Prediction of dinucleotide-specific RNA-binding sites in proteins.

abstract：BACKGROUND:The imputation of missing values is necessary for the efficient use of DNA microarray data, because many clustering algorithms and some statistical analysis require a complete data set. A few imputation methods for DNA microarray data have been introduced, but the efficiency of the methods was low and the va...

journal_title：BMC bioinformatics

authors： Kim KY,Kim BJ,Yi GS

更新日期：2004-10-26 00:00:00

abstract：:Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...

journal_title：BMC bioinformatics

authors： Li YF,Radivojac P

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such networks have been successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a n...

journal_title：BMC bioinformatics

authors： Margolin AA,Nemenman I,Basso K,Wiggins C,Stolovitzky G,Dalla Favera R,Califano A

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caeno...

journal_title：BMC bioinformatics

authors： Blei DM,Franks K,Jordan MI,Mian IS

更新日期：2006-05-08 00:00:00

abstract：BACKGROUND:Mammalian germ cells undergo meiosis to produce sperm or eggs, haploid cells that are primed to meet and propagate life. Meiosis is initiated by retinoic acid and meiotic prophase is the first and most complex stage of meiosis when homologous chromosomes pair to exchange genetic information. Errors in meiosi...

journal_title：BMC bioinformatics

authors： Li Y,Ray D,Ye P

更新日期：2013-02-27 00:00:00

abstract：BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...

journal_title：BMC bioinformatics

authors： Tan YD,Fornage M,Xu H

更新日期：2008-03-06 00:00:00

abstract：BACKGROUND:Parametric feature selection methods for machine learning and association studies based on genetic data are not robust with respect to outliers or influential observations. While rank-based, distribution-free statistics offer a robust alternative to parametric methods, their practical utility can be limited,...

journal_title：BMC bioinformatics

authors： Lin J,Sibley A,Shterev I,Nixon A,Innocenti F,Chan C,Owzar K

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible. RESULTS:In this paper, we present TPMS (Tree Pattern-...

journal_title：BMC bioinformatics

authors： Bigot T,Daubin V,Lassalle F,Perrière G

更新日期：2013-03-27 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:Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate ...

journal_title：BMC bioinformatics

authors： Cimmaruta C,Citro V,Andreotti G,Liguori L,Cubellis MV,Hay Mele B

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range o...

journal_title：BMC bioinformatics

authors： Iacoangeli A,Al Khleifat A,Sproviero W,Shatunov A,Jones AR,Morgan SL,Pittman A,Dobson RJ,Newhouse SJ,Al-Chalabi A

更新日期：2019-04-27 00:00:00

abstract：BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...

journal_title：BMC bioinformatics

authors： Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SY

更新日期：2020-12-17 00:00:00

abstract：BACKGROUND:Schizophrenia, bipolar disorder, and major depression are devastating mental diseases, each with distinctive yet overlapping epidemiologic characteristics. Microarray and proteomics data have revealed genes which expressed abnormally in patients. Several single nucleotide polymorphisms (SNPs) and mutations a...

journal_title：BMC bioinformatics

authors： Lee SA,Tsao TT,Yang KC,Lin H,Kuo YL,Hsu CH,Lee WK,Huang KC,Kao CY

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino ac...

journal_title：BMC bioinformatics

authors： Pan C,Park BH,McDonald WH,Carey PA,Banfield JF,VerBerkmoes NC,Hettich RL,Samatova NF

更新日期：2010-03-05 00:00:00

abstract：BACKGROUND:Expression quantitative trait loci (eQTL) mapping is often used to identify genetic loci and candidate genes correlated with traits. Although usually a group of genes affect complex traits, genes in most eQTL mapping methods are considered as independent. Recently, some eQTL mapping methods have accounted fo...

journal_title：BMC bioinformatics

authors： Wang Y,Richard R,Pan Y

更新日期：2016-12-13 00:00:00

abstract：BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...

journal_title：BMC bioinformatics

authors： Zhang W,Sun F,Jiang R

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to p...

journal_title：BMC bioinformatics

authors： Cipriano GM,Phillips GN Jr,Gleicher M

更新日期：2012-11-24 00:00:00

abstract：BACKGROUND:RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment. RESULTS:Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at...

journal_title：BMC bioinformatics

authors： Gadepalli VS,Ozer HG,Yilmaz AS,Pietrzak M,Webb A

更新日期：2019-12-20 00:00:00

abstract：BACKGROUND:There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and des...

journal_title：BMC bioinformatics

authors： Kahn AB,Ryan MC,Liu H,Zeeberg BR,Jamison DC,Weinstein JN

更新日期：2007-03-05 00:00:00

abstract：BACKGROUND:REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presence of two related proteins are not fully understood. Here, a variety of computational studies were p...

journal_title：BMC bioinformatics

authors： Mian IS,Worthey EA,Salavati R

更新日期：2006-06-16 00:00:00

abstract：BACKGROUND:Gene expression measurements from breast cancer (BrCa) tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely to have disease recurrence. However, diverse breast cancer datasets in conjunction with diagnostic cl...

journal_title：BMC bioinformatics

authors： Smith DD,Saetrom P,Snøve O Jr,Lundberg C,Rivas GE,Glackin C,Larson GP

更新日期：2008-01-28 00:00:00

abstract：BACKGROUND:The double-cut-and-join (DCJ) is a model that is able to efficiently sort a genome into another, generalizing the typical mutations (inversions, fusions, fissions, translocations) to which genomes are subject, but allowing the existence of circular chromosomes at the intermediate steps. In the general model ...

journal_title：BMC bioinformatics

authors： da Silva PH,Machado R,Dantas S,Braga MD

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The creation of a complete genome-wide map of transcription factor binding sites is essential for understanding gene regulatory networks in vivo. However, current prediction methods generally rely on statistical models that imperfectly model transcription factor binding. Generation of new prediction methods ...

journal_title：BMC bioinformatics

authors： Hill JT,Anderson KR,Mastracci TL,Kaestner KH,Sussel L

更新日期：2011-02-25 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:In the last decade, a significant improvement in detecting remote similarity between protein sequences has been made by utilizing alignment profiles in place of amino-acid strings. Unfortunately, no analytical theory is available for estimating the significance of a gapped alignment of two profiles. Many exp...

journal_title：BMC bioinformatics

authors： Poleksic A

更新日期：2009-04-20 00:00:00

abstract：BACKGROUND:Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target proteins. In recent studies, handcrafted features, similarity metrics and machine learning methods have...

journal_title：BMC bioinformatics

authors： Eslami Manoochehri H,Nourani M

更新日期：2020-07-06 00:00:00

abstract：BACKGROUND:Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of ...

journal_title：BMC bioinformatics

authors： Rahmatallah Y,Emmert-Streib F,Glazko G

更新日期：2014-12-05 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 developments of high-throughput genotyping technologies, which enable the simultaneous genotyping of hundreds of thousands of single nucleotide polymorphisms (SNP) have the potential to increase the benefits of genetic epidemiology studies. Although the enhanced resolution of these platforms increases th...

journal_title：BMC bioinformatics

authors： Chai HS,Sicotte H,Bailey KR,Turner ST,Asmann YW,Kocher JP

更新日期：2009-04-03 00:00:00

abstract：BACKGROUND:Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved acc...

journal_title：BMC bioinformatics

authors： Kuksa P,Huang PH,Pavlovic V

更新日期：2009-04-29 00:00:00