0035. 2001
    ..On the basis of this new information, an updated version of the annotated chromosome has been generated...
  7. pmc Genes and proteins of Escherichia coli K-12
    M Riley
    Marine Biology Laboratory, Woods Hole, MA 02540, USA
    Nucleic Acids Res 26:54. 1998
    ..coli proteins, representing groups of paralogous genes, with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can be accessed at the URL http://www.mbl.edu/html/ecoli.html..
  8. ncbi request reprint Systems for categorizing functions of gene products
    M Riley
    Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Curr Opin Struct Biol 8:388-92. 1998
    ..As much as possible, the same systems should be applicable to all organisms, so that when comparability exists among organisms the connections will become clear...
  9. ncbi request reprint Interim report on genomics of Escherichia coli
    M Riley
    The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
    Annu Rev Microbiol 54:341-411. 2000
    ..We also address classification of functions of gene products and avenues of insight into the history of protein evolution...
  10. ncbi request reprint Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome
    Margrethe H Serres
    Marine Biological Laboratory, Woods Hole, Massachusetts 02543 1015, USA
    OMICS 8:306-21. 2004
    ..Making use of several approaches not commonly used in annotation, we have been able to enrich our understanding of the functions encoded by the S. oneidensis genome...
  11. pmc Gene fusions and gene duplications: relevance to genomic annotation and functional analysis
    Margrethe H Serres
    Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543 1015, USA
    BMC Genomics 6:33. 2005
    ..Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes...
  12. pmc Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments
    Margrethe H Serres
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    J Bacteriol 188:4601-9. 2006
    ..This is an example of how a biochemically oriented sequence analysis can generate questions and direct further experimental investigation...
  13. pmc Evolution by leaps: gene duplication in bacteria
    Margrethe H Serres
    Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Biol Direct 4:46. 2009
    ..Comparing protein families of different organisms give insight into functional differences and similarities...
  14. pmc GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
    Margrethe H Serres
    Marine Biological Laboratory, Woods Hole, MA 02540, USA
    Nucleic Acids Res 32:D300-2. 2004
    ..We now use a rich system of characterizing cell roles which accents the fact that many proteins play more than one cellular role and therefore carry more than one designation from our detailed catalog of roles, MultiFun...
  15. ncbi request reprint Domain evolution and functional diversification of sulfite reductases
    Ashita Dhillon
    Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts 02543, USA
    Astrobiology 5:18-29. 2005
    ..aSiR, asrC, and alSir) suggest that their functional diversification during evolution may have preceded the bacterial/archaeal divergence...
  16. ncbi request reprint Physiological genomics of Escherichia coli protein families
    Ping Liang
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
    Physiol Genomics 9:15-26. 2002
    ..Data for the complete list of paralogous protein families and updated functional annotation for E. coli K-12 are accessible in GenProtEC (http://genprotec.mbl.edu)...
  17. pmc Eco Cyc: encyclopedia of Escherichia coli genes and metabolism
    P D Karp
    Pangea Systems Inc, 4040 Campbell Avenue, Menlo Park, CA 94025, USA and Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Nucleic Acids Res 27:55-8. 1999
    ..EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/..
  18. pmc Divergence of function in sequence-related groups of Escherichia coli proteins
    L A Nahum
    The Josephine Bay Paul Center-Marine Biological Laboratory, Woods Hole, Massachusetts 02543-1015, USA
    Genome Res 11:1375-81. 2001
    ..This information has relevance to the area of functional genomics in which the activities of gene products of unknown reading frames are attributed by analogy to the functions of sequence-related proteins of known function...
  19. pmc The MetaCyc Database
    Peter D Karp
    Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA
    Nucleic Acids Res 30:59-61. 2002
    ..org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info@ai.sri.com for information on obtaining a local copy of MetaCyc...
  20. pmc The EcoCyc Database
    Peter D Karp
    Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA
    Nucleic Acids Res 30:56-8. 2002
    ..EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/...
  21. pmc Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Proc Natl Acad Sci U S A 102:2099-104. 2005
    ..We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome...

Research Grants1

  1. E. coli Annotation Workshop
    Monica Riley; Fiscal Year: 2005
    ..coli information as it is fragmented into several databases with different objectives and there is contradictions.The output of a workshop and a follow-up smaller meeting will meet and solve this serious problem. ..