Promoting ranking diversity for genomics search with relevance-novelty combined model.

abstract：BACKGROUND:Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molec...

journal_title：BMC bioinformatics

authors： Steffen M,Petti A,Aach J,D'haeseleer P,Church G

更新日期：2002-11-01 00:00:00

abstract：BACKGROUND:The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced,...

journal_title：BMC bioinformatics

authors： Lischer HEL,Shimizu KK

更新日期：2017-11-10 00:00:00

abstract：BACKGROUND:The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The main network reconstruction approaches are either based on Bayesian scores, which enable the ranking...

journal_title：BMC bioinformatics

authors： Affeldt S,Verny L,Isambert H

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to populatio...

journal_title：BMC bioinformatics

authors： Brodin J,Krishnamoorthy M,Athreya G,Fischer W,Hraber P,Gleasner C,Green L,Korber B,Leitner T

更新日期：2013-08-21 00:00:00

abstract：BACKGROUND:Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly ass...

journal_title：BMC bioinformatics

authors： Gai X,Perin JC,Murphy K,O'Hara R,D'arcy M,Wenocur A,Xie HM,Rappaport EF,Shaikh TH,White PS

更新日期：2010-02-04 00:00:00

abstract：BACKGROUND:Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus ...

journal_title：BMC bioinformatics

authors： Kasprzak JM,Czerwoniec A,Bujnicki JM

更新日期：2012-06-28 00:00:00

abstract：BACKGROUND:Although protein-protein interaction networks determined with high-throughput methods are incomplete, they are commonly used to infer the topology of the complete interactome. These partial networks often show a scale-free behavior with only a few proteins having many and the majority having only a few conne...

journal_title：BMC bioinformatics

authors： Friedel CC,Zimmer R

更新日期：2006-11-30 00:00:00

abstract：BACKGROUND:DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arr...

journal_title：BMC bioinformatics

authors： Yu F,Xu C,Deng HW,Shen H

更新日期：2020-12-01 00:00:00

abstract：BACKGROUND:Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction h...

journal_title：BMC bioinformatics

authors： Su EC,Chiu HS,Lo A,Hwang JK,Sung TY,Hsu WL

更新日期：2007-09-08 00:00:00

abstract：BACKGROUND:Researchers involved in the annotation of large numbers of gene, clone or protein identifiers are usually required to perform a one-by-one conversion for each identifier. When the field of research is one such as microarray experiments, this number may be around 30,000. RESULTS:To help researchers map acces...

journal_title：BMC bioinformatics

authors： Alibés A,Yankilevich P,Cañada A,Díaz-Uriarte R

更新日期：2007-01-10 00:00:00

abstract：BACKGROUND:Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They are are actually coupled beause the integration of omic information may provide better means to detec...

journal_title：BMC bioinformatics

authors： Bardozzo F,Lió P,Tagliaferri R

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...

journal_title：BMC bioinformatics

authors： Henriques R,Ferreira FL,Madeira SC

更新日期：2017-02-02 00:00:00

abstract：BACKGROUND:The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed a...

journal_title：BMC bioinformatics

authors： Stubben CJ,Challacombe JF

更新日期：2014-02-05 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:The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software t...

journal_title：BMC bioinformatics

authors： Xi L,Fondufe-Mittendorf Y,Xia L,Flatow J,Widom J,Wang JP

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such studies, sequence annotations frequently play an essential role, and reliable results depend on metadata...

journal_title：BMC bioinformatics

authors： Miotto O,Tan TW,Brusic V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the hierarchy. This scenario is typically found in protein function prediction, considering that each pr...

journal_title：BMC bioinformatics

authors： Cerri R,Barros RC,P L F de Carvalho AC,Jin Y

更新日期：2016-09-15 00:00:00

abstract：BACKGROUND:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...

journal_title：BMC bioinformatics

authors： González JR,Carrasco JL,Armengol L,Villatoro S,Jover L,Yasui Y,Estivill X

更新日期：2008-06-04 00:00:00

abstract：BACKGROUND:Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships between lncRNAs and diseases. Due to the high costs and time complexity of traditional bio-experiments, ...

journal_title：BMC bioinformatics

authors： Xiao Y,Xiao Z,Feng X,Chen Z,Kuang L,Wang L

更新日期：2020-12-02 00:00:00

abstract：BACKGROUND:The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advance...

journal_title：BMC bioinformatics

authors： Matey-Hernandez ML,Danish Pan Genome Consortium.,Brunak S,Izarzugaza JMG

更新日期：2018-06-25 00:00:00

abstract：BACKGROUND:With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceabilit...

journal_title：BMC bioinformatics

authors： Thallinger GG,Baumgartner K,Pirklbauer M,Uray M,Pauritsch E,Mehes G,Buck CR,Zatloukal K,Trajanoski Z

更新日期：2007-03-07 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:Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent b...

journal_title：BMC bioinformatics

authors： Cohen-Boulakia S,Chen J,Missier P,Goble C,Williams AR,Froidevaux C

更新日期：2014-01-01 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:Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction ...

journal_title：BMC bioinformatics

authors： Zahurak M,Parmigiani G,Yu W,Scharpf RB,Berman D,Schaeffer E,Shabbeer S,Cope L

更新日期：2007-05-01 00:00:00

abstract：BACKGROUND:Biological data often originate from samples containing mixtures of subpopulations, corresponding e.g. to distinct cellular phenotypes. However, identification of distinct subpopulations may be difficult if biological measurements yield distributions that are not easily separable. RESULTS:We present Multire...

journal_title：BMC bioinformatics

authors： Feigelman J,Theis FJ,Marr C

更新日期：2014-07-11 00:00:00

abstract：BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...

journal_title：BMC bioinformatics

authors： Camacho C,Coulouris G,Avagyan V,Ma N,Papadopoulos J,Bealer K,Madden TL

更新日期：2009-12-15 00:00:00

abstract：:Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference, heritability estimation, and mapping disease loci. Simultaneous detection of IBD over multiple haplotypes has...

journal_title：BMC bioinformatics

authors： Park DS,Baran Y,Hormozdiari F,Eng C,Torgerson DG,Burchard EG,Zaitlen N

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to ac...

journal_title：BMC bioinformatics

authors： Lemaitre C,Barré A,Citti C,Tardy F,Thiaucourt F,Sirand-Pugnet P,Thébault P

更新日期：2011-11-24 00:00:00

abstract：BACKGROUND:In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image ac...

journal_title：BMC bioinformatics

authors： Hartmann A,Czauderna T,Hoffmann R,Stein N,Schreiber F

更新日期：2011-05-12 00:00:00