Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy.

abstract：BACKGROUND:In omics data integration studies, it is common, for a variety of reasons, for some individuals to not be present in all data tables. Missing row values are challenging to deal with because most statistical methods cannot be directly applied to incomplete datasets. To overcome this issue, we propose a multip...

journal_title：BMC bioinformatics

authors： Voillet V,Besse P,Liaubet L,San Cristobal M,González I

更新日期：2016-10-03 00:00:00

abstract：BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...

journal_title：BMC bioinformatics

authors： Chelaru F,Corrada Bravo H

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, γH2AX immunoassays have become the gold standard for studying DSB induction and repair. One o...

journal_title：BMC bioinformatics

authors： Memmel S,Sisario D,Zimmermann H,Sauer M,Sukhorukov VL,Djuzenova CS,Flentje M

更新日期：2020-01-28 00:00:00

abstract：BACKGROUND:Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be taken into account. Hence, increasingly modern computationally expensive regression methods are employed...

journal_title：BMC bioinformatics

authors： Zuber V,Duarte Silva AP,Strimmer K

更新日期：2012-10-31 00:00:00

abstract：BACKGROUND:InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using a variety of profile-based, hidden markov model and positional specific score matrix methods. It not...

journal_title：BMC bioinformatics

authors： Kelly RJ,Vincent DE,Friedberg I

更新日期：2010-12-21 00:00:00

abstract：BACKGROUND:Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to ar...

journal_title：BMC bioinformatics

authors： Doherty KM,Nakka P,King BM,Rhee SY,Holmes SP,Shafer RW,Radhakrishnan ML

更新日期：2011-12-15 00:00:00

abstract：BACKGROUND:Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientation allows us to study the complex relationship between sequence, structure and the lipid environment...

journal_title：BMC bioinformatics

authors： Nugent T,Jones DT

更新日期：2013-09-18 00:00:00

abstract：BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...

journal_title：BMC bioinformatics

authors： Wenskovitch JE Jr,Harris LA,Tapia JJ,Faeder JR,Marai GE

更新日期：2014-09-25 00:00:00

abstract：BACKGROUND:Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for predi...

journal_title：BMC bioinformatics

authors： Blum T,Briesemeister S,Kohlbacher O

更新日期：2009-09-01 00:00:00

abstract：BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...

journal_title：BMC bioinformatics

authors： Peng ZL,Yang JY,Chen X

更新日期：2010-08-09 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

authors： Jeffries NO

更新日期：2004-11-19 00:00:00

abstract：BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

journal_title：BMC bioinformatics

authors： He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...

journal_title：BMC bioinformatics

authors： Wang W,Sun W,Wang W,Szatkiewicz J

更新日期：2018-03-01 00:00:00

abstract：BACKGROUND:A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of ...

journal_title：BMC bioinformatics

authors： Alachiotis N,Berger S,Flouri T,Pissis SP,Stamatakis A

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public...

journal_title：BMC bioinformatics

authors： Nilsson RH,Kristiansson E,Ryberg M,Larsson KH

更新日期：2005-07-18 00:00:00

abstract：BACKGROUND:Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the missing heritability, i.e. heritability of phenotypes so far not accounted for by single genetic vari...

journal_title：BMC bioinformatics

authors： Zhong K,Karssen LC,Kayser M,Liu F

更新日期：2016-04-08 00:00:00

abstract：BACKGROUND:Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replica...

journal_title：BMC bioinformatics

authors： Zynda GJ,Song J,Concia L,Wear EE,Hanley-Bowdoin L,Thompson WF,Vaughn MW

更新日期：2017-08-07 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are a kind of small noncoding RNA molecules that are direct posttranscriptional regulations of mRNA targets. Studies have indicated that miRNAs play key roles in complex diseases by taking part in many biological processes, such as cell growth, cell death and so on. Therefore, in order to ...

journal_title：BMC bioinformatics

authors： Yan C,Wu FX,Wang J,Duan G

更新日期：2020-03-18 00:00:00

abstract：:Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data...

journal_title：BMC bioinformatics

authors： Pimentel H,Sturmfels P,Bray N,Melsted P,Pachter L

更新日期：2016-12-01 00:00:00

abstract：BACKGROUND:Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the im...

journal_title：BMC bioinformatics

authors： Liu K,He L,Liu Z,Xu J,Liu Y,Kuang Q,Wen Z,Li M

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been im...

journal_title：BMC bioinformatics

authors： Podell S,Gaasterland T,Allen EE

更新日期：2008-10-07 00:00:00

abstract：BACKGROUND:A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts ...

journal_title：BMC bioinformatics

authors： Kedzierska AM,Casanellas M

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only du...

journal_title：BMC bioinformatics

authors： Rocha M,Maia P,Mendes R,Pinto JP,Ferreira EC,Nielsen J,Patil KR,Rocha I

更新日期：2008-11-27 00:00:00

abstract：BACKGROUND:Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and hel...

journal_title：BMC bioinformatics

authors： Chen R,Chen W,Yang S,Wu D,Wang Y,Tian Y,Shi Y

更新日期：2011-07-29 00:00:00

abstract：BACKGROUND:The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics...

journal_title：BMC bioinformatics

authors： Widmer C,Toussaint NC,Altun Y,Rätsch G

更新日期：2010-10-26 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating ...

journal_title：BMC bioinformatics

authors： Doran AG,Creevey CJ

更新日期：2013-02-08 00:00:00

abstract：BACKGROUND:One of the major challenges in biology is the correct identification of promoter regions. Computational methods based on motif searching have been the traditional approach taken. Recent studies have shown that DNA structural properties, such as curvature, stacking energy, and stress-induced duplex destabiliz...

journal_title：BMC bioinformatics

authors： Bland C,Newsome AS,Markovets AA

更新日期：2010-10-07 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

authors： Wu TY,Hsieh CC,Hong JJ,Chen CY,Tsai YS

更新日期：2009-05-27 00:00:00

abstract：BACKGROUND:Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and...

journal_title：BMC bioinformatics

authors： Liany H,Rajapakse JC,Karuturi RKM

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have problems with small genes (either over-predicting or under-predicting). Therefore the question ari...

journal_title：BMC bioinformatics

authors： Warren AS,Archuleta J,Feng WC,Setubal JC

更新日期：2010-03-15 00:00:00