A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes.

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:Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in transcription factor databases, as well as to represent the po...

journal_title：BMC bioinformatics

authors： Kankainen M,Löytynoja A

更新日期：2007-06-08 00:00:00

abstract：BACKGROUND:During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused. METHODS:We investi...

journal_title：BMC bioinformatics

authors： Attie O,Darling AE,Yancopoulos S

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:Viral zoonosis, the transmission of a virus from its primary vertebrate reservoir species to humans, requires ubiquitous cellular proteins known as receptor proteins. Zoonosis can occur not only through direct transmission from vertebrates to humans, but also through intermediate reservoirs or other environm...

journal_title：BMC bioinformatics

authors： Bae SE,Son HS

更新日期：2011-04-13 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

abstract：BACKGROUND:Protein remote homology detection is one of the central problems in bioinformatics, which is important for both basic research and practical application. Currently, discriminative methods based on Support Vector Machines (SVMs) achieve the state-of-the-art performance. Exploring feature vectors incorporating...

journal_title：BMC bioinformatics

authors： Liu B,Xu J,Zou Q,Xu R,Wang X,Chen Q

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of ...

journal_title：BMC bioinformatics

authors： Spirito G,Mangoni D,Sanges R,Gustincich S

更新日期：2019-11-22 00:00:00

abstract：BACKGROUND:It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opp...

journal_title：BMC bioinformatics

authors： Borozan I,Wilson S,Blanchette P,Laflamme P,Watt SN,Krzyzanowski PM,Sircoulomb F,Rottapel R,Branton PE,Ferretti V

更新日期：2012-08-17 00:00:00

abstract：BACKGROUND:Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature ...

journal_title：BMC bioinformatics

authors： Song L,Langfelder P,Horvath S

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

journal_title：BMC bioinformatics

authors： von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

更新日期：2006-02-06 00:00:00

abstract：:DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancer...

journal_title：BMC bioinformatics

authors： Qiu P,Zhang L

更新日期：2012-01-01 00:00:00

abstract：:Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...

journal_title：BMC bioinformatics

authors： Li YF,Radivojac P

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is crucial to assess in silico the options as well as the impact of various crossing schemes and breedi...

journal_title：BMC bioinformatics

authors： Sun X,Mumm RH

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis work...

journal_title：BMC bioinformatics

authors： Saggese I,Bona E,Conway M,Favero F,Ladetto M,Liò P,Manzini G,Mignone F

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the micro...

journal_title：BMC bioinformatics

authors： Bengtsson H,Jönsson G,Vallon-Christersson J

更新日期：2004-11-12 00:00:00

abstract：BACKGROUND:Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA's 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incor...

journal_title：BMC bioinformatics

authors： Kleinkauf R,Houwaart T,Backofen R,Mann M

更新日期：2015-11-18 00:00:00

abstract：BACKGROUND:Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and...

journal_title：BMC bioinformatics

authors： Sarkar A,Kumar S,Sundar D

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Recent advances in global genomic profiling methodologies have enabled multi-dimensional characterization of biological systems. Complete analysis of these genomic profiles require an in depth look at parallel profiles of segmental DNA copy number status, DNA methylation state, single nucleotide polymorphism...

journal_title：BMC bioinformatics

authors： Chi B,deLeeuw RJ,Coe BP,Ng RT,MacAulay C,Lam WL

更新日期：2008-05-20 00:00:00

abstract：BACKGROUND:Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D model...

journal_title：BMC bioinformatics

authors： Antczak M,Kasprzak M,Lukasiak P,Blazewicz J

更新日期：2016-09-17 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:The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can h...

journal_title：BMC bioinformatics

authors： Zampieri G,Tran DV,Donini M,Navarin N,Aiolli F,Sperduti A,Valle G

更新日期：2018-01-25 00:00:00

abstract：BACKGROUND:Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, ...

journal_title：BMC bioinformatics

authors： Li Z,Lin J,Sibley AB,Truong T,Chua KC,Jiang Y,McCarthy J,Kroetz DL,Allen A,Owzar K

更新日期：2019-05-28 00:00:00

abstract：BACKGROUND:Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmann's recent review, we compared statistical performance of three methods, namely Global Tes...

journal_title：BMC bioinformatics

authors： Liu Q,Dinu I,Adewale AJ,Potter JD,Yasui Y

更新日期：2007-11-07 00:00:00

abstract：BACKGROUND:Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attribute...

journal_title：BMC bioinformatics

authors： Andrade AQ,Blondé W,Hastings J,Schulz S

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactio...

journal_title：BMC bioinformatics

authors： Oda K,Kim JD,Ohta T,Okanohara D,Matsuzaki T,Tateisi Y,Tsujii J

更新日期：2008-04-11 00:00:00

abstract：BACKGROUND:Many statistical algorithms combine microarray expression data and genome sequence data to identify transcription factor binding motifs in the low eukaryotic genomes. Finding cis-regulatory elements in higher eukaryote genomes, however, remains a challenge, as searching in the promoter regions of genes with ...

journal_title：BMC bioinformatics

authors： Kim RS,Ji H,Wong WH

更新日期：2006-01-26 00:00:00

abstract：BACKGROUND:A common feature of microarray experiments is the occurrence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative backgro...

journal_title：BMC bioinformatics

authors： Tom BD,Gilks WR,Brooke-Powell ET,Ajioka JW

更新日期：2005-09-26 00:00:00

abstract：BACKGROUND:Genome-wide transcriptional profiling of patient blood samples offers a powerful tool to investigate underlying disease mechanisms and personalized treatment decisions. Most studies are based on analysis of total peripheral blood mononuclear cells (PBMCs), a mixed population. In this case, accuracy is inhere...

journal_title：BMC bioinformatics

authors： Bolen CR,Uduman M,Kleinstein SH

更新日期：2011-06-24 00:00:00

abstract：BACKGROUND:Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams. RESULTS:Our primary contribution is a local sliding-...

journal_title：BMC bioinformatics

authors： Sarkar A,Soueidan H,Nikolski M

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptio...

journal_title：BMC bioinformatics

authors： Chevenet F,Brun C,Bañuls AL,Jacq B,Christen R

更新日期：2006-10-10 00:00:00