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Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines,...
Correctly merged data sets that have been independently genotyped can increase statistical power in linkage and association studies. However, alleles from microsatellite data sets genotyped with different expe...
A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgu...
The Related Article to this article has been published in Nature Protocols 2015 11:nprot.2015.133
Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers provide opportunities to detect epistatic SNPs associated with quantitative traits and to detect the exact mode of an e...
A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that ...
Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays....
Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is...
Many common disorders have multiple genetic components which convey increased susceptibility. SNPs have been used to identify genetic components which are associated with a disease. Unfortunately, many studies...
Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undisc...
Large-scale genetic association studies can test hundreds of thousands of genetic markers for association with a trait. Since the genetic markers may be correlated, a Bonferroni correction is typically too str...
Biomedical researchers often want to explore pathogenesis and pathways regulated by abnormally expressed genes, such as those identified by microarray analyses. Literature mining is an important way to assist ...
Random forests are becoming increasingly popular in many scientific fields because they can cope with "small n large p" problems, complex interactions and even highly correlated predictor variables. Their vari...
We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algo...
Gene expression profiling has the potential to unravel molecular mechanisms behind gene regulation and identify gene targets for therapeutic interventions. As microarray technology matures, the number of micro...
Two problems complicate the study of selection in viral genomes: Firstly, the presence of genes in overlapping reading frames implies that selection in one reading frame can bias our estimates of neutral mutat...
False discovery rate (FDR) methods play an important role in analyzing high-dimensional data. There are two types of FDR, tail area-based FDR and local FDR, as well as numerous statistical algorithms for estim...
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
This article is part of a Supplement: Volume 9 Supplement 7
The amount of information stemming from proteomics experiments involving (multi dimensional) separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an...
Protein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated ...
Identification of biomarkers among thousands of genes arrayed for disease classification has been the subject of considerable research in recent years. These studies have focused on disease classification, com...
Pseudogenes, nonfunctional copies of genes, evolve fast due the lack of evolutionary pressures and thus appear in several different forms. PseudoGeneQuest is an online tool to search the human genome for a giv...
Nonnegative matrix factorization (NMF) is a feature extraction method that has the property of intuitive part-based representation of the original features. This unique ability makes NMF a potentially promisin...
As the number of non-synonymous single nucleotide polymorphisms (nsSNPs), also known as single amino acid polymorphisms (SAPs), increases rapidly, computational methods that can distinguish disease-causing SAP...
Sequence searches are routinely employed to detect and annotate related proteins. However, a rapid growth of databases necessitates a frequent repetition of sequence searches and subsequent analysis of obtaine...
Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable ind...
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