Rob Knight

Summary

Affiliation: University of Colorado
Country: USA

Publications

  1. 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
  2. pmc The mind-body-microbial continuum
    Antonio Gonzalez
    Department of Computer Science, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Dialogues Clin Neurosci 13:55-62. 2011
  3. pmc TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
    Meg Pirrung
    Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
    Bioinformatics 27:3067-9. 2011
  4. pmc Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions
    Laura Wegener Parfrey
    Department of Chemistry and Biochemistry, University of Colorado Boulder, CO, USA
    Front Microbiol 2:153. 2011
  5. pmc Cohabiting family members share microbiota with one another and with their dogs
    Se Jin Song
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, United States
    elife 2:e00458. 2013
  6. pmc The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    Daniel McDonald
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    Gigascience 1:7. 2012
  7. pmc Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)
    Andrea R Ottesen
    FDA Center for Food Safety and Applied Nutrition, Division of Microbiology, Molecular Methods and Subtyping, 5100 Paint Branch Parkway, College Park, MD 20740, USA
    BMC Microbiol 13:114. 2013
  8. pmc Unlocking the potential of metagenomics through replicated experimental design
    Rob Knight
    Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA
    Nat Biotechnol 30:513-20. 2012
  9. pmc Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
    Gary D Wu
    Division of Gastroenterology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6076 USA
    BMC Microbiol 10:206. 2010
  10. 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

