| |
Abstract
There are well documented links between close relationships and physical health, such that those who have supportive close relationships have lower rates of morbidity and mortality compared to those who do not. Inflammation is one mechanism that may help to explain this link. Chronically high levels of inflammation predict disease. Across the lifespan, people who have supportive close relationships have lower levels of systemic inflammation ...
|
| |
The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, Vol. 61, No. 10. (1 October 2006), pp. 1051-1052, doi:10.1093/gerona/61.10.1051
posted to inflammation primer
by Zephyrus
on 2013-05-16 19:52:19
|
| |
|
| |
Abstract
A number of human diseases such as obesity and diabetes are associated with changes or imbalances in the gut microbiota (GM). Laboratory mice are commonly used as experimental models for such disorders. The introduction and dynamic development of next generation sequencing techniques have enabled detailed mapping of the GM of both humans and animal models. Nevertheless there is still a significant knowledge gap regarding the human and mouse common GM core and thus the applicability of the latter as an animal ...
|
| |
Abstract
Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa (“core”), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic ...
|
| |
Abstract
BACKGROUND:Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have a better understanding of how these two parameters differ in various organism types. In this study, the number of ribosomal operons and genome size were separately mapped onto a Bacterial phylogenetic tree.RESULTS:A representative Bacterial tree was constructed using 31 marker genes found in 578 ...
|
| |
Abstract
In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as ...
|
| |
The Journal of clinical pediatric dentistry, Vol. 37, No. 2. (2012), pp. 167-170
posted to candida microbiome saliva
by Zephyrus
on 2013-05-14 05:27:15
Abstract
Candida species are common inhabitants of the normal oral microbiota. A few studies founded a relationship between high levels of Candida albicans in the oral cavity and high DMF scores. Toothbrushes can also be reservoirs of microorganisms, the proliferation of these microorganism on a toothbrush could be a major factor for its distribution in the oral cavity. ...
|
| |
Abstract
Next generation sequencing (NGS) enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test several simple and complex workflows, including frequently used as well as recently published tools, and report on their respective accuracy and efficiency under various conditions covering different sequence lengths, number of sequences and real world experimental data ...
|
| |
Abstract
Radiotherapy is the primary treatment modality used for patients with head-and-neck cancers, but inevitably causes microorganism-related oral complications. This study aims to explore the dynamic core microbiome of oral microbiota in supragingival plaque during the course of head-and-neck radiotherapy. Eight subjects aged 26 to 70 were recruited. Dental plaque samples were collected (over seven sampling time points for each patient) before and during radiotherapy. The ...
|
| |
(11 Sep 2012)
Abstract
We propose a new procedure for estimating high dimensional Gaussian graphical models. Our approach is asymptotically tuning-free and non-asymptotically tuning-insensitive: it requires very few efforts to choose the tuning parameter in finite sample settings. Computationally, our procedure is significantly faster than existing methods due to its tuning-insensitive property. Theoretically, the obtained estimator is simultaneously minimax optimal for precision matrix estimation under different norms. Empirically, we illustrate the advantages of our method using thorough simulated and real examples. The R package bigmatrix implementing the proposed methods is available on the Comprehensive ...
|
| |
(10 Feb 2011)
Abstract
A constrained L1 minimization method is proposed for estimating a sparse inverse covariance matrix based on a sample of $n$ iid $p$-variate random variables. The resulting estimator is shown to enjoy a number of desirable properties. In particular, it is shown that the rate of convergence between the estimator and the true $s$-sparse precision matrix under the spectral norm is $s\sqrt\log p/n$ when the population distribution has either exponential-type tails or polynomial-type tails. Convergence rates under the elementwise $L_∞$ norm and Frobenius norm are also presented. In addition, ...
|
| |
|
| |
Abstract
We propose a pivotal method for estimating high-dimensional sparse linear regression models, where the overall number of regressors $p$ is large, possibly much larger than $n$, but only $s$ regressors are significant. The method is a modification of the lasso, called the square-root lasso. The method is pivotal in that it neither relies on the knowledge of the standard deviation $σ$ or nor does it need to pre-estimate $σ$. Moreover, the method does not rely on normality or sub-Gaussianity of noise. It achieves near-oracle performance, attaining the convergence ...
