SDAR: a practical tool for graphical analysis of two-dimensional data.

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:Analysis of cellular processes with microscopic bright field defocused imaging has the advantage of low phototoxicity and minimal sample preparation. However bright field images lack the contrast and nuclei reporting available with florescent approaches and therefore present a challenge to methods that segme...

journal_title：BMC bioinformatics

authors： Mohamadlou H,Shope JC,Flann NS

更新日期：2014-01-30 00:00:00

abstract：BACKGROUND:Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. RESULTS:In this paper, we have proposed a Vertical...

journal_title：BMC bioinformatics

authors： Naznin F,Sarker R,Essam D

更新日期：2011-08-25 00:00:00

abstract：BACKGROUND:Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as...

journal_title：BMC bioinformatics

authors： Peters B,Sette A

更新日期：2005-05-31 00:00:00

abstract：BACKGROUND:Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the assoc...

journal_title：BMC bioinformatics

authors： Sikdar S,Datta S

更新日期：2017-02-02 00:00:00

abstract：BACKGROUND:Antibiotics are the widely prescribed drugs for children and most likely to be related with adverse reactions. Record on adverse reactions and allergies from antibiotics considerably affect the prescription choices. We consider this a biomedical decision-making problem and explore hidden knowledge in survey ...

journal_title：BMC bioinformatics

authors： Yildirim P,Majnarić L,Ekmekci O,Holzinger A

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area through ballast water and biofouling. Aiming at aquatic bioinvasion issue, people proposed various sug...

journal_title：BMC bioinformatics

authors： Wang S,Wang C,Wang S,Ma L

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the programs are made for a specific task, hence the user often needs to combine multiple programs in order to reach a goal. This can make the data proc...

journal_title：BMC bioinformatics

authors： Kunzmann P,Hamacher K

更新日期：2018-10-01 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:Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at...

journal_title：BMC bioinformatics

authors： Andersson CR,Isaksson A,Gustafsson MG

更新日期：2006-02-09 00:00:00

abstract：BACKGROUND:Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are di...

journal_title：BMC bioinformatics

authors： Li Z,He Y,Liu Q,Zhao L,Wong L,Kwoh CK,Nguyen H,Li J

更新日期：2013-01-01 00:00:00

abstract：:Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data...

journal_title：BMC bioinformatics

authors： Pimentel H,Sturmfels P,Bray N,Melsted P,Pachter L

更新日期：2016-12-01 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:Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. RESULTS:He...

journal_title：BMC bioinformatics

authors： Sanli K,Karlsson FH,Nookaew I,Nielsen J

更新日期：2013-02-01 00:00:00

abstract：BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...

journal_title：BMC bioinformatics

authors： Kong W,Mou X,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of pr...

journal_title：BMC bioinformatics

authors： Ayub U,Haider I,Naveed H

更新日期：2020-11-04 00:00:00

abstract：BACKGROUND:A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts ...

journal_title：BMC bioinformatics

authors： Kedzierska AM,Casanellas M

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcript...

journal_title：BMC bioinformatics

authors： Angelini C,De Canditiis D,De Feis I

更新日期：2014-05-09 00:00:00

abstract：BACKGROUND:Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, int...

journal_title：BMC bioinformatics

authors： Yu C,Zavaljevski N,Desai V,Johnson S,Stevens FJ,Reifman J

更新日期：2008-01-25 00:00:00

abstract：BACKGROUND:The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein wit...

journal_title：BMC bioinformatics

authors： Ray S,Craven M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafi...

journal_title：BMC bioinformatics

authors： Kang CP,Tu HC,Fu TF,Wu JM,Chu PH,Chang DT

更新日期：2018-05-09 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:The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering, the process of grouping of original fragments according to their annotation, similarity to known genomic DNA or each other. Cluste...

journal_title：BMC bioinformatics

authors： Ptitsyn A,Hide W

更新日期：2005-07-15 00:00:00

abstract：BACKGROUND:As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constraint on variation due to shared selective pressures. In comparative sequence analysis, for example, sequence s...

journal_title：BMC bioinformatics

authors： Stone EA,Sidow A

更新日期：2007-06-26 00:00:00

abstract：BACKGROUND:Gene expression data can be analyzed by summarizing groups of individual gene expression profiles based on GO annotation information. The mean expression profile per group can then be used to identify interesting GO categories in relation to the experimental settings. However, the expression profiles present...

journal_title：BMC bioinformatics

authors： De Haan JR,Piek E,van Schaik RC,de Vlieg J,Bauerschmidt S,Buydens LM,Wehrens R

更新日期：2010-03-26 00:00:00

abstract：BACKGROUND:The median of k≥3 genomes was originally defined to find a compromise genome indicative of a common ancestor. However, in gene order comparisons, the usual definitions based on minimizing the sum of distances to the input genomes lead to degenerate medians reflecting only one of the input genomes. "Near-medi...

journal_title：BMC bioinformatics

authors： Larlee CA,Brandts A,Sankoff D

更新日期：2016-12-15 00:00:00

abstract：BACKGROUND:Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. RESULTS:We ...

journal_title：BMC bioinformatics

authors： Chang HH,McGeachie M,Alterovitz G,Ramoni MF

更新日期：2010-10-28 00:00:00

abstract：BACKGROUND:The misregulation of microRNA (miRNA) has been shown to cause diseases. Recently, we have proposed a computational method based on a random walk framework on a miRNA-target gene network to predict disease-associated miRNAs. The prediction performance of our method is better than that of some existing state-o...

journal_title：BMC bioinformatics

authors： Le DH,Tran TTH

更新日期：2020-06-15 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:The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have...

journal_title：BMC bioinformatics

authors： Veuthey AL,Bridge A,Gobeill J,Ruch P,McEntyre JR,Bougueleret L,Xenarios I

更新日期：2013-03-22 00:00:00