271 research outputs found
Dataset for 53 gene families from 16 eukaryotes
No full text<p>NEXUS file representing Guigo et al.'s (1996) dataset for 53 gene families from 16 eukaryotes, used in a number of gene tree reconciliation studies. Original data from Guigo et al., this NEXUS encoding by Roderic Page.</p>
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
No full textShotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease
The expedition of Humphry Clinker. [electronic resource] : By the author of Roderic [sic] Random. In two volumes. ... Cooke's edition. Embellished with superb engravings.
No full textAuthor of Roderic Random = Tobias George Smollett.- Plates are dated 1794.Electronic reproduction.English Short Title Catalog,Reproduction of original from British Library
De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function.
No full textThe splicing regulator Polypyrimidine Tract Binding Protein (PTBP1) has four RNA binding domains that each binds a short pyrimidine element, allowing recognition of diverse pyrimidine-rich sequences. This variation makes it difficult to evaluate PTBP1 binding to particular sites based on sequence alone and thus to identify target RNAs. Conversely, transcriptome-wide binding assays such as CLIP identify many in vivo targets, but do not provide a quantitative assessment of binding and are informative only for the cells where the analysis is performed. A general method of predicting PTBP1 binding and possible targets in any cell type is needed. We developed computational models that predict the binding and splicing targets of PTBP1. A Hidden Markov Model (HMM), trained on CLIP-seq data, was used to score probable PTBP1 binding sites. Scores from this model are highly correlated (ρ = -0.9) with experimentally determined dissociation constants. Notably, we find that the protein is not strictly pyrimidine specific, as interspersed Guanosine residues are well tolerated within PTBP1 binding sites. This model identifies many previously unrecognized PTBP1 binding sites, and can score PTBP1 binding across the transcriptome in the absence of CLIP data. Using this model to examine the placement of PTBP1 binding sites in controlling splicing, we trained a multinomial logistic model on sets of PTBP1 regulated and unregulated exons. Applying this model to rank exons across the mouse transcriptome identifies known PTBP1 targets and many new exons that were confirmed as PTBP1-repressed by RT-PCR and RNA-seq after PTBP1 depletion. We find that PTBP1 dependent exons are diverse in structure and do not all fit previous descriptions of the placement of PTBP1 binding sites. Our study uncovers new features of RNA recognition and splicing regulation by PTBP1. This approach can be applied to other multi-RRM domain proteins to assess binding site degeneracy and multifactorial splicing regulation
An Investigation of the Crystal Structure of dichloro-μ-tetra(n-butyrato)dirhenium(III)
No full textTitle: An Investigation of the Crystal Structure of dichloro-μ-tetra(n-butyrato)dirhenium(III), Author: Roderic J. Restivo, Location: ThodeDichloro-μ-tetra(n-butyrato)dirhenium(III) was examined by x-rays and found to consist of a centrosymmetric dimeric unit in an eclipsed rotomeric configuration with a short rhenium-rhenium bond length of 2.20(2)Å. A long rhenium-chlorine bond 2.53(1)Å is present in the molecular unit. The bonding in Re2(O2C.C3H7-N)4CL2 is discussed with reference to similar carboxylate dimer structures. A preliminary report on the structure of Re2(O4C.C3H7-N)2 is also presented.ThesisMaster of Science (MS
Supplemental materials for paper: Correlation between scientific production and democracy
No full textSobre la llengua a les universitats
No full text<p>An essay about the use of the Catalan language in Catalan universities.</p>
Supplemental materials for paper: Correlation between scientific production and democracy
No full textFaculty Opinions recommendation of Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.
No full textSupplemental materials for paper: Correlation between scientific production and democracy
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