Providing visualisation support for the analysis of anatomy ontology data.

abstract：BACKGROUND:Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. ...

journal_title：BMC bioinformatics

authors： Wu X,Wei Z,Chen K,Zhang Q,Su J,Liu H,Zhang L,Meng J

更新日期：2019-05-02 00:00:00

abstract：BACKGROUND:Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the defa...

journal_title：BMC bioinformatics

authors： Ong E,Xie J,Ni Z,Liu Q,Sarntivijai S,Lin Y,Cooper D,Terryn R,Stathias V,Chung C,Schürer S,He Y

更新日期：2017-12-21 00:00:00

abstract：BACKGROUND: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 been widely used for this purpose. In many settings, it may be important to incorporate ancillary biolo...

journal_title：BMC bioinformatics

authors： Hill SM,Neve RM,Bayani N,Kuo WL,Ziyad S,Spellman PT,Gray JW,Mukherjee S

更新日期：2012-05-11 00:00:00

abstract：BACKGROUND:Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local...

journal_title：BMC bioinformatics

authors： Koren S,Miller JR,Walenz BP,Sutton G

更新日期：2010-09-10 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

authors： Sheikhizadeh Anari S,de Ridder D,Schranz ME,Smit S

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human cells into malignant cancer cells. Interrogation of cancer genomes holds the promise of understandi...

journal_title：BMC bioinformatics

authors： Sanchez-Garcia F,Akavia UD,Mozes E,Pe'er D

更新日期：2010-04-14 00:00:00

abstract：BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...

journal_title：BMC bioinformatics

authors： Li C

更新日期：2008-05-08 00:00:00

abstract：BACKGROUND:Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the regulatory relationships, High-Order Dynamic Bayesian Network (HO-DBN) is a good model of GRN. Howeve...

journal_title：BMC bioinformatics

authors： Lo LY,Wong ML,Lee KH,Leung KS

更新日期：2015-11-25 00:00:00

abstract：BACKGROUND:Wise et al. introduced a rank-based statistical technique for meta-analysis of genome scans, the Genome Scan Meta-Analysis (GSMA) method. Levinson et al. recently described two generalizations of the GSMA statistic: (i) a weighted version of the GSMA statistic, so that different studies could be ascribed dif...

journal_title：BMC bioinformatics

authors： Koziol JA,Feng AC

更新日期：2005-02-17 00:00:00

abstract：BACKGROUND:Direct in vivo investigation of human metabolism is complicated by the distinct metabolic functions of various sub-cellular organelles. Diverse micro-environments in different organelles may lead to distinct functions of the same protein and the use of different enzymes for the same metabolic reaction. To be...

journal_title：BMC bioinformatics

authors： Hao T,Ma HW,Zhao XM,Goryanin I

更新日期：2010-07-22 00:00:00

abstract：BACKGROUND:Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native...

journal_title：BMC bioinformatics

authors： Corona RI,Sudarshan S,Aluru S,Guo JT

更新日期：2018-12-21 00:00:00

abstract：:Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far lim...

journal_title：BMC bioinformatics

authors： Ay F,Dang M,Kahveci T

更新日期：2012-03-21 00:00:00

abstract：BACKGROUND:The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challeng...

journal_title：BMC bioinformatics

authors： Eggle D,Debey-Pascher S,Beyer M,Schultze JL

更新日期：2009-06-18 00:00:00

abstract：BACKGROUND:Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacte...

journal_title：BMC bioinformatics

authors： Lata S,Sharma BK,Raghava GP

更新日期：2007-07-23 00:00:00

abstract：BACKGROUND:Understanding the relationship between the protein sequence and the 3D structure is a major research area in bioinformatics. The prediction of complete protein tertiary structure based only on sequence information is still an impractical work. This paper aims at revealing the hidden knowledge of the sequence...

journal_title：BMC bioinformatics

authors： Chen B,Johnson M

更新日期：2009-10-08 00:00:00

abstract：BACKGROUND:In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however...

journal_title：BMC bioinformatics

authors： Peng J,Wang Y,Chen J

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....

journal_title：BMC bioinformatics

authors： Bayerlová M,Jung K,Kramer F,Klemm F,Bleckmann A,Beißbarth T

更新日期：2015-10-22 00:00:00

abstract：BACKGROUND:Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking t...

journal_title：BMC bioinformatics

authors： Fu LM,Fu-Liu CS

更新日期：2005-03-22 00:00:00

abstract：BACKGROUND:In many biomedical applications, there is a need for developing classification models based on noisy annotations. Recently, various methods addressed this scenario by relaying on unreliable annotations obtained from multiple sources. RESULTS:We proposed a probabilistic classification algorithm based on labe...

journal_title：BMC bioinformatics

authors： Zhang P,Cao W,Obradovic Z

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...

journal_title：BMC bioinformatics

authors： Choo-Wosoba H,Albert PS,Zhu B

更新日期：2018-11-14 00:00:00

abstract：BACKGROUND:High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise ...

journal_title：BMC bioinformatics

authors： Lawless C,Wilkinson DJ,Young A,Addinall SG,Lydall DA

更新日期：2010-05-28 00:00:00

abstract：:Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate E...

journal_title：BMC bioinformatics

authors： Ander C,Schulz-Trieglaff OB,Stoye J,Cox AJ

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequenc...

journal_title：BMC bioinformatics

authors： Kracht D,Schober S

更新日期：2015-02-18 00:00:00

abstract：BACKGROUND:Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiolog...

journal_title：BMC bioinformatics

authors： Lemmin T,Soto C

更新日期：2019-10-22 00:00:00

abstract：BACKGROUND:Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinations are limited in their scope, e.g. to the identification of combinations falling within individual...

journal_title：BMC bioinformatics

authors： McLaughlin WA,Chen K,Hou T,Wang W

更新日期：2007-10-16 00:00:00

abstract：BACKGROUND:The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been develo...

journal_title：BMC bioinformatics

authors： Li GH,Huang JF

更新日期：2010-08-27 00:00:00

abstract：BACKGROUND:Researchers involved in the annotation of large numbers of gene, clone or protein identifiers are usually required to perform a one-by-one conversion for each identifier. When the field of research is one such as microarray experiments, this number may be around 30,000. RESULTS:To help researchers map acces...

journal_title：BMC bioinformatics

authors： Alibés A,Yankilevich P,Cañada A,Díaz-Uriarte R

更新日期：2007-01-10 00:00:00

abstract：BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...

journal_title：BMC bioinformatics

authors： Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes....

journal_title：BMC bioinformatics

authors： Yeturu K,Utriainen T,Kemp GJ,Chandra N

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:The Triplex cell vaccine is a cancer cellular vaccine that can prevent almost completely the mammary tumor onset in HER-2/neu transgenic mice. In a translational perspective, the activity of the Triplex vaccine was also investigated against lung metastases showing that the vaccine is an effective treatment a...

journal_title：BMC bioinformatics

authors： Pennisi M,Pappalardo F,Palladini A,Nicoletti G,Nanni P,Lollini PL,Motta S

更新日期：2010-10-15 00:00:00