Sequence-structure relations of pseudoknot RNA.

abstract：BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...

journal_title：BMC bioinformatics

authors： Zhang W,Sun F,Jiang R

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathol...

journal_title：BMC bioinformatics

authors： Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer U

更新日期：2009-10-15 00:00:00

abstract：BACKGROUND:Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. It is interesting to identify and represent relevant CNVs from a genome-wide data due to high data volume and the complexity of interactions. RESULTS:In this paper, we incorporate the ...

journal_title：BMC bioinformatics

authors： Liu Y,Lee YF,Ng MK

更新日期：2011-01-01 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:Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known bindi...

journal_title：BMC bioinformatics

authors： Thomson K,Amin I,Morales E,Winters-Hilt S

更新日期：2007-11-01 00:00:00

abstract：BACKGROUND:Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional natur...

journal_title：BMC bioinformatics

authors： Arakawa K,Tamaki S,Kono N,Kido N,Ikegami K,Ogawa R,Tomita M

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. RESULTS:Qxpak is a package for versatile statistical genomics, specificall...

journal_title：BMC bioinformatics

authors： Pérez-Enciso M,Misztal I

更新日期：2011-05-25 00:00:00

abstract：BACKGROUND:Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-based prediction of some of these so-called one-dimensional features. However, there is little expla...

journal_title：BMC bioinformatics

authors： Ahmad S,Singh YH,Paudel Y,Mori T,Sugita Y,Mizuguchi K

更新日期：2010-10-27 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:Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to pre...

journal_title：BMC bioinformatics

authors： Piippo M,Lietzén N,Nevalainen OS,Salmi J,Nyman TA

更新日期：2010-06-15 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:The definition of a distance measure plays a key role in the evaluation of different clustering solutions of gene expression profiles. In this empirical study we compare different clustering solutions when using the Mutual Information (MI) measure versus the use of the well known Euclidean distance and Pears...

journal_title：BMC bioinformatics

authors： Priness I,Maimon O,Ben-Gal I

更新日期：2007-03-30 00:00:00

abstract：BACKGROUND:Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control ...

journal_title：BMC bioinformatics

authors： Nilsson R,Björkegren J,Tegnér J

更新日期：2009-01-29 00:00:00

abstract：BACKGROUND:Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. The growing volume of gene expression data in open data repositories such as the N...

journal_title：BMC bioinformatics

authors： Gower AC,Spira A,Lenburg ME

更新日期：2011-09-27 00:00:00

abstract：BACKGROUND:DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS:Here, we describe a method to detect copy number varia...

journal_title：BMC bioinformatics

authors： Xie C,Tammi MT

更新日期：2009-03-06 00:00:00

abstract：BACKGROUND AND GOAL:The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing with logistic regression in many innovation-friendly scientific fields. RESULTS:In this conte...

journal_title：BMC bioinformatics

authors： Couronné R,Probst P,Boulesteix AL

更新日期：2018-07-17 00:00:00

abstract：BACKGROUND:Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are established techniques that combine parameter estimation and variable selection. One big challenge is to i...

journal_title：BMC bioinformatics

authors： Sariyar M,Hoffmann I,Binder H

更新日期：2014-02-26 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactom...

journal_title：BMC bioinformatics

authors： Caufield JH,Wimble C,Shary S,Wuchty S,Uetz P

更新日期：2017-03-16 00:00:00

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:Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potential multimolecular complex. However, the tri-dimensional structure of urokinase, urokinase receptor a...

journal_title：BMC bioinformatics

authors： Degryse B,Fernandez-Recio J,Citro V,Blasi F,Cubellis MV

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Periodic phenomena are widespread in biology. The problem of finding periodicity in biological time series can be viewed as a multiple hypothesis testing of the spectral content of a given time series. The exact noise characteristics are unknown in many bioinformatics applications. Furthermore, the observed ...

journal_title：BMC bioinformatics

authors： Ahdesmäki M,Lähdesmäki H,Pearson R,Huttunen H,Yli-Harja O

更新日期：2005-05-13 00:00:00

abstract：BACKGROUND:Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to s...

journal_title：BMC bioinformatics

authors： Weber Zendrera A,Sokolovska N,Soula HA

更新日期：2019-10-15 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:The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise and contaminant peaks. It is widely accepted that a valid primary peak tends to have high intensity an...

journal_title：BMC bioinformatics

authors： Zhang S,Wang Y,Bu D,Zhang H,Sun S

更新日期：2011-08-17 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:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

journal_title：BMC bioinformatics

authors： Ryan BC,Werner TS,Howard PL,Chow RL

更新日期：2016-04-27 00:00:00

abstract：BACKGROUND:Transcriptome sequencing is a powerful tool for measuring gene expression, but as well as some other technologies, various artifacts and biases affect the quantification. In order to correct some of them, several normalization approaches have emerged, differing both in the statistical strategy employed and i...

journal_title：BMC bioinformatics

authors： Filloux C,Cédric M,Romain P,Lionel F,Christophe K,Dominique R,Abderrahman M,Daniel P

更新日期：2014-06-14 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:Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences s...

journal_title：BMC bioinformatics

authors： Arenas M,Posada D

更新日期：2007-11-20 00:00:00

abstract：BACKGROUND:High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknes...

journal_title：BMC bioinformatics

authors： Bian X,Zhu B,Wang M,Hu Y,Chen Q,Nguyen C,Hicks B,Meerzaman D

更新日期：2018-11-19 00:00:00