SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes.

abstract：BACKGROUND:Discovering patterns from gene expression levels is regarded as a classification problem when tissue classes of the samples are given and solved as a discrete-data problem by discretizing the expression levels of each gene into intervals maximizing the interdependence between that gene and the class labels. ...

journal_title：BMC bioinformatics

authors： Wu GP,Chan KC,Wong AK

更新日期：2011-01-01 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:One of key issues in the post-genomic era is to assign functions to uncharacterized proteins. Since proteins seldom act alone; rather, they must interact with other biomolecular units to execute their functions. Thus, the functions of unknown proteins may be discovered through studying their interactions wit...

journal_title：BMC bioinformatics

authors： Hu P,Jiang H,Emili A

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the dif...

journal_title：BMC bioinformatics

authors： Maji RK,Sarkar A,Khatua S,Dasgupta S,Ghosh Z

更新日期：2014-06-04 00:00:00

abstract：BACKGROUND:As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological results from the aspects of whole-genome coverage, variant discovery power and the quality of varian...

journal_title：BMC bioinformatics

authors： Jiang Y,Jiang Y,Wang S,Zhang Q,Ding X

更新日期：2019-11-08 00:00:00

abstract：BACKGROUND:Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the development of effective statistical methods to calibrat...

journal_title：BMC bioinformatics

authors： Komorowski M,Finkenstädt B,Harper CV,Rand DA

更新日期：2009-10-19 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...

journal_title：BMC bioinformatics

authors： Liu L,Zhu X,Ma Y,Piao H,Yang Y,Hao X,Fu Y,Wang L,Peng J

更新日期：2020-12-16 00:00:00

abstract：BACKGROUND:Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to ar...

journal_title：BMC bioinformatics

authors： Doherty KM,Nakka P,King BM,Rhee SY,Holmes SP,Shafer RW,Radhakrishnan ML

更新日期：2011-12-15 00:00:00

abstract：BACKGROUND:Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., conti...

journal_title：BMC bioinformatics

authors： Taskesen E,Beekman R,de Ridder J,Wouters BJ,Peeters JK,Touw IP,Reinders MJ,Delwel R

更新日期：2010-05-21 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:Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealth of available human genomic information. This raises the question whether it can be done with less ...

journal_title：BMC bioinformatics

authors： Groß C,de Ridder D,Reinders M

更新日期：2018-10-12 00:00:00

abstract：BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...

journal_title：BMC bioinformatics

authors： Che D,Guo S,Jiang Q,Chen L

更新日期：2020-07-14 00:00:00

abstract：BACKGROUND:Hidden variability is a fundamentally important issue in the context of gene expression studies. Collected tissue samples may have a wide variety of hidden effects that may alter their transcriptional landscape significantly. As a result their actual differential expression pattern can be potentially distort...

journal_title：BMC bioinformatics

authors： Chakraborty S,Datta S,Datta S

更新日期：2013-07-24 00:00:00

abstract：BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...

journal_title：BMC bioinformatics

authors： Sievers F,Hughes GM,Higgins DG

更新日期：2014-10-04 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:Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific ...

journal_title：BMC bioinformatics

authors： Allhoff M,Schönhuth A,Martin M,Costa IG,Rahmann S,Marschall T

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequencing methods now becoming accessible, general network inference algorithms that were initially dev...

journal_title：BMC bioinformatics

authors： Chen S,Mar JC

更新日期：2018-06-19 00:00:00

abstract：BACKGROUND:Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying protein folds and domains. Although some methods have been presented to the protein solvent accessibilit...

journal_title：BMC bioinformatics

authors： Fan C,Liu D,Huang R,Chen Z,Deng L

更新日期：2016-01-11 00:00:00

abstract：BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...

journal_title：BMC bioinformatics

authors： Zhang X,Gao L,Liu ZP,Chen L

更新日期：2015-03-18 00:00:00

abstract：BACKGROUND:Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional s...

journal_title：BMC bioinformatics

authors： Ibrahim M,Jassim S,Cawthorne MA,Langlands K

更新日期：2014-11-04 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:Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, ...

journal_title：BMC bioinformatics

authors： Thakur S,Guttman DS

更新日期：2016-06-30 00:00:00

abstract：BACKGROUND:In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve extra effort and cost and may yield invalid EAs. Alternatively, EA can be extracted from individual ...

journal_title：BMC bioinformatics

authors： Batsch A,Noetel A,Fork C,Urban A,Lazic D,Lucas T,Pietsch J,Lazar A,Schömig E,Gründemann D

更新日期：2008-02-12 00:00:00

abstract：BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...

journal_title：BMC bioinformatics

authors： Bui VK,Wei C

更新日期：2020-10-20 00:00:00

abstract：BACKGROUND:Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map con...

journal_title：BMC bioinformatics

authors： Dias Z,Dias U,Setubal JC

更新日期：2012-05-14 00:00:00

abstract：BACKGROUND:Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. RESULTS:A Java program was developed for retrieval of protein and nucleic acid s...

journal_title：BMC bioinformatics

authors： Büssow K,Hoffmann S,Sievert V

更新日期：2002-12-19 00:00:00

abstract：BACKGROUND:Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification ...

journal_title：BMC bioinformatics

authors： Tempel S,Rousseau C,Tahi F,Nicolas J

更新日期：2010-09-22 00:00:00

abstract：BACKGROUND:The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accurately acquiring the synaptic connectivity, and they cannot effectively alleviate the burden of synaps...

journal_title：BMC bioinformatics

authors： Xiao C,Li W,Deng H,Chen X,Yang Y,Xie Q,Han H

更新日期：2018-07-13 00:00:00

abstract：BACKGROUND:The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for model...

journal_title：BMC bioinformatics

authors： Angarica VE,Pérez AG,Vasconcelos AT,Collado-Vides J,Contreras-Moreira B

更新日期：2008-10-16 00:00:00