SplicerAV: a tool for mining microarray expression data for changes in RNA processing.

abstract：BACKGROUND:Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemic...

journal_title：BMC bioinformatics

authors： Chae M,Shmookler Reis RJ,Thaden JJ

更新日期：2008-08-12 00:00:00

abstract：BACKGROUND:Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleo...

journal_title：BMC bioinformatics

authors： Wang Y,Wu H,Cai Y

更新日期：2018-12-31 00:00:00

abstract：BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

journal_title：BMC bioinformatics

authors： Choo KH,Tan TW,Ranganathan S

更新日期：2005-10-13 00:00:00

abstract：BACKGROUND:The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the simila...

journal_title：BMC bioinformatics

authors： Zhang M,Yang L,Ren J,Ahlgren NA,Fuhrman JA,Sun F

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniq...

journal_title：BMC bioinformatics

authors： Bhattacharya S,Bhattacharyya C,Chandra NR

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography coupled to mass spectrometry (GC/MS) is a well-established analytical method in metabolomics study, an...

journal_title：BMC bioinformatics

authors： Tsugawa H,Tsujimoto Y,Arita M,Bamba T,Fukusaki E

更新日期：2011-05-04 00:00:00

abstract：BACKGROUND:Computational gene finding algorithms have proven their robustness in identifying genes in complete genomes. However, metagenomic sequencing has presented new challenges due to the incomplete and fragmented nature of the data. During the last few years, attempts have been made to extract complete and incompl...

journal_title：BMC bioinformatics

authors： El Allali A,Rose JR

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool wh...

journal_title：BMC bioinformatics

authors： David MP,Lapid CM,Daria VR

更新日期：2008-04-28 00:00:00

abstract：BACKGROUND:The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running ti...

journal_title：BMC bioinformatics

authors： Meyer F,Kurtz S,Backofen R,Will S,Beckstette M

更新日期：2011-05-27 00:00:00

abstract：BACKGROUND:Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure ...

journal_title：BMC bioinformatics

authors： Tharatipyakul A,Numnark S,Wichadakul D,Ingsriswang S

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...

journal_title：BMC bioinformatics

authors： Jaiswal M,Crabtree N,Bauer MA,Hall R,Raney KD,Zybailov BL

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. R...

journal_title：BMC bioinformatics

authors： Beccati A,Gerken J,Quast C,Yilmaz P,Glöckner FO

更新日期：2017-09-30 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:Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV da...

journal_title：BMC bioinformatics

authors： Vandeweyer G,Reyniers E,Wuyts W,Rooms L,Kooy RF

更新日期：2011-01-05 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：:Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...

journal_title：BMC bioinformatics

authors： Nahnsen S,Kohlbacher O

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in transcription factor databases, as well as to represent the po...

journal_title：BMC bioinformatics

authors： Kankainen M,Löytynoja A

更新日期：2007-06-08 00:00:00

abstract：BACKGROUND:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and a...

journal_title：BMC bioinformatics

authors： Signorelli M,Vinciotti V,Wit EC

更新日期：2016-09-05 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:Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human cells into malignant cancer cells. Interrogation of cancer genomes holds the promise of understandi...

journal_title：BMC bioinformatics

authors： Sanchez-Garcia F,Akavia UD,Mozes E,Pe'er D

更新日期：2010-04-14 00:00:00

abstract：BACKGROUND:In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene express...

journal_title：BMC bioinformatics

authors： Acharya S,Cui L,Pan Y

更新日期：2020-12-30 00:00:00

abstract：BACKGROUND:Determining a suitable sample size is an important step in the planning of microarray experiments. Increasing the number of arrays gives more statistical power, but adds to the total cost of the experiment. Several approaches for sample size determination have been developed for expression array studies, but...

journal_title：BMC bioinformatics

authors： Scheinin I,Ferreira JA,Knuutila S,Meijer GA,van de Wiel MA,Ylstra B

更新日期：2010-06-17 00:00:00

abstract：:We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists work...

journal_title：BMC bioinformatics

authors： Ranganathan S,Gribskov M,Tan TW

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order t...

journal_title：BMC bioinformatics

authors： Corradi L,Fato M,Porro I,Scaglione S,Torterolo L

更新日期：2008-11-13 00:00:00

abstract：BACKGROUND:Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large". RESULTS:Using the multispecies coalescent model, we report a general an...

journal_title：BMC bioinformatics

authors： Uricchio LH,Warnow T,Rosenberg NA

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local corre...

journal_title：BMC bioinformatics

authors： Wang WL,Yu Z,Castillo-Menendez LR,Sodroski J,Mao Y

更新日期：2019-04-03 00:00:00

abstract：:Following last year's computational vaccinology workshop in Shanghai, China, the third ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013) was held in Barcelona, Spain. ICoVax 2013 provided an international platform for the attendees to showcase their research and discuss problems and solutions in the ...

journal_title：BMC bioinformatics

authors： De Groot AS,De Groot P,He Y

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Health Organization (WHO) proposed classification that assigns multi-level codes to compounds based on th...

journal_title：BMC bioinformatics

authors： Olson T,Singh R

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:People with an autistic spectrum disorder (ASD) display a variety of characteristic behavioral traits, including impaired social interaction, communication difficulties and repetitive behavior. This complex neurodevelopment disorder is known to be associated with a combination of genetic and environmental fa...

journal_title：BMC bioinformatics

authors： Patel S,Roncaglia P,Lovering RC

更新日期：2015-06-06 00:00:00

abstract：BACKGROUND:Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model ...

journal_title：BMC bioinformatics

authors： Cao R,Bhattacharya D,Hou J,Cheng J

更新日期：2016-12-05 00:00:00