Can Zipf's law be adapted to normalize microarrays?

abstract：BACKGROUND:The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS:...

journal_title：BMC bioinformatics

authors： Müller HM,Van Auken KM,Li Y,Sternberg PW

更新日期：2018-03-09 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:The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. RESULTS:We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the ...

journal_title：BMC bioinformatics

authors： Shah A,Tenzen T,McMahon AP,Woolf PJ

更新日期：2009-12-18 00:00:00

abstract：BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...

journal_title：BMC bioinformatics

authors： Bartoli L,Calabrese R,Fariselli P,Mita DG,Casadio R

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing. RESULTS:We propose s...

journal_title：BMC bioinformatics

authors： Rudra P,Shi WJ,Vestal B,Russell PH,Odell A,Dowell RD,Radcliffe RA,Saba LM,Kechris K

更新日期：2017-03-02 00:00:00

abstract：BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...

journal_title：BMC bioinformatics

authors： Varadi M,Guharoy M,Zsolyomi F,Tompa P

更新日期：2015-05-13 00:00:00

abstract：BACKGROUND:Gene expression experiments are common in molecular biology, for example in order to identify genes which play a certain role in a specified biological framework. For that purpose expression levels of several thousand genes are measured simultaneously using DNA microarrays. Comparing two distinct groups of t...

journal_title：BMC bioinformatics

authors： Jung K,Friede T,Beissbarth T

更新日期：2011-07-15 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:Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the databas...

journal_title：BMC bioinformatics

authors： Shimizu K,Nuida K,Arai H,Mitsunari S,Attrapadung N,Hamada M,Tsuda K,Hirokawa T,Sakuma J,Hanaoka G,Asai K

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...

journal_title：BMC bioinformatics

authors： Chanumolu SK,Albahrani M,Otu HH

更新日期：2019-08-15 00:00:00

abstract：BACKGROUND:The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is d...

journal_title：BMC bioinformatics

authors： Wang L,Stein LD

更新日期：2010-11-08 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...

journal_title：BMC bioinformatics

authors： Yang F,Fan K,Song D,Lin H

更新日期：2020-07-21 00:00:00

abstract：BACKGROUND:Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate ...

journal_title：BMC bioinformatics

authors： Cimmaruta C,Citro V,Andreotti G,Liguori L,Cubellis MV,Hay Mele B

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression tra...

journal_title：BMC bioinformatics

authors： Cheng W,Shi Y,Zhang X,Wang W

更新日期：2015-01-16 00:00:00

abstract：BACKGROUND:Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investiga...

journal_title：BMC bioinformatics

authors： Zhu H,Domingues FS,Sommer I,Lengauer T

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:Accurately prioritizing candidate disease genes is an important and challenging problem. Various network-based methods have been developed to predict potential disease genes by utilizing the disease similarity network and molecular networks such as protein interaction or gene co-expression networks. Although...

journal_title：BMC bioinformatics

authors： Ni J,Koyuturk M,Tong H,Haines J,Xu R,Zhang X

更新日期：2016-11-10 00:00:00

abstract：BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...

journal_title：BMC bioinformatics

authors： Schönenberger F,Deutzmann A,Ferrando-May E,Merhof D

更新日期：2015-05-29 00:00:00

abstract：BACKGROUND:We aim to solve the problem of determining word senses for ambiguous biomedical terms with minimal human effort. METHODS:We build a fully automated system for Word Sense Disambiguation by designing a system that does not require manually-constructed external resources or manually-labeled training examples e...

journal_title：BMC bioinformatics

authors： Duan W,Song M,Yates A

更新日期：2009-03-19 00:00:00

abstract：BACKGROUND:Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize line has accelerated the pace of development of superior commercial seed varieties and has been tran...

journal_title：BMC bioinformatics

authors： Veeramani B,Raymond JW,Chanda P

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...

journal_title：BMC bioinformatics

authors： Rivas E,Eddy SR

更新日期：2015-12-10 00:00:00

abstract：BACKGROUND:Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to p...

journal_title：BMC bioinformatics

authors： Cipriano GM,Phillips GN Jr,Gleicher M

更新日期：2012-11-24 00:00:00

abstract：BACKGROUND:Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS:A non-parametric Bayesian ap...

journal_title：BMC bioinformatics

authors： Beam AL,Motsinger-Reif A,Doyle J

更新日期：2014-11-21 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:In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for ...

journal_title：BMC bioinformatics

authors： Aberer AJ,Stamatakis A

更新日期：2013-07-09 00:00:00

abstract：BACKGROUND:The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug...

journal_title：BMC bioinformatics

authors： Singh I,Kuscuoglu M,Harkins DM,Sutton G,Fouts DE,Nelson KE

更新日期：2019-01-07 00:00:00

abstract：BACKGROUND:Community structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a system's functional components and the impact of local structures on dynamics at a global scale. Choosing an a...

journal_title：BMC bioinformatics

authors： Sah P,Singh LO,Clauset A,Bansal S

更新日期：2014-06-25 00:00:00

abstract：BACKGROUND:Reliability and Reproducibility of differentially expressed genes (DEGs) are essential for the biological interpretation of microarray data. The microarray quality control (MAQC) project launched by US Food and Drug Administration (FDA) elucidated that the lists of DEGs generated by intra- and inter-platform...

journal_title：BMC bioinformatics

authors： Zhang L,Zhang J,Yang G,Wu D,Jiang L,Wen Z,Li M

更新日期：2013-04-29 00:00:00

abstract：:Following publication of the original article [1], the author reported that there are several errors in the original article. ...

journal_title：BMC bioinformatics

authors： Ranjard L,Wong TKF,Rodrigo AG

更新日期：2020-01-22 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:The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutat...

journal_title：BMC bioinformatics

authors： Santos J,Monteagudo Á

更新日期：2017-03-27 00:00:00