iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes.

abstract：BACKGROUND:Knowledge of when and in which cells each gene is expressed across multicellular organisms is critical in understanding both gene function and regulation of cell type diversity. However, methods for measuring expression typically involve a trade-off between imaging-based methods, which give the precise locat...

journal_title：BMC bioinformatics

authors： Burdick JT,Murray JI

更新日期：2013-06-22 00:00:00

abstract：BACKGROUND:Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the micro...

journal_title：BMC bioinformatics

authors： Bengtsson H,Jönsson G,Vallon-Christersson J

更新日期：2004-11-12 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:determining beforehand specific positions to align (anchor points) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biological expertise, or automatically, usually by pairwise similarity searches. Multiple local similar...

journal_title：BMC bioinformatics

authors： Pitschi F,Devauchelle C,Corel E

更新日期：2010-09-02 00:00:00

abstract：BACKGROUND:To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibriu...

journal_title：BMC bioinformatics

authors： Shi M,Umbach DM,Wise AS,Weinberg CR

更新日期：2018-01-02 00:00:00

abstract：BACKGROUND:In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding...

journal_title：BMC bioinformatics

authors： Wang X,Wu D,Zheng S,Sun J,Tao L,Li Y,Cao Z

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...

journal_title：BMC bioinformatics

authors： Schönenberger F,Deutzmann A,Ferrando-May E,Merhof D

更新日期：2015-05-29 00:00:00

abstract：BACKGROUND:Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the missing heritability, i.e. heritability of phenotypes so far not accounted for by single genetic vari...

journal_title：BMC bioinformatics

authors： Zhong K,Karssen LC,Kayser M,Liu F

更新日期：2016-04-08 00:00:00

abstract：BACKGROUND:Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of ap...

journal_title：BMC bioinformatics

authors： Hsu JT,Peng CH,Hsieh WP,Lan CY,Tang CY

更新日期：2011-07-12 00:00:00

abstract：BACKGROUND:Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for th...

journal_title：BMC bioinformatics

authors： Meng G,Mosig A,Vingron M

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, the...

journal_title：BMC bioinformatics

authors： Karlen Y,McNair A,Perseguers S,Mazza C,Mermod N

更新日期：2007-04-20 00:00:00

abstract：BACKGROUND:Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide only a single answer and in practice do not produce good results. RESULTS:We explore an alternative...

journal_title：BMC bioinformatics

authors： Brown DG,Golod D

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, protein functional annotation, prediction of molecular interactions, etc. These applications, however sop...

journal_title：BMC bioinformatics

authors： Vanhoutreve R,Kress A,Legrand B,Gass H,Poch O,Thompson JD

更新日期：2016-07-07 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:The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relations...

journal_title：BMC bioinformatics

authors： Gutiérrez FI,Rodriguez-Valenzuela F,Ibarra IL,Devos DP,Melo F

更新日期：2016-01-05 00:00:00

abstract：BACKGROUND:We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interp...

journal_title：BMC bioinformatics

authors： Zeeberg BR,Qin H,Narasimhan S,Sunshine M,Cao H,Kane DW,Reimers M,Stephens RM,Bryant D,Burt SK,Elnekave E,Hari DM,Wynn TA,Cunningham-Rundles C,Stewart DM,Nelson D,Weinstein JN

更新日期：2005-07-05 00:00:00

abstract：BACKGROUND:DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such...

journal_title：BMC bioinformatics

authors： Ryan DP,Ehninger D

更新日期：2014-10-18 00:00:00

abstract：BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...

journal_title：BMC bioinformatics

authors： Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

更新日期：2010-10-07 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:Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, most existi...

journal_title：BMC bioinformatics

authors： Xiong W,Liu H,Guan J,Zhou S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with...

journal_title：BMC bioinformatics

authors： Bandyopadhyay S,Bhattacharyya M

更新日期：2009-05-28 00:00:00

abstract：BACKGROUND:The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious pro...

journal_title：BMC bioinformatics

authors： Xiao A,Wu Z,Dong S

更新日期：2019-02-14 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:Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expression alterations. The growing volume of gene expression data in open data repositories such as the N...

journal_title：BMC bioinformatics

authors： Gower AC,Spira A,Lenburg ME

更新日期：2011-09-27 00:00:00

abstract：BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...

journal_title：BMC bioinformatics

authors： Hofmeister BT,Schmitz RJ

更新日期：2018-04-25 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:Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for ...

journal_title：BMC bioinformatics

authors： Shen YQ,Burger G

更新日期：2007-10-29 00:00:00

abstract：BACKGROUND:Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors fr...

journal_title：BMC bioinformatics

authors： Sleep JA,Schreiber AW,Baumann U

更新日期：2013-12-18 00:00:00

abstract：BACKGROUND:Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On...

journal_title：BMC bioinformatics

authors： Yuan Y,Li CT,Wilson R

更新日期：2008-06-18 00:00:00

abstract：BACKGROUND:Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objectiv...

journal_title：BMC bioinformatics

authors： Zuyderduyn SD,Jones SJ

更新日期：2003-10-28 00:00:00