Oxford Index Search Results

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sensitive species x Bioinformatics and Computational Biology x clear all

sensitive species

Overview page. Subjects: Environmental Science.

Plant or animal species which are susceptible to changes in habitat or to impacts from human activities.

See overview in Oxford Index

A general species delimitation method with applications to phylogenetic placements

Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis and Alexandros Stamatakis.

in Bioinformatics

November 2013; p ublished online August 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6705 words.

Motivation: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on...

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Optimal algorithms for local vertex quartet cleaning

Gianluca Della Vedova and H. Todd Wareham.

in Bioinformatics

October 2002; p ublished online October 2002 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Motivation: Reconstructing evolutionary trees is an important problem in biology. A response to the computational intractability of most of the traditional criteria for inferring...

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DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent

Graham Jones, Zeynep Aydin and Bengt Oxelman.

in Bioinformatics

April 2015; p ublished online November 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5944 words.

Motivation: The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches...

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Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles

Marko Sysi-Aho, Aki Vehtari, Vidya R. Velagapudi, Jukka Westerbacka, Laxman Yetukuri, Robert Bergholm, Marja-Riitta Taskinen, Hannele Yki-Järvinen and Matej Orešič.

in Bioinformatics

July 2007; p ublished online July 2007 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6431 words.

Motivation: Serum lipids have been traditionally studied in the context of lipoprotein particles. Today's emerging lipidomics technologies afford sensitive detection of...

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Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Christophe Dessimoz, Brigitte Boeckmann, Alexander C. J. Roth and Gaston H. Gonnet.

in Nucleic Acids Research

July 2006; p ublished online July 2006 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5548 words.

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome...

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Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

P. Kapli, S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis and T. Flouri.

in Bioinformatics

June 2017; p ublished online January 2017 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7178 words.

Abstract

Motivation: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity....

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miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data

Jikai Lei and Yanni Sun.

in Bioinformatics

October 2014; p ublished online June 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1487 words.

Summary: Plant microRNA prediction tools that use small RNA-sequencing data are emerging quickly. These existing tools have at least one of the following problems: (i) high...

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The systematic analysis of ultraconserved genomic regions in the budding yeast

Zhi-Kai Yang and Feng Gao.

in Bioinformatics

February 2018; p ublished online September 2017 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4253 words.

Abstract

Motivation

In the evolution of species, a kind of special sequences, termed ultraconserved sequences...

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EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes

Khalid Mahmood, Arun S. Konagurthu, Jiangning Song, Ashley M. Buckle, Geoffrey I. Webb and James C. Whisstock.

in Bioinformatics

September 2010; p ublished online June 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6815 words.

Motivation: Identification of functionally equivalent genes in different species is essential to understand the evolution of biological pathways and processes. At the same...

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Large-scale machine learning for metagenomics sequence classification

Kévin Vervier, Pierre Mahé, Maud Tournoud, Jean-Baptiste Veyrieras and Jean-Philippe Vert.

in Bioinformatics

April 2016; p ublished online November 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7923 words.

Motivation: Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in...

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Exon discovery by genomic sequence alignment

Burkhard Morgenstern, Oliver Rinner, Saïd Abdeddaïm, Dirk Haase, Klaus F. X. Mayer, Andreas W. M. Dress and Hans-Werner Mewes.

in Bioinformatics

June 2002; p ublished online June 2002 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Motivation: During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating ‘junk DNA’ so local sequence similarity often indicates...

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Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets

Dennis J. Hazelett, Daniel L. Lakeland and Joseph B. Weiss.

in Bioinformatics

July 2009; p ublished online April 2009 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6419 words.

Methods: A new method was developed for identifying novel transcription factor regulatory targets based on calculating Local Affinity Density. Techniques from the...

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Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes

David M. Curran, John S. Gilleard and James D. Wasmuth.

in Bioinformatics

November 2014; p ublished online August 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1309 words.

Motivation: Gene models from draft genome assemblies of metazoan species are often incorrect, missing exons or entire genes, particularly for large gene families. Consequently,...

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A bioinformatic screen for novel A–I RNA editing sites reveals recoding editing in BC10

D. R. Clutterbuck, A. Leroy, M. A. O'Connell and C. A. M. Semple.

in Bioinformatics

June 2005; p ublished online March 2005 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5575 words.

Motivation: Recent studies have demonstrated widespread adenosine–inosine RNA editing in non-coding sequence. However, the extent of editing in coding sequences has remained...

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De novo identification of repeat families in large genomes

Alkes L. Price, Neil C. Jones and Pavel A. Pevzner.

in Bioinformatics

June 2005; p ublished online June 2005 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Every time we compare two species that are closer to each other than either is to humans, we get nearly killed by unmasked repeats.

Webb Miller (Personal...

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Pareto-optimal phylogenetic tree reconciliation

Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal and Manolis Kellis.

in Bioinformatics

June 2014; p ublished online June 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7780 words.

Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other...

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UCHIME improves sensitivity and speed of chimera detection

Robert C. Edgar, Brian J. Haas, Jose C. Clemente, Christopher Quince and Rob Knight.

in Bioinformatics

August 2011; p ublished online June 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4883 words.

Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal...

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panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data

Panisa Treepong, Christophe Guyeux, Alexandre Meunier, Charlotte Couchoud, Didier Hocquet and Benoit Valot.

Edited by Inanc Birol.

in Bioinformatics

November 2018; p ublished online June 2018 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4402 words.

Abstract

Motivation

The advent of next-generation sequencing has boosted the analysis of bacterial genome...

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BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach

Anqi Wang, Zhanyu Wang, Zheng Li and Lei M Li.

Edited by Bonnie Berger.

in Bioinformatics

June 2018; p ublished online January 2018 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 8384 words.

Abstract

Motivation

It is highly desirable to assemble genomes of high continuity and consistency at low cost. The...

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Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures

Hiroshi Matsui, Kengo Sato and Yasubumi Sakakibara.

in Bioinformatics

June 2005; p ublished online March 2005 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5135 words.

Motivation: Since the whole genome sequences of many species have been determined, computational prediction of RNA secondary structures and computational identification of...

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