Page 145 of 249
Gene finding is a complicated procedure that encapsulates algorithms for coding sequence modeling, identification of promoter regions, issues concerning overlapping genes and more. In the present study we focu...
Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome compariso...
An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have bee...
Microorganisms are used as cell factories to produce valuable compounds in pharmaceuticals, biofuels, and other industrial processes. Incorporating heterologous metabolic pathways into well-characterized hosts...
A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been propos...
The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and...
The estimation of parameter values for mathematical models of biological systems is an optimization problem that is particularly challenging due to the nonlinearities involved. One major difficulty is the exis...
RNA molecules play diverse functional and structural roles in cells. They function as messengers for transferring genetic information from DNA to proteins, as the primary genetic material in many viruses, as c...
A central goal of genomics is to predict phenotypic variation from genetic variation. Fitting predictive models to genome-wide and whole genome single nucleotide polymorphism (SNP) profiles allows us to estima...
With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results neede...
There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessment...
Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation...
The rabbit is an important model organism used in a wide range of biomedical research. However, the rabbit genome is still sparsely annotated, thus prohibiting extensive functional analysis of gene sets derive...
Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The us...
Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the ...
This article is part of a Supplement: Volume 13 Supplement 7
Biclustering aims at finding subgroups of genes that show highly correlated behaviors across a subgroup of conditions. Biclustering is a very useful tool for mining microarray data and has various practical ap...
This article is part of a Supplement: Volume 13 Supplement 7
In recent years the genome-wide microarray-based gene expression profiles and diffusion tensor images (DTI) in human brain have been made available with accompanying anatomic and histology data. The challenge ...
This article is part of a Supplement: Volume 13 Supplement 7
DNA microarray data are used to identify genes which could be considered prognostic markers. However, due to the limited sample size of each study, the signatures are unstable in terms of the composing genes a...
This article is part of a Supplement: Volume 13 Supplement 7
Reconstructing gene regulatory networks (GRNs) from expression data is one of the most important challenges in systems biology research. Many computational models and methods have been proposed to automate the...
This article is part of a Supplement: Volume 13 Supplement 7
Drug combination that consists of distinctive agents is an attractive strategy to combat complex diseases and has been widely used clinically with improved therapeutic effects. However, the identification of e...
This article is part of a Supplement: Volume 13 Supplement 7
Mycobacterium tuberculosis is an infectious bacterium posing serious threats to human health. Due to the difficulty in performing molecular biology experiments to detect protein interactions, reconstruction of a ...
This article is part of a Supplement: Volume 13 Supplement 7
Several computational methods have been developed to predict protein-protein interactions from amino acid sequences, but most of those methods are intended for the interactions within a species rather than for...
This article is part of a Supplement: Volume 13 Supplement 7
Previous studies have shown modular structures in PPI (protein-protein interaction) networks. More recently, many genome and metagenome investigations have focused on identifying modules in PPI networks. Howev...
This article is part of a Supplement: Volume 13 Supplement 7
Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted ...
This article is part of a Supplement: Volume 13 Supplement 7
The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise...
This article is part of a Supplement: Volume 13 Supplement 7
Olfactory receptors are key components in signal transduction. Mutations in olfactory receptors alter the odor response, which is a fundamental response of organisms to their immediate environment. Understandi...
This article is part of a Supplement: Volume 13 Supplement 7
This article is part of a Supplement: Volume 13 Supplement 7
Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction ...
For gene expression or gene association studies with a large number of hypotheses the number of measurements per marker in a conventional single-stage design is often low due to limited resources. Two-stage de...
An increasing number of genomic studies interrogating more than one molecular level is published. Bioinformatics follows biological practice, and recent years have seen a surge in methodology for the integrati...
As numerous experimental factors drive the acquisition, identification, and interpretation of protein-protein interactions (PPIs), aggregated assemblies of human PPI data invariably contain experiment-dependen...
Stochastic Context–Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs pot...
Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained accept...
Contact network models have become increasingly common in epidemiology, but we lack a flexible programming framework for the generation and analysis of epidemiological contact networks and for the simulation o...
Public resources of chemical compound are in a rapid growth both in quantity and the types of data-representation. To comprehensively understand the relationship between the intrinsic features of chemical comp...
Label-free quantitative proteomics holds a great deal of promise for the future study of both medicine and biology. However, the data generated is extremely intricate in its correlation structure, and its prop...
Genome-wide expression profiling using microarrays or sequence-based technologies allows us to identify genes and genetic pathways whose expression patterns influence complex traits. Different methods to prior...
Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs) is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Indi...
Gene expression profiling technologies have gradually become a community standard tool for clinical applications. For example, gene expression data has been analyzed to reveal novel disease subtypes (class dis...
Stratification of patients according to their clinical prognosis is a desirable goal in cancer treatment in order to achieve a better personalized medicine. Reliable predictions on the basis of gene signatures...
A prerequisite for the mechanistic simulation of a biochemical system is detailed knowledge of its kinetic parameters. Despite recent experimental advances, the estimation of unknown parameter values from obse...
Hidden Markov Models (HMMs) are a powerful tool for protein domain identification. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in new sequ...
Type III Secretion System (T3SS), which plays important roles in pathogenesis or symbiosis, is widely expressed in a variety of gram negative bacteria. However, lack of unique nomenclature for T3SS genes has h...
As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these pro...
Alignment of protein sequences (MPSA) is the starting point for a multitude of applications in molecular biology. Here, we present a novel MPSA program based on the SeqAn sequence alignment library. Our implem...
Outer membrane proteins (OMPs) of Pasteurella multocida have various functions related to virulence and pathogenesis and represent important targets for vaccine development. Various bioinformatic algorithms can p...
In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mu...
Manual annotation of enzymatic functions cannot keep up with automatic genome sequencing. In this work we explore the capacity of InterPro sequence signatures to automatically predict enzymatic function.
The 27k Illumina Infinium Methylation Beadchip is a popular high-throughput technology that allows the methylation state of over 27,000 CpGs to be assayed. While feature selection and classification methods ha...
View featured videos from across the BMC-series journals
Citation Impact 2023
Journal Impact Factor: 2.9
5-year Journal Impact Factor: 3.6
Source Normalized Impact per Paper (SNIP): 0.821
SCImago Journal Rank (SJR): 1.005
Speed 2023
Submission to first editorial decision (median days): 12
Submission to acceptance (median days): 146
Usage 2023
Downloads: 5,987,678
Altmetric mentions: 4,858