Robin Knight

Summary

Affiliation: University of Colorado
Country: USA

Publications

  1. doi request reprint Supervised classification of human microbiota
    Dan Knights
    Department of Computer Science, University of Colorado, Boulder, CO, USA
    FEMS Microbiol Rev 35:343-59. 2011
  2. pmc Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    J Gregory Caporaso
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    ISME J 6:1621-4. 2012
  3. pmc Evolutionary rates vary among rRNA structural elements
    S Smit
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Nucleic Acids Res 35:3339-54. 2007
  4. pmc Do universal codon-usage patterns minimize the effects of mutation and translation error?
    Roberto Marquez
    Department of Computer Science, New Mexico State University, MSC CS, Las Cruces, NM 88003, USA
    Genome Biol 6:R91. 2005
  5. pmc MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    Genome Biol 9:R128. 2008
  6. pmc Activating and inhibiting connections in biological network dynamics
    Daniel McDonald
    Department of Physics, University of Colorado, 390 UCB, Boulder, CO 80309, USA
    Biol Direct 3:49. 2008
  7. pmc Insights and inferences about integron evolution from genomic data
    Diana R Nemergut
    Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
    BMC Genomics 9:261. 2008
  8. pmc Fast-Find: a novel computational approach to analyzing combinatorial motifs
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:1. 2006
  9. pmc Using the nucleotide substitution rate matrix to detect horizontal gene transfer
    Micah Hamady
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:476. 2006
  10. pmc UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context
    Catherine Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:371. 2006