|
| |
(28 Feb 2012)
Abstract
In this paper, the high-dimensional sparse linear regression model is considered, where the overall number of variables is larger than the number of observations. We investigate the L1 penalized least absolute deviation method. Different from most of other methods, the L1 penalized LAD method does not need any knowledge of standard deviation of the noises or any moment assumptions of the noises. Our analysis shows that the method achieves near oracle performance, i.e. with large probability, the L2 norm of the estimation error is of order $O(\sqrtk \log ...
|
| |
Abstract
Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate ESS data on a large scale, but computationally efficient methods for analysing such data sets are needed.Here we present metaBEETL, a fast taxonomic classifier for environmental shotgun sequences. It uses a Burrows-Wheeler Transform (BWT) index of the ...
|
| |
Abstract
BACKGROUND:Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizable, high-resolution Venn and Euler diagrams in the R statistical environment. To fill this gap we introduce VennDiagram, an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams with up to three sets.RESULTS:The VennDiagram package offers the user the ability to customize essentially all aspects of the generated diagrams, ...
|
| |
Abstract
Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High-throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly ...
|
| |
posted to background biology il22
by Zephyrus
on 2013-04-21 17:46:48
Abstract
Several cell types, in particular epithelial cells, express the receptor for the cytokine IL-22 and upon its recognition produce molecules that are active both locally and systemically. Many different types of lymphocyte secrete IL-22. Th17 cells produce IL-22 although the optimal conditions for secretion of IL-17 or IL-22 by Th17 cells differ, as do the transcription factors involved. Aryl hydrocarbon receptor is required for IL-22 production by Th17, Th22 and γδ T cells. Th22 cells produce IL-22 in response to IL-6 ...
|
| |
Journal of Computer Science and Technology In Journal of Computer Science and Technology, Vol. 27, No. 2. (1 March 2012), pp. 225-239, doi:10.1007/s11390-012-1219-y
Abstract
With the rapid development of next-generation sequencing technologies, bacterial identification becomes a very important and essential step in processing genomic data, especially for metagenomic data. Many computational methods have been developed and some of them are widely used to address the problems in bacterial identification. In this article we review the algorithms of these methods, discuss their drawbacks, and propose future computational methods that use genomic data to characterize bacteria. In addition, we tackle two specific computational problems in bacterial identification, ...
|
| |
Abstract
Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies. ...
|
| |
Abstract
"Binning" (or taxonomic classification) of DNA sequence reads is an initial step to analyzing an environmental biological sample. Currently, a homology-based tool, BLAST, is one of the most commonly used tools to label DNA reads, but it is argued that BLAST will quickly lose its classification ability as the genome databases grow. In this paper, we compare the accuracies of a naïve Bayes classifier (NBC) ...
|
| |
Bioinformatics (Oxford, England), Vol. 17, No. 11. (November 2001), pp. 1077-1083
Abstract
Multi Locus Sequence Typing (MLST) is a newly developed typing method for bacteria based on the sequence determination of internal fragments of seven house-keeping genes. It has proved useful in characterizing and monitoring disease-causing and antibiotic resistant lineages of bacteria. The strength of this approach is that unlike data obtained using most other typing methods, sequence data are unambiguous, can be held on a central ...
|
| |
Abstract
BACKGROUND:Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet.RESULTS:The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions. This separation enables isolate databases to be established by individual laboratories, each customised to the needs of the particular project ...
|
| |
Abstract
Summary: Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50 000 isolates in over 50 different species. Here, we present a coalescent method to jointly simulate MLST data and the clonal genealogy that gave rise to the sample. ...
|
| |
Abstract
BACKGROUND:Multilocus Sequence Typing (MLST) is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence of housekeeping genes that result in each strain having a distinct numerical allelic profile, which is abbreviated to a unique identifier: the sequence type (ST). The relatedness between two strains can then be inferred by the differences between allelic profiles. For a more comprehensive analysis of the possible patterns of ...
|
| |
posted to background bacteria methods mlst
by Zephyrus
on 2013-04-12 05:12:51
Abstract
We consider the problem Maximum Leaf Spanning Tree (MLST) on digraphs, which is defined as follows. Given a digraph G, find a directed spanning tree of G that maximizes the number of leaves. MLST is NP-hard. Existing approximation algorithms for MLST have ratios of $O(\sqrt OPT)$ ...