Detail Information

Publications103 found, 100 shown here

  1. 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
    ....
  2. pmc The mind-body-microbial continuum
    Antonio Gonzalez
    Department of Computer Science, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Dialogues Clin Neurosci 13:55-62. 2011
    ..Better understanding of microbiome-encoded pathways for xenobiotic metabolism also has important implications for improving the efficacy of pharmacologic interventions with neuromodulatory agents...
  3. pmc TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
    Meg Pirrung
    Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
    Bioinformatics 27:3067-9. 2011
    ....
  4. pmc Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions
    Laura Wegener Parfrey
    Department of Chemistry and Biochemistry, University of Colorado Boulder, CO, USA
    Front Microbiol 2:153. 2011
    ....
  5. pmc Cohabiting family members share microbiota with one another and with their dogs
    Se Jin Song
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, United States
    elife 2:e00458. 2013
    ..DOI:http://dx.doi.org/10.7554/eLife.00458.001...
  6. pmc The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    Daniel McDonald
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    Gigascience 1:7. 2012
    ....
  7. pmc Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)
    Andrea R Ottesen
    FDA Center for Food Safety and Applied Nutrition, Division of Microbiology, Molecular Methods and Subtyping, 5100 Paint Branch Parkway, College Park, MD 20740, USA
    BMC Microbiol 13:114. 2013
    ....
  8. pmc Unlocking the potential of metagenomics through replicated experimental design
    Rob Knight
    Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA
    Nat Biotechnol 30:513-20. 2012
    ..Improvements in comparability of data will facilitate the study of biotechnologically relevant processes, such as bioprospecting for new glycoside hydrolases or identifying novel energy sources...
  9. pmc Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
    Gary D Wu
    Division of Gastroenterology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6076 USA
    BMC Microbiol 10:206. 2010
    ....
  10. 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...
  11. 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...
  12. pmc Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients
    Noah Fierer
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
    ISME J 6:1007-17. 2012
    ....
  13. pmc Moving pictures of the human microbiome
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
    Genome Biol 12:R50. 2011
    ..Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints...
  14. pmc Experimental and analytical tools for studying the human microbiome
    Justin Kuczynski
    Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, 347 UCB, Boulder, Colorado 80309, USA
    Nat Rev Genet 13:47-58. 2012
    ..Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis...
  15. 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...
  16. 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
    ....
  17. 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
    ....
  18. 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...
  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 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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
    ....
  25. pmc Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation
    Jesse R R Zaneveld
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Trends Microbiol 19:472-82. 2011
    ..Phylogenetic approaches and detailed information about each environmental sample will be crucial as the ability to collect genome sequences continues to expand...
  26. pmc Examining the global distribution of dominant archaeal populations in soil
    Scott T Bates
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    ISME J 5:908-17. 2011
    ..This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups...
  27. pmc Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 108:4516-22. 2011
    ..The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution...
  28. pmc Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
    J Kirk Harris
    Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO, USA
    ISME J 7:50-60. 2013
    ....
  29. pmc Meta-analyses of studies of the human microbiota
    Catherine A Lozupone
    Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
    Genome Res 23:1704-14. 2013
    ....
  30. pmc Using QIIME to analyze 16S rRNA gene sequences from microbial communities
    Justin Kuczynski
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Curr Protoc Microbiol . 2012
    ..The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities...
  31. pmc Diversity, distribution and sources of bacteria in residential kitchens
    Gilberto E Flores
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Environ Microbiol 15:588-96. 2013
    ..These results also illustrate the ease with which human- and food-associated bacteria can be transferred in residential settings to kitchen surfaces...
  32. pmc RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    RNA 18:1319-27. 2012
    ..The improved alignments have been contributed to the Rfam database...
  33. pmc PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
    William A Walters
    Department of Molecular, Cellular, and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO 80309, USA
    Bioinformatics 27:1159-61. 2011
    ..PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task...
  34. 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...
  35. doi request reprint Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    Science 342:621-4. 2013
    ....
  36. 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
    ....
  37. 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)...
  38. pmc Global biogeography of highly diverse protistan communities in soil
    Scott T Bates
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    ISME J 7:652-9. 2013
    ..However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability...
  39. pmc Boulder ALignment Editor (ALE): a web-based RNA alignment tool
    Jesse Stombaugh
    Department of Chemistry and Biochemistry, University of Colorado, CO, USA
    Bioinformatics 27:1706-7. 2011
    ....
  40. pmc Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments
    Robert M Bowers
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 0216, USA
    ISME J 5:601-12. 2011
    ..This work furthers our understanding of bacterial diversity in the atmosphere, the terrestrial controls on this diversity and potential approaches for source tracking of airborne bacteria...
  41. 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...
  42. 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
    ....
  43. 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...
  44. pmc Defining the human microbiome
    Luke K Ursell
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Nutr Rev 70:S38-44. 2012
    ..Additional advances in sequencing technology and in our understanding of the microbiome will provide exciting prospects for exploiting the microbiota for personalized medicine...
  45. pmc Characterizing microbial communities through space and time
    Antonio Gonzalez
    Department of Computer Science, University of Colorado at Boulder, Boulder, CO 80309, USA
    Curr Opin Biotechnol 23:431-6. 2012
    ..The fusion of proper spatio-temporal sampling, combined with modern multi-omics and computational tools, will provide insight into the tracking, development and manipulation of microbial communities...
  46. pmc A meta-analysis of changes in bacterial and archaeal communities with time
    Ashley Shade
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
    ISME J 7:1493-506. 2013
    ..These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and 'macro'-bial communities alike. ..
