Research Topics
| Robin KnightSummaryAffiliation: University of Colorado Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Supervised classification of human microbiotaDan Knights
Department of Computer Science, University of Colorado, Boulder, CO, USA
FEMS Microbiol Rev 35:343-59. 2011....- 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... - MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifsMicah 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... - Activating and inhibiting connections in biological network dynamicsDaniel McDonald
Department of Physics, University of Colorado, 390 UCB, Boulder, CO 80309, USA
Biol Direct 3:49. 2008.... - Insights and inferences about integron evolution from genomic dataDiana 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... - Fast-Find: a novel computational approach to analyzing combinatorial motifsMicah 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... - Using the nucleotide substitution rate matrix to detect horizontal gene transferMicah 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... - UniFrac--an online tool for comparing microbial community diversity in a phylogenetic contextCatherine 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... - Pathological rate matrices: from primates to pathogensHarold 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... - Species divergence and the measurement of microbial diversityCatherine 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... - Analyzing partially randomized nucleic acid pools: straight dope on dopingRob 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... - PyCogent: a toolkit for making sense from sequenceRob 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... - Abundance of correctly folded RNA motifs in sequence space, calculated on computational gridsRob 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... - Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samplesChristian 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... - Natural and artificial RNAs occupy the same restricted region of sequence spaceRyan 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... - Bacterial community variation in human body habitats across space and timeElizabeth 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... - CodonExplorer: an interactive online database for the analysis of codon usage and sequence compositionJesse 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... - Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relativesJesse R Zaneveld
Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
Nucleic Acids Res 38:3869-79. 2010.... - BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequencesRob 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... - Stable tRNA-based phylogenies using only 76 nucleotidesJeremy Widmann
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
RNA 16:1469-77. 2010.... - Size, constant sequences, and optimal selectionMichal 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... - The convergence of carbohydrate active gene repertoires in human gut microbesCatherine 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.... - Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metricsJ 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... - Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communitiesCatherine 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... - Information, probability, and the abundance of the simplest RNA active sitesRyan 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... - Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip dataMicah 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... - Short pyrosequencing reads suffice for accurate microbial community analysisZongzhi Liu
Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
Nucleic Acids Res 35:e120. 2007.... - Microbial community resemblance methods differ in their ability to detect biologically relevant patternsJustin 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... - Comparison of methods for estimating the nucleotide substitution matrixMaribeth 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... - The influence of sex, handedness, and washing on the diversity of hand surface bacteriaNoah 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.... - Global patterns in the biogeography of bacterial taxaDiana R Nemergut
Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
Environ Microbiol 13:135-44. 2011.... - Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNAIrene 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... - Changes through time: integrating microorganisms into the study of successionNoah Fierer
Dept of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
Res Microbiol 161:635-42. 2010.... - A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analysesRyan T Jones
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
ISME J 3:442-53. 2009.... - Forensic identification using skin bacterial communitiesNoah 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.... - PyNAST: a flexible tool for aligning sequences to a template alignmentJ 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)... - Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nucleiRobert 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... - Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scaleChristian L Lauber
Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, 80309, USA
Appl Environ Microbiol 75:5111-20. 2009.... - RNA-amino acid binding: a stereochemical era for the genetic codeMichael 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... - Bacterial communities of disease vectors sampled across time, space, and speciesRyan T Jones
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
ISME J 4:223-31. 2010.... - CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomesMicah Hamady
Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
Bioinformatics 25:1331-2. 2009.... - Origins of the genetic code: the escaped triplet theoryMichael 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... - Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acidsAlexey 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... - Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categoriesSandra 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... - DivergentSet, a tool for picking non-redundant sequences from large sequence collectionsJeremy 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... - 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... - Global patterns in bacterial diversityCatherine 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... - Multiple pattern matching: a Markov chain approachManuel 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... - Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soilNoah 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... - Short-term temporal variability in airborne bacterial and fungal populationsNoah 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... - Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencersZongzhi Liu
Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
Nucleic Acids Res 36:e120. 2008.... - Bioinformatics assessment of beta-myosin mutations reveals myosin's high sensitivity to mutationsMassimo 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... - UniFrac: a new phylogenetic method for comparing microbial communitiesCatherine Lozupone
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
Appl Environ Microbiol 71:8228-35. 2005.... - Simple, recurring RNA binding sites for L-arginineTeresa 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... - Direct sequencing of the human microbiome readily reveals community differencesJustin Kuczynski
Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
Genome Biol 11:210. 2010.... - Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplexMicah Hamady
Department of Computer Science, UCB 430, University of Colorado, Boulder, Colorado 80309, USA
Nat Methods 5:235-7. 2008.... - Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patternsJesse 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... - A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteinsChia 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.... - tRNA creation by hairpin duplicationJeremy 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... - Host-bacterial coevolution and the search for new drug targetsJesse 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... - Key challenges in proteomics and proteoinformatics. Progress in proteinsMicah Hamady
Department of Computer Science, University of Colorado at Boulder, USA
IEEE Eng Med Biol Mag 24:34-40. 2005 - Does protein structure influence trypsin miscleavage? Using structural properties to predict the behavior of related proteinsMicah Hamady
Department of Computer Science, University of Colorado at Boulder, USA
IEEE Eng Med Biol Mag 24:58-66. 2005 - Error minimization and coding triplet/binding site associations are independent features of the canonical genetic codeJ 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... - The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitisPhilip 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... - The human microbiome projectPeter 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... - From knotted to nested RNA structures: a variety of computational methods for pseudoknot removalSandra 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... - Evolution of mammals and their gut microbesRuth E Ley
Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
Science 320:1647-51. 2008.... - The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecologyRuth E Ley
Center for Genome Sciences, Washington University, St Louis, MO, USA
Environ Microbiol 9:3-4. 2007 - Worlds within worlds: evolution of the vertebrate gut microbiotaRuth E Ley
Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
Nat Rev Microbiol 6:776-88. 2008....
Research Grants
- New Tools for Understanding the Composition and Dynamics of Microbial CommunitiesRobin Knight; Fiscal Year: 2009....
- New Tools for Understanding the Composition and Dynamics of Microbial CommunitiesRobin Knight; Fiscal Year: 2009..The investigators intend to work closely with other researchers involved in the HMP in order to ensure rapid progress. ..
- New Tools for Understanding the Composition and Dynamics of Microbial CommunitiesRobin Knight; Fiscal Year: 2010....