SAMSA: a comprehensive metatranscriptome analysis pipeline.

abstract：BACKGROUND:Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. RESULTS:In thi...

journal_title：BMC bioinformatics

authors： Deng X,Cheng J

更新日期：2014-07-25 00:00:00

abstract：BACKGROUND:A major goal of the analysis of high-dimensional RNA expression data from tumor tissue is to identify prognostic signatures for discriminating patient subgroups. For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and lo...

journal_title：BMC bioinformatics

authors： Hellwig B,Hengstler JG,Schmidt M,Gehrmann MC,Schormann W,Rahnenführer J

更新日期：2010-05-25 00:00:00

abstract：BACKGROUND:Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze t...

journal_title：BMC bioinformatics

authors： Lopes Ide O,Schliep A,de Carvalho AC

更新日期：2014-05-02 00:00:00

abstract：BACKGROUND:Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene express...

journal_title：BMC bioinformatics

authors： Zhang SD,Gant TW

更新日期：2008-06-02 00:00:00

abstract：BACKGROUND:Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phe...

journal_title：BMC bioinformatics

authors： Lee JY,Fujimoto GM,Wilson R,Wiley HS,Payne SH

更新日期：2018-06-11 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：: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:Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data co...

journal_title：BMC bioinformatics

authors： Bagheri H,Muppirala U,Masonbrink RE,Severin AJ,Rajan H

更新日期：2019-08-22 00:00:00

abstract：BACKGROUND:The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS:In the present work, individual cluste...

journal_title：BMC bioinformatics

authors： Sen TZ,Kloczkowski A,Jernigan RL

更新日期：2006-07-24 00:00:00

abstract：BACKGROUND:Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the similarities between tw...

journal_title：BMC bioinformatics

authors： Sato K,Mituyama T,Asai K,Sakakibara Y

更新日期：2008-07-22 00:00:00

abstract：BACKGROUND:Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each...

journal_title：BMC bioinformatics

authors： Starmer J,Magnuson T

更新日期：2016-03-24 00:00:00

abstract：BACKGROUND:Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putati...

journal_title：BMC bioinformatics

authors： Stuart GW,Berry MW

更新日期：2004-12-17 00:00:00

abstract：:Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...

journal_title：BMC bioinformatics

authors： Yang JY,Dunker A,Liu JS,Qin X,Arabnia HR,Yang W,Niemierko A,Chen Z,Luo Z,Wang L,Liu Y,Xu D,Deng Y,Tong W,Yang M

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Fluorescence microscopy is widely used to determine the subcellular location of proteins. Efforts to determine location on a proteome-wide basis create a need for automated methods to analyze the resulting images. Over the past ten years, the feasibility of using machine learning methods to recognize all maj...

journal_title：BMC bioinformatics

authors： Chebira A,Barbotin Y,Jackson C,Merryman T,Srinivasa G,Murphy RF,Kovacević J

更新日期：2007-06-19 00:00:00

abstract：BACKGROUND:Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiolog...

journal_title：BMC bioinformatics

authors： Lemmin T,Soto C

更新日期：2019-10-22 00:00:00

abstract：BACKGROUND:Analyzing Variance heterogeneity in genome wide association studies (vGWAS) is an emerging approach for detecting genetic loci involved in gene-gene and gene-environment interactions. vGWAS analysis detects variability in phenotype values across genotypes, as opposed to typical GWAS analysis, which detects v...

journal_title：BMC bioinformatics

authors： Al Kawam A,Alshawaqfeh M,Cai JJ,Serpedin E,Datta A

更新日期：2018-03-21 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes and form the basis of biological mechanisms. Although large amount of PPIs data for different species has been generated by high-throughput experimental techniques, current PPI pairs obtained with experiment...

journal_title：BMC bioinformatics

authors： You ZH,Lei YK,Zhu L,Xia J,Wang B

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, ma...

journal_title：BMC bioinformatics

authors： Cherkasov A,Ho Sui SJ,Brunham RC,Jones SJ

更新日期：2004-07-26 00:00:00

abstract：BACKGROUND:Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated,...

journal_title：BMC bioinformatics

authors： de Brevern AG,Hazout S,Malpertuy A

更新日期：2004-08-23 00:00:00

abstract：BACKGROUND:Automatic quantification of neuronal morphology from images of fluorescence microscopy plays an increasingly important role in high-content screenings. However, there exist very few freeware tools and methods which provide automatic neuronal morphology quantification for pharmacological discovery. RESULTS:T...

journal_title：BMC bioinformatics

authors： Ho SY,Chao CY,Huang HL,Chiu TW,Charoenkwan P,Hwang E

更新日期：2011-06-08 00:00:00

abstract：BACKGROUND:Differences in cell-type composition across subjects and conditions often carry biological significance. Recent advancements in single cell sequencing technologies enable cell-types to be identified at the single cell level, and as a result, cell-type composition of tissues can now be studied in exquisite de...

journal_title：BMC bioinformatics

authors： Cao Y,Lin Y,Ormerod JT,Yang P,Yang JYH,Lo KK

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics...

journal_title：BMC bioinformatics

authors： Widmer C,Toussaint NC,Altun Y,Rätsch G

更新日期：2010-10-26 00:00:00

abstract：BACKGROUND:Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype s...

journal_title：BMC bioinformatics

authors： Peng J,Hui W,Shang X

更新日期：2018-04-11 00:00:00

abstract：BACKGROUND:Recent advances in genomics and proteomics have allowed us to study the nuances of the Warburg effect--a long-standing puzzle in cancer energy metabolism--at an unprecedented level of detail. While modern next-generation sequencing technologies are extremely powerful, the lack of appropriate data analysis to...

journal_title：BMC bioinformatics

authors： Markovets AA,Herman D

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functi...

journal_title：BMC bioinformatics

authors： Tchagang AB,Gawronski A,Bérubé H,Phan S,Famili F,Pan Y

更新日期：2010-05-06 00:00:00

abstract：BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...

journal_title：BMC bioinformatics

authors： Paten B,Zerbino DR,Hickey G,Haussler D

更新日期：2014-06-19 00:00:00

abstract：BACKGROUND:Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation. Despite the kinetic information generated by real-time PCR, most popular analysis methods assume c...

journal_title：BMC bioinformatics

authors： Alvarez MJ,Vila-Ortiz GJ,Salibe MC,Podhajcer OL,Pitossi FJ

更新日期：2007-03-09 00:00:00

abstract：BACKGROUNDS:Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgentl...

journal_title：BMC bioinformatics

authors： Joo T,Choi JH,Lee JH,Park SE,Jeon Y,Jung SH,Woo HG

更新日期：2019-02-20 00:00:00

abstract：BACKGROUND:Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientifi...

journal_title：BMC bioinformatics

authors： Durrant JD,Amaro RE

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public...

journal_title：BMC bioinformatics

authors： Nilsson RH,Kristiansson E,Ryberg M,Larsson KH

更新日期：2005-07-18 00:00:00