Abstract:
:Information Integrator is an extension to IBM's relational database DB2, which uses data federation to provide benefits to molecular biology researchers through two unique capabilities: increased flexibility in combining data from disparate sources, and SQL access to non-SQL data, easing the task of automating data analysis.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Arenson ADdoi
10.1093/bib/4.4.375keywords:
subject
Has Abstractpub_date
2003-12-01 00:00:00pages
375-81issue
4eissn
1467-5463issn
1477-4054journal_volume
4pub_type
杂志文章abstract::Integrative analyses of genomic, epigenomic and transcriptomic features for human and various model organisms have revealed that many such features are nonrandomly distributed in the genome. Significant enrichment (or depletion) of genomic features is anticipated to be biologically important. Detection of genomic regi...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt053
更新日期:2014-11-01 00:00:00
abstract::Prognostic tests using expression profiles of several dozen genes help provide treatment choices for prostate cancer (PCa). However, these tests require improvement to meet the clinical need for resolving overtreatment, which continues to be a pervasive problem in PCa management. Genomic selection (GS) methodology, wh...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa197
更新日期:2020-09-08 00:00:00
abstract::A number of supervised machine learning models have recently been introduced for the prediction of drug-target interactions based on chemical structure and genomic sequence information. Although these models could offer improved means for many network pharmacology applications, such as repositioning of drugs for new t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbu010
更新日期:2015-03-01 00:00:00
abstract::Numerous studies have shown that copy number variation (CNV) in lncRNA regions play critical roles in the initiation and progression of cancer. However, our knowledge about their functionalities is still limited. Here, we firstly provided a computational method to identify lncRNAs with copy number variation (lncRNAs-C...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz113
更新日期:2020-12-01 00:00:00
abstract::Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have gene...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbv080
更新日期:2016-07-01 00:00:00
abstract::Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, w...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbp046
更新日期:2010-03-01 00:00:00
abstract:MOTIVATION:With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bby072
更新日期:2019-11-27 00:00:00
abstract::Computational and mathematical modelling has become a valuable tool for investigating biological systems. Modelling enables prediction of how biological components interact to deliver system-level properties and extrapolation of biological system performance to contexts and experimental conditions where this is unknow...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bby092
更新日期:2018-09-18 00:00:00
abstract::Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/5.4.339
更新日期:2004-12-01 00:00:00
abstract::Accurately identifying the interactions between genomic factors and the response of cancer drugs plays important roles in drug discovery, drug repositioning and cancer treatment. A number of studies revealed that interactions between genes and drugs were 'many-genes-to-many drugs' interactions, i.e. common modules, op...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa087
更新日期:2020-06-26 00:00:00
abstract:MOTIVATION:The functional changes of the genes, RNAs and proteins will eventually be reflected in the metabolic level. Increasing number of researchers have researched mechanism, biomarkers and targeted drugs by metabolites. However, compared with our knowledge about genes, RNAs, and proteins, we still know few about d...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa212
更新日期:2020-10-13 00:00:00
abstract::The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by d...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs049
更新日期:2014-01-01 00:00:00
abstract::Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the 'uncertainty' of a solution, that is, the probability of the solution is extremely small. This situation arises for estimation problems on high-dimen...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt038
更新日期:2014-09-01 00:00:00
abstract::Whole-organism metabolic rate co-varies allometrically with body mass, and is also affected by temperature through different biochemical mechanisms. Here we implement a computational platform to map specific quantitative trait loci (QTLs) that govern the dependence of metabolic rate on size and temperature. The model ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbv116
更新日期:2017-01-01 00:00:00
abstract::Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-inc...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa322
更新日期:2020-12-18 00:00:00
abstract::In therapeutic research, the safety and efficacy of pharmaceutical products are necessarily tested on humans via clinical trials after an extensive and expensive preclinical development period. Methodologies such as computer modeling and clinical trial simulation (CTS) might represent a valuable option to reduce anima...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx055
更新日期:2018-11-27 00:00:00
abstract::The use of multiple testing procedures in the context of gene-set testing is an important but relatively underexposed topic. If a multiple testing method is used, this is usually a standard familywise error rate (FWER) or false discovery rate (FDR) controlling procedure in which the logical relationships that exist be...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbv091
更新日期:2016-09-01 00:00:00
abstract::Systems pharmacology is an emerging field that integrates systems biology and pharmacology to advance the process of drug discovery, development and the understanding of therapeutic mechanisms. The aim of the present work is to highlight the role that the systems pharmacology plays across the traditional herbal medici...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt035
更新日期:2014-09-01 00:00:00
abstract::Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become incre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbw072
更新日期:2017-11-01 00:00:00
abstract::The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tool...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/3.1.18
更新日期:2002-03-01 00:00:00
abstract::The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of ...
journal_title:Briefings in bioinformatics
pub_type: 历史文章,杂志文章
doi:10.1093/bib/bbu022
更新日期:2015-03-01 00:00:00
abstract::Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior year...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa349
更新日期:2020-12-30 00:00:00
abstract::Next generation sequencers have greatly improved our ability to mine polymorphisms and mutations out of entire (or portions of) genomes. The reliability of their outputs, though, showed to be very related to the sequencing chemistry and to deeply affect the quality of the downstream analyses. We focus here on the two-...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs048
更新日期:2013-11-01 00:00:00
abstract::The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether r...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz146
更新日期:2021-01-18 00:00:00
abstract::Drug-drug interactions (DDIs) constitute an important concern in drug development and postmarketing pharmacovigilance. They are considered the cause of many adverse drug effects exposing patients to higher risks and increasing public health system costs. Methods to follow-up and discover possible DDIs causing harm to ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbx010
更新日期:2018-09-28 00:00:00
abstract::Posttranscriptional crosstalk and communication between RNAs yield large regulatory competing endogenous RNA (ceRNA) networks via shared microRNAs (miRNAs), as well as miRNA synergistic networks. The ceRNA crosstalk represents a novel layer of gene regulation that controls both physiological and pathological processes...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx137
更新日期:2019-07-19 00:00:00
abstract::The bipartite network representation of the drug-target interactions (DTIs) in a biosystem enhances understanding of the drugs' multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational pre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx041
更新日期:2018-11-27 00:00:00
abstract::Protein remote homology detection is one of the most fundamental and central problems for the studies of protein structures and functions, aiming to detect the distantly evolutionary relationships among proteins via computational methods. During the past decades, many computational approaches have been proposed to sol...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbw108
更新日期:2018-03-01 00:00:00
abstract::In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these pre...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa160
更新日期:2020-08-07 00:00:00
abstract::RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a numb...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt086
更新日期:2015-01-01 00:00:00