Collaborators

Detail Information

Publications71

  1. doi request reprint Supervised classification of human microbiota
    Dan Knights
    Department of Computer Science, University of Colorado, Boulder, CO, USA
    FEMS Microbiol Rev 35:343-59. 2011
    ....
  2. pmc Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    J Gregory Caporaso
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    ISME J 6:1621-4. 2012
    ....
  3. pmc Evolutionary rates vary among rRNA structural elements
    S Smit
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Nucleic Acids Res 35:3339-54. 2007
    ..The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions...
  4. pmc Do universal codon-usage patterns minimize the effects of mutation and translation error?
    Roberto Marquez
    Department of Computer Science, New Mexico State University, MSC CS, Las Cruces, NM 88003, USA
    Genome Biol 6:R91. 2005
    ..We tested whether codon and amino-acid usages from 457 bacteria, 264 eukaryotes, and 33 archaea minimize errors compared to random usages, and whether changes in genome G+C content influence these error values...
  5. pmc MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    Genome Biol 9:R128. 2008
    ..We demonstrate MotifCluster's accuracy using gold-standard protein superfamilies; using recommended settings, families were assigned to the correct superfamilies with 0.17% false positive and no false negative assignments...
  6. pmc Activating and inhibiting connections in biological network dynamics
    Daniel McDonald
    Department of Physics, University of Colorado, 390 UCB, Boulder, CO 80309, USA
    Biol Direct 3:49. 2008
    ....
  7. pmc Insights and inferences about integron evolution from genomic data
    Diana R Nemergut
    Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
    BMC Genomics 9:261. 2008
    ..Here, we provide a systematic analysis of the distribution and diversity of integron intI genes and integron-containing bacteria...
  8. pmc Fast-Find: a novel computational approach to analyzing combinatorial motifs
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:1. 2006
    ..Identifying transcripts that contain meaningful combinations of patterns is thus an important problem, which existing tools address poorly...
  9. pmc Using the nucleotide substitution rate matrix to detect horizontal gene transfer
    Micah Hamady
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:476. 2006
    ..Existing sequence-based methods for detecting HGT focus on changes in nucleotide composition or on differences between gene and genome phylogenies; these methods have high error rates...
  10. pmc UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context
    Catherine Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    BMC Bioinformatics 7:371. 2006
    ..Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses...
  11. pmc Pathological rate matrices: from primates to pathogens
    Harold W Schranz
    John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
    BMC Bioinformatics 9:550. 2008
    ..Here we tested whether pathological rate matrices exist in nature, and consider the suitability of different algorithms to their computation...
  12. pmc Species divergence and the measurement of microbial diversity
    Catherine A Lozupone
    Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    FEMS Microbiol Rev 32:557-78. 2008
    ..Consequently, divergence-based methods are providing new insights into microbial community structure and function...
  13. pmc PyCogent: a toolkit for making sense from sequence
    Rob Knight
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
    Genome Biol 8:R171. 2007
    ..The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent...
  14. pmc Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids
    Rob Knight
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Nucleic Acids Res 33:5924-35. 2005
    ..1 x 10(9) for the isoleucine aptamer and 1.6 x 10(10) for the hammerhead ribozyme. These figures are consistent with the facile recovery of these motifs from SELEX experiments...
  15. pmc Analyzing partially randomized nucleic acid pools: straight dope on doping
    Rob Knight
    Department of Molecular, Cellular and Developmental Biology, Campus Box 347, University of Colorado, Boulder, CO 80309, USA
    Nucleic Acids Res 31:e30. 2003
    ..A web form is provided for customized calculations...
  16. pmc Natural and artificial RNAs occupy the same restricted region of sequence space
    Ryan Kennedy
    Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
    RNA 16:280-9. 2010
    ..These universal evolved sequence features are therefore intrinsic in RNA molecules that bind small-molecule targets or catalyze reactions...
  17. pmc Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples
    Christian L Lauber
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 0216, USA
    FEMS Microbiol Lett 307:80-6. 2010
    ..These results suggest that many samples collected and stored under field conditions without refrigeration may be useful for microbial community analyses...
  18. pmc CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition
    Jesse Zaneveld
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
    Methods Mol Biol 537:207-32. 2009
    ..CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses...
  19. pmc Stable tRNA-based phylogenies using only 76 nucleotides
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    RNA 16:1469-77. 2010
    ....
  20. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
    ..These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease...
  21. pmc BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences
    Rob Knight
    Department of Molecular, Cellular, and Developmental Biology, Campus Box 347, University of Colorado, Boulder 80309, USA
    RNA 10:1323-36. 2004
    ..The Web interface, available at http://bayes.colorado.edu/fold/, includes the flexibility to thread any of the sequences (or the consensus sequence) through any of the structures, including the one judged most probable...
  22. pmc Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
    Jesse R Zaneveld
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Nucleic Acids Res 38:3869-79. 2010
    ....
  23. pmc Size, constant sequences, and optimal selection
    Michal Legiewicz
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 80309 0347, USA
    RNA 11:1701-9. 2005
    ..Differing random tract lengths also determined the probable motif permutation and the most abundant helix lengths. These data support a significant but lesser role for primer sequences in the outcome of selections...
  24. pmc The convergence of carbohydrate active gene repertoires in human gut microbes
    Catherine A Lozupone
