Bioinformatics (Oxford, England)

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Charge asymmetry in the proteins of the outer membrane
Bioinformatics (Oxford, England) - Tập 29 Số 17 - Trang 2122-2128 - 2013
Joanna S.G. Slusky, Roland L. Dunbrack
Abstract Motivation: Outer membrane beta-barrels (OMBBs) are the proteins found in the outer membrane of bacteria, mitochondria and chloroplasts. There are thousands of beta-barrels reported in genomic databases with ∼2–3% of the genes in gram-negative bacteria encoding these proteins. These proteins have a wide variety of biological functions includ...... hiện toàn bộ
FIMO: scanning for occurrences of a given motif
Bioinformatics (Oxford, England) - Tập 27 Số 7 - Trang 1017-1018 - 2011
Charles E. Grant, Timothy L. Bailey, William Stafford Noble
AbstractSummary: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to ...... hiện toàn bộ
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
Bioinformatics (Oxford, England) - Tập 22 Số 9 - Trang 1096-1102 - 2006
Ana Conesa, María José Nueda, Alberto Ferrer, Manuel Talón
Abstract Motivation: Multi-series time-course microarray experiments are useful approaches for exploring biological processes. In this type of experiments, the researcher is frequently interested in studying gene expression changes along time and in evaluating trend differences between the various experimental groups. The large amount of data, multip...... hiện toàn bộ
Combining multiple microarray studies and modeling interstudy variation
Bioinformatics (Oxford, England) - Tập 19 Số suppl_1 - Trang i84-i90 - 2003
Jung Kyoon Choi, Ung-Sik Yu, Sang Soo Kim, Ook Joon Yoo
Abstract We have established a method for systematic integration of multiple microarray datasets. The method was applied to two different sets of cancer profiling studies. The change of gene expression in cancer was expressed as ’ effect size’, a standardized index measuring the magnitude of a treatment or covariate effect. The effect sizes were comb...... hiện toàn bộ
Moderated effect size and P-value combinations for microarray meta-analyses
Bioinformatics (Oxford, England) - Tập 25 Số 20 - Trang 2692-2699 - 2009
Guillemette Marot, Jean‐Louis Foulley, Claus Mayer, Florence Jaffrézic
Abstract Motivation: With the proliferation of microarray experiments and their availability in the public domain, the use of meta-analysis methods to combine results from different studies increases. In microarray experiments, where the sample size is often limited, meta-analysis offers the possibility to considerably increase the statistical power ...... hiện toàn bộ
Functional microRNA targets in protein coding sequences
Bioinformatics (Oxford, England) - Tập 28 Số 6 - Trang 771-776 - 2012
Martin Reczko, Manolis Maragkakis, Panagiotis Alexiou, Ivo Große, Artemis G. Hatzigeorgiou
Abstract Motivation: Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression. Results: Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian hi...... hiện toàn bộ
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Bioinformatics (Oxford, England) - Tập 22 Số 14 - Trang e124-e131 - 2006
Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry
Abstract Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical proper...... hiện toàn bộ
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics (Oxford, England) - Tập 26 Số 7 - Trang 873-881 - 2010
Thomas D. Wu, Şerban Nacu
Abstract Motivation: Next-generation sequencing captures sequence differences in reads relative to a reference genome or transcriptome, including splicing events and complex variants involving multiple mismatches and long indels. We present computational methods for fast detection of complex variants and splicing in short reads, based on a successive...... hiện toàn bộ
JOY: protein sequence-structure representation and analysis.
Bioinformatics (Oxford, England) - Tập 14 Số 7 - Trang 617-623 - 1998
Kenji Mizuguchi, Charlotte M. Deane, T.L. Blundell, Mark S. Johnson, John P. Overington
Abstract MOTIVATION: JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments. RESULTS:: The JOY representation now constitutes an es...... hiện toàn bộ
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
Bioinformatics (Oxford, England) - Tập 34 Số 6 - Trang 1037-1039 - 2018
Yasuhiro Tanizawa, Takatomo Fujisawa, Yasukazu Nakamura
Abstract Summary We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch i...... hiện toàn bộ
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