Comparative evaluation of gene set analysis approaches for RNA-Seq data.

abstract：BACKGROUND:Meta-analysis (MA) is widely used to pool genome-wide association studies (GWASes) in order to a) increase the power to detect strong or weak genotype effects or b) as a result verification method. As a consequence of differing SNP panels among genotyping chips, imputation is the method of choice within GWAS...

journal_title：BMC bioinformatics

authors： Meesters C,Leber M,Herold C,Angisch M,Mattheisen M,Drichel D,Lacour A,Becker T

更新日期：2012-09-12 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect...

journal_title：BMC bioinformatics

authors： Bauer-Mehren A,Furlong LI,Rautschka M,Sanz F

更新日期：2009-08-27 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:Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our motivation is inspired by label propagation algorithm and the false positive protein-protein intera...

journal_title：BMC bioinformatics

authors： Zhang Y,Liu J,Liu X,Fan X,Hong Y,Wang Y,Huang Y,Xie M

更新日期：2018-02-08 00:00:00

abstract：BACKGROUND:Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. RESULTS:We pres...

journal_title：BMC bioinformatics

authors： Kharchenko P,Chen L,Freund Y,Vitkup D,Church GM

更新日期：2006-03-29 00:00:00

abstract：BACKGROUND:Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting...

journal_title：BMC bioinformatics

authors： Kelly WP,Stumpf MP

更新日期：2010-09-20 00:00:00

abstract：BACKGROUND:RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence o...

journal_title：BMC bioinformatics

authors： Li B,Dewey CN

更新日期：2011-08-04 00:00:00

abstract：BACKGROUND:Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i...

journal_title：BMC bioinformatics

authors： Lu T,Costello CM,Croucher PJ,Häsler R,Deuschl G,Schreiber S

更新日期：2005-02-23 00:00:00

abstract：BACKGROUND:DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data s...

journal_title：BMC bioinformatics

authors： Kim J,Kim H

更新日期：2017-10-12 00:00:00

abstract：BACKGROUND:X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it's well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as ...

journal_title：BMC bioinformatics

authors： Ul-Haq Z,Iqbal S,Moin ST

更新日期：2012-11-01 00:00:00

abstract：BACKGROUND:The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly similar reactions evolved on different, i. e. non-homologous protein folds and how similar their 3D pos...

journal_title：BMC bioinformatics

authors： Žváček C,Friedrichs G,Heizinger L,Merkl R

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...

journal_title：BMC bioinformatics

authors： Hofmeister BT,Schmitz RJ

更新日期：2018-04-25 00:00:00

abstract：:Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H)...

journal_title：BMC bioinformatics

authors： Mirhaji P,Zhu M,Vagnoni M,Bernstam EV,Zhang J,Smith JW

更新日期：2009-02-05 00:00:00

abstract：BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...

journal_title：BMC bioinformatics

authors： You ZH,Yin Z,Han K,Huang DS,Zhou X

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in man...

journal_title：BMC bioinformatics

authors： Misselwitz B,Strittmatter G,Periaswamy B,Schlumberger MC,Rout S,Horvath P,Kozak K,Hardt WD

更新日期：2010-01-14 00:00:00

abstract：BACKGROUND:Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little simila...

journal_title：BMC bioinformatics

authors： Nojoomi S,Koehl P

更新日期：2017-08-25 00:00:00

abstract：BACKGROUND:In the biomedical domain, the desired information of a question (query) asked by biologists usually is a list of a certain type of entities covering different aspects that are related to the question, such as genes, proteins, diseases, mutations, etc. Hence it is important for a biomedical information retrie...

journal_title：BMC bioinformatics

authors： Yin X,Li Z,Huang JX,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classi...

journal_title：BMC bioinformatics

authors： Chen JL,Liu Y,Sam LT,Li J,Lussier YA

更新日期：2007-05-09 00:00:00

abstract：BACKGROUND:Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great ...

journal_title：BMC bioinformatics

authors： Stoltzfus A,Lapp H,Matasci N,Deus H,Sidlauskas B,Zmasek CM,Vaidya G,Pontelli E,Cranston K,Vos R,Webb CO,Harmon LJ,Pirrung M,O'Meara B,Pennell MW,Mirarab S,Rosenberg MS,Balhoff JP,Bik HM,Heath TA,Midford PE,Brown

更新日期：2013-05-13 00:00:00

abstract：BACKGROUND:Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a g...

journal_title：BMC bioinformatics

authors： Reddy HM,Sharma A,Dehzangi A,Shigemizu D,Chandra AA,Tsunoda T

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigene...

journal_title：BMC bioinformatics

authors： Delatola EI,Lebarbier E,Mary-Huard T,Radvanyi F,Robin S,Wong J

更新日期：2017-07-11 00:00:00

abstract：BACKGROUND:For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional too...

journal_title：BMC bioinformatics

authors： Keller O,Odronitz F,Stanke M,Kollmar M,Waack S

更新日期：2008-06-13 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:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibil...

journal_title：BMC bioinformatics

authors： Deng M,Brägelmann J,Schultze JL,Perner S

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experimen...

journal_title：BMC bioinformatics

authors： Cutillo L,Boukouvalas A,Marinopoulou E,Papalopulu N,Rattray M

更新日期：2020-08-21 00:00:00

abstract：BACKGROUND:Research related to cancer is vast, and continues in earnest in many directions. Due to the complexity of cancer, a better understanding of tumor growth dynamics can be gleaned from a dynamic computational model. We present a comprehensive, fully executable, spatial and temporal 3D computational model of the...

journal_title：BMC bioinformatics

authors： Bloch N,Harel D

更新日期：2016-08-24 00:00:00

abstract：BACKGROUND:Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number...

journal_title：BMC bioinformatics

authors： Sauta E,Demartini A,Vitali F,Riva A,Bellazzi R

更新日期：2020-05-29 00:00:00

abstract：BACKGROUND:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...

journal_title：BMC bioinformatics

authors： Skums P,Dimitrova Z,Campo DS,Vaughan G,Rossi L,Forbi JC,Yokosawa J,Zelikovsky A,Khudyakov Y

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND:Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of effic...

journal_title：BMC bioinformatics

authors： Coutant S,Cabot C,Lefebvre A,Léonard M,Prieur-Gaston E,Campion D,Lecroq T,Dauchel H

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model...

journal_title：BMC bioinformatics

authors： Cobbs G

更新日期：2012-08-16 00:00:00