Blar i Fakultet for medisin og helsevitenskap (MH) på tidsskrift "BMC Bioinformatics"
Viser treff 1-20 av 21
-
A two-step site and mRNA-level model for predicting microRNA targets
(Journal article; Peer reviewed, 2010)Background: Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA targeting, most existing methods focus on identifying individual miRNA target sites and do not model contributions ... -
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis
(Peer reviewed; Journal article, 2022)Background Transcription factor (TF) binding motifs are identified by high throughput sequencing technologies as means to capture Protein-DNA interactions. These motifs are often represented by consensus sequences in form ... -
Assessment of composite motif discovery methods
(Journal article; Peer reviewed, 2008)Background: Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have ... -
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
(Journal article; Peer reviewed, 2019)Background For more than a decade, gene expression data sets have been used as basis for the construction of co-expression networks used in systems biology investigations, leading to many important discoveries in a wide ... -
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
(Journal article; Peer reviewed, 2018)Background Constraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The starting point and cornerstone of all such modeling is a genome-scale ... -
Compo: composite motif discovery using discrete models
(Journal article; Peer reviewed, 2008)Background: Computational discovery of motifs in biomolecular sequences is an established field, with applications both in the discovery of functional sites in proteins and regulatory sites in DNA. In recent years there ... -
csdR, an R package for differential co-expression analysis
(Peer reviewed; Journal article, 2022)Background Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networks ... -
Enhanced identification of significant regulators of gene expression
(Peer reviewed; Journal article, 2020)Background Diseases like cancer will lead to changes in gene expression, and it is relevant to identify key regulatory genes that can be linked directly to these changes. This can be done by computing a Regulatory Impact ... -
An ensemble framework for identifying essential proteins
(Peer reviewed; Journal article, 2016)Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy,and the number ... -
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function.
(Peer reviewed; Journal article, 2016)Background Transcription factors are key proteins in the regulation of gene transcription. An important step in this process is the opening of chromatin in order to make genomic regions available for transcription. Data ... -
Finding gene regulatory network candidates using the gene expression knowledge base
(Journal article; Peer reviewed, 2014)Background: Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ?omics? data can ... -
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
(Peer reviewed; Journal article, 2023)Background - Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce ... -
Identification of Metabolites from 2D 1H-13C HSQC NMR using Peak Correlation Plots
(Journal article; Peer reviewed, 2014)Background Identification of individual components in complex mixtures is an important and sometimes daunting task in several research areas like metabolomics and natural product studies. NMR spectroscopy is an excellent ... -
Improved benchmarks for computational motif discovery
(Journal article; Peer reviewed, 2007-06-08)Background An important step in annotation of sequenced genomes is the identification of transcription factor binding sites. More than a hundred different computational methods have been proposed, and it is difficult ... -
Measures of co-expression for improved function prediction of long non-coding RNAs
(Journal article; Peer reviewed, 2018)Background Almost 16,000 human long non-coding RNA (lncRNA) genes have been identified in the GENCODE project. However, the function of most of them remains to be discovered. The function of lncRNAs and other novel genes ... -
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation
(Journal article; Peer reviewed, 2008)Background: Gene expression measurements from breast cancer (BrCa) tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely ... -
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions
(Journal article; Peer reviewed, 2019)Background Genome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of ... -
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis
(Journal article; Peer reviewed, 2013)Background: Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional ... -
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
(Journal article; Peer reviewed, 2012)Background: Chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-Seq) is the most frequently used method to identify the binding sites of transcription factors. Active binding sites can be seen ... -
TopoICSim: A new semantic similarity measure based on gene ontology
(Peer reviewed; Journal article, 2016)Background The Gene Ontology (GO) is a dynamic, controlled vocabulary that describes the cellular function of genes and proteins according to tree major categories: biological process, molecular function and cellular ...