Abstract:
BACKGROUND:The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular level, the adaptations of the immune system in host defense and its dysregulation in pathological conditions. A critical aspect of intersecting and investigating complex datasets is determining how to best integrate genomic data from diverse platforms and heterogeneous sample populations to capture immunological signatures in health and disease. RESULT:We focus on gene signatures, representing highly enriched genes of immune cell subsets from both diseased and healthy tissues. From these, we construct a series of biomaps that illustrate the molecular linkages between cell subsets from different lineages, the connectivity between different immunological diseases, and the enrichment of cell subset signatures in diseased tissues. Finally, we overlay the downstream genes of drug targets with disease gene signatures to display the potential therapeutic applications for these approaches. CONCLUSION:An in silico approach has been developed to characterize immune cell subsets and diseases based on the gene signatures that most differentiate them from other biological states. This modular 'biomap' reveals the linkages between different diseases and immune subtypes, and provides evidence for the presence of specific immunocyte subsets in mixed tissues. The over-represented genes in disease signatures of interest can be further investigated for their functions in both host defense and disease.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Liu H,Liu J,Toups M,Soos T,Arendt Cdoi
10.1186/s12859-016-1012-ysubject
Has Abstractpub_date
2016-04-18 00:00:00pages
171issn
1471-2105pii
10.1186/s12859-016-1012-yjournal_volume
17pub_type
杂志文章abstract:BACKGROUND:Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evo...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0688-8
更新日期:2015-08-14 00:00:00
abstract:BACKGROUND:For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-orde...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-255
更新日期:2012-10-03 00:00:00
abstract:BACKGROUND:Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (Arabidopsis thaliana). However, these networks are usually constructed and analyzed in an ad hoc manner. In this study, we propose a completely...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S12-S2
更新日期:2011-11-24 00:00:00
abstract:BACKGROUND:Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., conti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-275
更新日期:2010-05-21 00:00:00
abstract:BACKGROUND:Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2DE images. To reduce the errors of spot quantification in 2DE images, a novel brightness correction m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3432-y
更新日期:2020-03-19 00:00:00
abstract:BACKGROUND:Multiple co-inertia analysis (mCIA) is a multivariate analysis method that can assess relationships and trends in multiple datasets. Recently it has been used for integrative analysis of multiple high-dimensional -omics datasets. However, its estimated loading vectors are non-sparse, which presents challenge...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3455-4
更新日期:2020-04-15 00:00:00
abstract:BACKGROUND:Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss-of-function mutations and/o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S1-S3
更新日期:2009-01-30 00:00:00
abstract:BACKGROUND:Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-286
更新日期:2013-10-01 00:00:00
abstract:BACKGROUND:Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS:We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Wa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-48
更新日期:2004-04-29 00:00:00
abstract:BACKGROUND:Enhancers are stretches of DNA (100-1000 bp) that play a major role in development gene expression, evolution and disease. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (CRMs). Although the binding ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0980-2
更新日期:2016-03-18 00:00:00
abstract:BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3155-0
更新日期:2019-11-28 00:00:00
abstract:BACKGROUND:Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging vari...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-248
更新日期:2014-07-21 00:00:00
abstract:BACKGROUND:Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03564-9
更新日期:2020-08-21 00:00:00
abstract:BACKGROUND:Knowledge of when and in which cells each gene is expressed across multicellular organisms is critical in understanding both gene function and regulation of cell type diversity. However, methods for measuring expression typically involve a trade-off between imaging-based methods, which give the precise locat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-204
更新日期:2013-06-22 00:00:00
abstract:BACKGROUND:Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to s...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3112-y
更新日期:2019-10-15 00:00:00
abstract:BACKGROUND:Schizophrenia, bipolar disorder, and major depression are devastating mental diseases, each with distinctive yet overlapping epidemiologic characteristics. Microarray and proteomics data have revealed genes which expressed abnormally in patients. Several single nucleotide polymorphisms (SNPs) and mutations a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S13-S20
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-160
更新日期:2009-05-27 00:00:00
abstract:BACKGROUND:Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2362-4
更新日期:2018-09-26 00:00:00
abstract:BACKGROUND:The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-346
更新日期:2010-06-24 00:00:00
abstract:BACKGROUND:Many statistical methods have been proposed to identify disease biomarkers from gene expression profiles. However, from gene expression profile data alone, statistical methods often fail to identify biologically meaningful biomarkers related to a specific disease under study. In this paper, we develop a nove...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-416
更新日期:2008-10-06 00:00:00
abstract:BACKGROUND:High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of pr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03827-5
更新日期:2020-11-04 00:00:00
abstract:BACKGROUND:The improvements of high throughput technologies have produced large amounts of multi-omics experiments datasets. Initial analysis of these data has revealed many concurrent gene alterations within single dataset or/and among multiple omics datasets. Although powerful bioinformatics pipelines have been devel...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3171-0
更新日期:2019-11-08 00:00:00
abstract:BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0394-y
更新日期:2014-12-14 00:00:00
abstract:BACKGROUND:Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2463-0
更新日期:2018-12-28 00:00:00
abstract:BACKGROUND:Analysis of cellular processes with microscopic bright field defocused imaging has the advantage of low phototoxicity and minimal sample preparation. However bright field images lack the contrast and nuclei reporting available with florescent approaches and therefore present a challenge to methods that segme...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-32
更新日期:2014-01-30 00:00:00
abstract:BACKGROUND:Recently, mass spectrometry data have been mined using a genetic algorithm to produce discriminatory models that distinguish healthy individuals from those with cancer. This algorithm is the basis for claims of 100% sensitivity and specificity in two related publicly available datasets. To date, no detailed ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-180
更新日期:2004-11-19 00:00:00
abstract:BACKGROUND:Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compound...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-168
更新日期:2009-06-02 00:00:00
abstract:BACKGROUND:Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically lin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S1-S20
更新日期:2009-01-30 00:00:00
abstract:BACKGROUND:The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test stati...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0496-1
更新日期:2015-02-20 00:00:00
abstract:BACKGROUND:Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows conve...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0759-x
更新日期:2015-11-04 00:00:00