|
| |
Abstract
BACKGROUND:The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online ...
|
| |
Abstract
BACKGROUND:The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner.RESULTS:The Bacterial Isolate Genome Sequence Database (BIGSDB) is a scalable, open source, web-accessible database system that meets these needs, enabling phenotype and sequence data, which can range from a single sequence read to whole genome data, to ...
|
| |
European Food Research and Technology In European Food Research and Technology, Vol. 233, No. 3. (28 June 2011), pp. 377-385, doi:10.1007/s00217-011-1526-5
posted to background bacteria methods mlst
by Zephyrus
on 2013-04-12 05:12:40
Abstract
Comparative typing analysis of 25 Lactobacillus delbrueckii subsp. bulgaricus strains, isolated from traditional yoghurts in Turkey, was performed by RAPD–PCR (randomly amplified polymorphic DNA–PCR) and MLST (multilocus sequence typing). RAPD–PCR analyses were performed using two primers; M13 and 1254. Primer 1254 produced better results than primer M13. The bands produced by primer 1254 were brighter and easier to interpret, and a higher number of bands were produced. In addition, clusters produced by primer 1254 were grouped according to the source of ...
|
| |
|
| |
Abstract
BACKGROUND:Worldwide effort on sampling and characterization of molecular variation within a large number of human and animal pathogens has lead to the emergence of multi-locus sequence typing (MLST) databases as an important tool for studying the epidemiology and evolution of pathogens. Many of these databases are currently harboring several thousands of multi-locus DNA sequence types (STs) enriched with metadata over traits such as serotype, antibiotic resistance, host organism etc of the isolates. Curators of the databases have thus the possibility of ...
|
| |
Abstract
We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake webcite. ...
|
| |
Abstract
Motivation: The continuing improvements to high-throughput sequencing (HTS) platforms have begun to unfold a myriad of new applications. As a result, error correction of sequencing reads remains an important problem. Though several tools do an excellent job of correcting datasets where the reads are sampled close to uniformly, the problem of correcting reads coming from drastically non-uniform datasets, such as those from single-cell sequencing, remains open. ...
|
| |
Abstract
BACKGROUND:Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of ...
|
| |
Abstract
High coverage whole genome sequencing provides near complete information about genetic variation. However, other technologies can be more efficient in some settings by (a) reducing redundant coverage within samples and (b) exploiting patterns of genetic variation across samples. To characterize as many samples as possible, many genetic studies therefore employ lower coverage sequencing or SNP array genotyping coupled to statistical imputation. To compare these approaches individually and in conjunction, we developed a statistical framework to estimate genotypes jointly from sequence reads, ...
|
| |
Abstract
Multidimensional scaling (MDS) is a technique which retrieves the locations of objects in a Euclidean space (the object configuration) from data consisting of the dissimilarities between pairs of objects. An important issue in MDS is finding an appropriate dimensionality underlying these dissimilarities. In this paper, we propose a simple and efficient Bayesian approach for selecting dimensionality in MDS. For each column (attribute) vector of an MDS configuration, we assume a prior that is a mixture of the point mass at 0 ...
|
| |
Abstract
We consider the problem of performing interpretable classification in the high-dimensional setting, in which the number of features is very large and the number of observations is limited. This setting has been studied extensively in the chemometrics literature, and more recently has become commonplace in biological and medical applications. In this setting, a traditional approach involves performing feature selection before classification. We propose sparse discriminant analysis, a method for performing linear discriminant analysis with a sparseness criterion imposed such that classification ...
|
| |
Abstract
A beneficial mutation that has nearly but not yet fixed in a population produces a characteristic haplotype configuration, called a partial selective sweep. Whether nonadaptive processes might generate similar haplotype configurations has not been extensively explored. Here, we consider 5 population genetic data sets taken from regions flanking high-frequency transposable elements in North American strains of Drosophila melanogaster, each of which appears to be consistent with the expectations of a partial selective sweep. We use coalescent simulations to explore whether incorporation ...