  47. doi request reprint The amphibian skin-associated microbiome across species, space and life history stages
    Jordan G Kueneman
    Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N 122, UCB 334, Boulder, CO, 80309, USA
    Mol Ecol 23:1238-50. 2014
    ....
  48. pmc Sources of bacteria in outdoor air across cities in the midwestern United States
    Robert M Bowers
    Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
    Appl Environ Microbiol 77:6350-6. 2011
    ..Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere...
  49. pmc An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    Daniel McDonald
    Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
    ISME J 6:610-8. 2012
    ..The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/...
  50. pmc The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites
    Luke K Ursell
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    J Allergy Clin Immunol 129:1204-8. 2012
    ....
  51. pmc Using QIIME to analyze 16S rRNA gene sequences from microbial communities
    Justin Kuczynski
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Curr Protoc Bioinformatics . 2011
    ..The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities...
  52. 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
    ....
  53. 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
    ....
  54. pmc Co-habiting amphibian species harbor unique skin bacterial communities in wild populations
    Valerie J McKenzie
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 0334, USA
    ISME J 6:588-96. 2012
    ..In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens...
  55. 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...
  56. pmc Advancing our understanding of the human microbiome using QIIME
    José A Navas-Molina
    Department of Computer Science, University of Colorado, Boulder, Colorado, USA
    Methods Enzymol 531:371-444. 2013
    ..We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses. ..
  57. 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...
  58. pmc Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
    Catherine Lozupone
    Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
    Genome Res 22:1974-84. 2012
    ....
  59. 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...
  60. 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...
  61. pmc A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system
    Jessica L Metcalf
    BioFrontiers Institute, University of Colorado at Boulder, Boulder, United States
    elife 2:e01104. 2013
    ..DOI:http://dx.doi.org/10.7554/eLife.01104.001. ..
  62. 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...
  63. pmc The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves
    Amanda J Redford
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    Environ Microbiol 12:2885-93. 2010
    ..ponderosa needles...
  64. 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...
  65. 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
    ....
  66. 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...
  67. pmc SitePainter: a tool for exploring biogeographical patterns
    Antonio Gonzalez
    Department of Computer Science, University of Colorado at Boulder and Howard Hughes Medical Institute, Boulder, CO 80309, USA
    Bioinformatics 28:436-8. 2012
    ..SitePainter thus increases the visual power and ability to explore spatially explicit studies...
  68. pmc Postprandial remodeling of the gut microbiota in Burmese pythons
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    ISME J 4:1375-85. 2010
    ..The Burmese python may provide a unique model for dissecting these interrelationships...
  69. 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...
  70. 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...
  71. doi request reprint Convergence of gut microbiomes in myrmecophagous mammals
    Frédéric Delsuc
    Institut des Sciences de l Evolution, UMR 5554 CNRS IRD, Universite Montpellier 2, Montpellier, France Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
    Mol Ecol 23:1301-17. 2014
    ..This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages...
  72. 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
    ....
  73. 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
  74. pmc The intestinal metabolome: an intersection between microbiota and host
    Luke K Ursell
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado
    Gastroenterology 146:1470-6. 2014
    ....
  75. 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...
  76. 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...
  77. 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...
  78. 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...
  79. 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...
  80. pmc Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch
    Colby D Stoddard
    Department of Chemistry and Biochemistry, 596 UCB, University of Colorado, Boulder, CO 80309 0596, USA
    J Mol Biol 425:1596-611. 2013
    ..The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs...
  81. pmc Microbial biogeography of public restroom surfaces
    Gilberto E Flores
    Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America
    PLoS ONE 6:e28132. 2011
    ....
  82. doi request reprint Biogeography and habitat modelling of high-alpine bacteria
    Andrew J King
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
    Nat Commun 1:53. 2010
    ..Furthermore, our global analysis of high-elevation soils from the Andes, Rockies, Himalayas and Alaskan range shows that habitat distribution models for bacteria have a strong predictive power across the entire globe...
  83. pmc Bayesian community-wide culture-independent microbial source tracking
    Dan Knights
    Department of Computer Science, University of Colorado, Boulder, Colorado, USA
    Nat Methods 8:761-3. 2011
    ..We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing...
  84. ncbi request reprint Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems
    Kelly S Ramirez
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
    Ecology 91:3463-70; discussion 3503-14. 2010
    ....
  85. pmc Human-associated microbial signatures: examining their predictive value
    Dan Knights
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    Cell Host Microbe 10:292-6. 2011
    ..We suggest turning to machine learning and discuss key directions toward harnessing human-associated microbial signatures...
  86. pmc Host-associated and free-living phage communities differ profoundly in phylogenetic composition
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, United States of America
    PLoS ONE 6:e16900. 2011
    ....
  87. 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
    ....
  88. pmc Bacterial communities associated with the lichen symbiosis
    Scott T Bates
    Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Rm 318, CIRES Bldg, Boulder, CO 80309, USA
    Appl Environ Microbiol 77:1309-14. 2011
    ..Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses...
  89. 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
    ....
  90. 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...
  91. ncbi request reprint Microbes do not follow the elevational diversity patterns of plants and animals
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
    Ecology 92:797-804. 2011
    ....
  92. doi 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
    ....
  93. pmc The impact of the gut microbiota on human health: an integrative view
    Jose C Clemente
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Cell 148:1258-70. 2012
    ....
  94. 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
    ....
  95. 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
    ....
  96. 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
    ....
  97. 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
    ....
  98. 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...
  99. 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...