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 105:15076-81. 2008
    ....
  25. pmc Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
    Justin Kuczynski
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Nat Methods 7:813-9. 2010
    ..These results also provide a basis for understanding tradeoffs between number of samples and depth of coverage, tradeoffs that are important to consider when designing studies to characterize microbial communities...
  26. pmc Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    BMC Evol Biol 8:327. 2008
    ..We further considered the influence of sequence recoding using reduced-state amino acid alphabets, a common tactic employed in coevolutionary analyses to improve both statistical and computational performance...
  27. pmc Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO, USA
    ISME J 4:17-27. 2010
    ..Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac...
  28. ncbi request reprint Information, probability, and the abundance of the simplest RNA active sites
    Ryan Kennedy
    Department of Computer Science, University of Colorado at Boulder, 430 UCB, Boulder, CO 80309 0430, USA
    Front Biosci 13:6060-71. 2008
    ..We show that all of the methods that take modularity into account provide far more accurate estimates of this probability than the informational methods, and that fast approximate methods are suitable for a wide range of RNA motifs...
  29. pmc Short pyrosequencing reads suffice for accurate microbial community analysis
    Zongzhi Liu
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    Nucleic Acids Res 35:e120. 2007
    ....
  30. pmc Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
    Catherine A Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Appl Environ Microbiol 73:1576-85. 2007
    ..We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny...
  31. pmc CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    Bioinformatics 25:1331-2. 2009
    ....
  32. pmc Finding specific RNA motifs: function in a zeptomole world?
    Rob Knight
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309 0347, USA
    RNA 9:218-30. 2003
    ..This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules...
  33. pmc Forensic identification using skin bacterial communities
    Noah Fierer
    Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 107:6477-81. 2010
    ....
  34. pmc A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses
    Ryan T Jones
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    ISME J 3:442-53. 2009
    ....
  35. ncbi request reprint Multiple pattern matching: a Markov chain approach
    Manuel E Lladser
    Department of Applied Mathematics, University of Colorado at Boulder, 526 UCB, Boulder, CO 80309 0526, USA
    J Math Biol 56:51-92. 2008
    ..The applications we present focus on the concept of synchronization of automata, as well as automata used to search for a finite number of keywords (including sets of patterns generated according to base pairing rules) in a general text...
  36. doi request reprint RNA-amino acid binding: a stereochemical era for the genetic code
    Michael Yarus
    Department of MCD Biology and Chemistry Biochemistry, University of Colorado, Boulder, CO 80309 0347, USA
    J Mol Evol 69:406-29. 2009
    ..A Direct RNA Template scheme embodying a credible early history for coded peptide synthesis is readily constructed based on these observations...
  37. ncbi request reprint DivergentSet, a tool for picking non-redundant sequences from large sequence collections
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
    Mol Cell Proteomics 5:1520-32. 2006
    ..This instability suggests that the types of sensitivity analysis enabled by DivergentSet may be widely useful for identifying the motifs of biological significance...
  38. pmc Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei
    Robert M Bowers
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, USA
    Appl Environ Microbiol 75:5121-30. 2009
    ..However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria...
  39. pmc Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
    Christian L Lauber
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, 80309, USA
    Appl Environ Microbiol 75:5111-20. 2009
    ....
  40. pmc Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories
    Sandra Smit
    Department of Chemistry and Biochemistry, Campus Box 215, University of Colorado at Boulder, Boulder, CO 80309, USA
    RNA 12:1-14. 2006
    ..They also suggest caution in interpreting differences in the rate of change of the GC content in different parts of the molecule as evidence of differential selection...
  41. ncbi request reprint Bacterial communities of disease vectors sampled across time, space, and species
    Ryan T Jones
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
    ISME J 4:223-31. 2010
    ....
  42. pmc Comparison of methods for estimating the nucleotide substitution matrix
    Maribeth Oscamou
    Department of Applied Mathematics, University of Colorado, Boulder, CO, USA
    BMC Bioinformatics 9:511. 2008
    ..However, the speed and accuracy of these methods has not been compared...
  43. pmc The influence of sex, handedness, and washing on the diversity of hand surface bacteria
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 105:17994-9. 2008
    ....
  44. pmc Global patterns in bacterial diversity
    Catherine A Lozupone
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 104:11436-40. 2007
    ..This work provides a framework for understanding the impact of environmental factors on bacterial evolution and for the direction of future sequencing efforts to discover new lineages...
  45. doi request reprint Global patterns in the biogeography of bacterial taxa
    Diana R Nemergut
    Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
    Environ Microbiol 13:135-44. 2011
    ....
  46. ncbi request reprint Origins of the genetic code: the escaped triplet theory
    Michael Yarus
    Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309 0347, USA
    Annu Rev Biochem 74:179-98. 2005
    ..These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself...
  47. ncbi request reprint Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids
    Alexey Wolfson
    Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, CO 80309, USA
    FEBS Lett 579:3467-72. 2005
    ..The significance of this association is discussed in terms of the structural organization of translation in the living cell...
  48. pmc Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA
    Irene Majerfeld
    Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    RNA 16:1915-24. 2010