|
| |
|
| |
posted to methods statistics
by Zephyrus
on 2013-04-07 17:26:37
Abstract
This manuscript describes a novel strategy to improve HIV DNA vaccine design. Employing a new information theory based bioinformatic algorithm, we identify a set of nucleotide motifs which are common in the coding region of HIV, but are under-represented in genes that are highly expressed in the human genome. We hypothesize that these motifs contribute to the poor protein expression of gag, pol, and env genes from the c-DNAs of HIV clinical isolates. Using this approach and beginning with a codon ...
|
| |
posted to methods statistics
by Zephyrus
on 2013-04-07 17:26:28
|
| |
Abstract
Mormon prophet Joseph Smith (1805–44) claimed that more than two-dozen ancient individuals (Nephi, Mormon, Alma, etc.) living from around 2200 BC to 421 AD authored the Book of Mormon (1830), and that he translated their inscriptions into English. Later researchers who analyzed selections from the Book of Mormon concluded that differences between selections supported Smith's claim of multiple authorship and ancient origins. We offer a new approach that employs two classification techniques: ‘delta’ commonly used to determine probable authorship and ‘nearest ...
|
| |
Abstract
The genetic programs that promote retention of self-renewing leukemia stem cells (LSCs) at the apex of cellular hierarchies in acute myeloid leukemia (AML) are not known. In a mouse model of human AML, LSCs exhibit variable frequencies that correlate with the initiating MLL oncogene and are maintained in a self-renewing state by a transcriptional subprogram more akin to that of embryonic stem cells (ESCs) than ...
|
| |
Abstract
Summary. We propose covariance-regularized regression, a family of methods for prediction in high dimensional settings that uses a shrunken estimate of the inverse covariance matrix of the features to achieve superior prediction. An estimate of the inverse covariance matrix is obtained by maximizing the log-likelihood of the data, under a multivariate normal model, subject to a penalty; it is then used to estimate coefficients for the regression of the response onto the features. We show that ridge regression, the lasso and ...
|
| |
Abstract
We present a penalized matrix decomposition (PMD), a new framework for computing a rank-K approximation for a matrix. We approximate the matrix X as , where dk, uk, and vk minimize the squared Frobenius norm of X, subject to penalties on uk and vk. This results in a regularized version of the singular value decomposition. Of particular interest is the use of L1-penalties on uk and vk, which yields a decomposition of X using sparse vectors. We show that when the ...
|
| |
by Andrew H. Beck, Ziming Weng, Daniela M. Witten, et al.Shirley Zhu, Joseph W. Foley, Phil Lacroute, Cheryl L. Smith, Robert Tibshirani, Matt van de Rijn, Arend Sidow, Robert B. West
Abstract
Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3â²-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and ...
|
| |
Abstract
In recent years, breakthroughs in biomedical technology have led to a wealth of data in which the number of features (for instance, genes on which expression measurements are available) exceeds the number of observations (e.g. patients). Sometimes survival outcomes are also available for those same observations. In this case, one might be interested in (a) identifying features that are associated with survival (in a univariate sense), and (b) developing a multivariate model for the relationship between the features and survival that ...
|
| |
by A. H. Beck, C. H. Lee, D. M. Witten, et al.B. C. Gleason, B. Edris, I. Espinosa, S. Zhu, R. Li, K. D. Montgomery, R. J. Marinelli, R. Tibshirani, T. Hastie, D. M. Jablons, B. P. Rubin, C. D. Fletcher, R. B. West, M. van de Rijn
posted to methods omics statistics
by Zephyrus
on 2013-04-07 17:25:01
Abstract
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling
Oncogene advance online publication, November 9, 2009. doi:10.1038/onc.2009.381
Authors: A H Beck, C-H Lee, D M Witten, B C Gleason, B Edris, I Espinosa, S Zhu, R Li, K D Montgomery, R J Marinelli, R Tibshirani, T Hastie, D M Jablons, B P Rubin, C D Fletcher, R B West
& M van de ...
|
| |
posted to methods statistics
by Zephyrus
on 2013-04-07 17:24:49
Abstract
Daniela M. Witten and Robert Tibshirani. Survival analysis with high-dimensional covariates. Statistical Methods in Medical Research 2010; 19: 29–51 (DOI: 10.1177/0962280209105024). On page 36, Figure 1 is incorrect. Please note the following correction in the figure: The ‘Modified Cox’ and ‘LPC’ legends in the artwork were reversed. The correct figure is given below. ...
|
Search