    ..Addition of the new element yields a sufficient binding site by the insertion criterion, binding tryptophan in 22 out of 23 tries. Random insertion testing for site sufficiency seems likely to be broadly revealing...
  49. doi request reprint Changes through time: integrating microorganisms into the study of succession
    Noah Fierer
    Dept of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    Res Microbiol 161:635-42. 2010
    ....
  50. pmc Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309 0216, USA
    Appl Environ Microbiol 73:7059-66. 2007
    ..Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse...
  51. pmc Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutations
    Massimo Buvoli
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Trends Cardiovasc Med 18:141-9. 2008
    ..Increasing knowledge of the characteristics of MH7 mutations may provide a valuable resource for scientists and clinicians studying diagnosis, risk stratification, and treatment of disease associated with these mutations...
  52. pmc Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
    Zongzhi Liu
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    Nucleic Acids Res 36:e120. 2008
    ....
  53. pmc Short-term temporal variability in airborne bacterial and fungal populations
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, 216 UCB, CIRES, Boulder, CO 80309 0216, USA
    Appl Environ Microbiol 74:200-7. 2008
    ..These results suggest that outdoor air may harbor similar types of bacteria regardless of location and that the short-term temporal variability in airborne bacterial assemblages can be very large...
  54. pmc PyNAST: a flexible tool for aligning sequences to a template alignment
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    Bioinformatics 26:266-7. 2010
    ..Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API)...
  55. doi request reprint Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns
    Jesse R Zaneveld
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Microbiology 154:1-15. 2008
    ..Finally, we describe software, databases and algorithms for identifying particular classes of mobile elements, and outline prospects for better detection of HGT based on specific mechanisms of transfer...
  56. pmc Direct sequencing of the human microbiome readily reveals community differences
    Justin Kuczynski
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Genome Biol 11:210. 2010
    ....
  57. pmc Simple, recurring RNA binding sites for L-arginine
    Teresa Janas
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    RNA 16:805-16. 2010
    ..An arginine coding triplet (codon/anticodon) is highly conserved within the largest family of Arg sites (72% of all sequences), as has also been found in minimal, most prevalent RNA binding sites for Ile, His, and Trp...
  58. pmc Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
    Micah Hamady
    Department of Computer Science, UCB 430, University of Colorado, Boulder, Colorado 80309, USA
    Nat Methods 5:235-7. 2008
    ....
  59. pmc UniFrac: a new phylogenetic method for comparing microbial communities
    Catherine Lozupone
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Appl Environ Microbiol 71:8228-35. 2005
    ....
  60. ncbi request reprint tRNA creation by hairpin duplication
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    J Mol Evol 61:524-30. 2005
    ..These results support the hypothesis that the modern tRNA cloverleaf arose from a single hairpin duplication prior to the divergence of modern tRNA specificities and the three domains of life...
  61. pmc A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins
    Chia Yu Yen
    Department of Chemistry and Biochemistry and paragraph signHoward Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
    Mol Cell Proteomics 8:857-69. 2009
    ....
  62. ncbi request reprint Does protein structure influence trypsin miscleavage? Using structural properties to predict the behavior of related proteins
    Micah Hamady
    Department of Computer Science, University of Colorado at Boulder, USA
    IEEE Eng Med Biol Mag 24:58-66. 2005
  63. pmc Host-bacterial coevolution and the search for new drug targets
    Jesse Zaneveld
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, United States
    Curr Opin Chem Biol 12:109-14. 2008
    ..Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities...
  64. ncbi request reprint Key challenges in proteomics and proteoinformatics. Progress in proteins
    Micah Hamady
    Department of Computer Science, University of Colorado at Boulder, USA
    IEEE Eng Med Biol Mag 24:34-40. 2005
  65. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007
    ..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...
  66. pmc The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis
    Philip McKenna
    Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
    PLoS Pathog 4:e20. 2008
    ..This work provides comprehensive data and improved methods for studying the role of commensal microbiota in macaque models of GI diseases and provides a model for the large-scale screening of the human gut microbiome...
  67. pmc From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal
    Sandra Smit
    Centre for Integrative Bioinformatics VU IBIVU, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
    RNA 14:410-6. 2008
    ..We provide access to reference implementations through a web interface (at http://www.ibi.vu.nl/programs/k2nwww), and the source code is available in the PyCogent project...
  68. ncbi request reprint Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Mail Stop 8303, P O Box 6511, Aurora, CO 80045, USA
    J Mol Evol 61:597-607. 2005
    ..We explicitly show that prior fixation of a stereochemical core is consistent with an effective later minimization of error...
  69. pmc Evolution of mammals and their gut microbes
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 320:1647-51. 2008
    ....
  70. pmc Worlds within worlds: evolution of the vertebrate gut microbiota
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nat Rev Microbiol 6:776-88. 2008
    ....
  71. ncbi request reprint The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology
    Ruth E Ley
    Center for Genome Sciences, Washington University, St Louis, MO, USA
    Environ Microbiol 9:3-4. 2007

Research Grants4

  1. New Tools for Understanding the Composition and Dynamics of Microbial Communities
    Robin Knight; Fiscal Year: 2009
    ....
  2. New Tools for Understanding the Composition and Dynamics of Microbial Communities
    Robin Knight; Fiscal Year: 2009
    ..The investigators intend to work closely with other researchers involved in the HMP in order to ensure rapid progress. ..
  3. New Tools for Understanding the Composition and Dynamics of Microbial Communities
    Robin Knight; Fiscal Year: 2010
    ....