ILP-based maximum likelihood genome scaffolding.

abstract：BACKGROUND:Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as...

journal_title：BMC bioinformatics

authors： Peters B,Sette A

更新日期：2005-05-31 00:00:00

abstract：BACKGROUND:Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and m...

journal_title：BMC bioinformatics

authors： Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, in The Cancer Genome Atlas, collects protein expressions in human cancers and it is a reference reso...

journal_title：BMC bioinformatics

authors： Sardina DS,Micale G,Ferro A,Pulvirenti A,Giugno R

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplicat...

journal_title：BMC bioinformatics

authors： Thierry-Mieg N

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...

journal_title：BMC bioinformatics

authors： Skums P,Dimitrova Z,Campo DS,Vaughan G,Rossi L,Forbi JC,Yokosawa J,Zelikovsky A,Khudyakov Y

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND AND GOAL:The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing with logistic regression in many innovation-friendly scientific fields. RESULTS:In this conte...

journal_title：BMC bioinformatics

authors： Couronné R,Probst P,Boulesteix AL

更新日期：2018-07-17 00:00:00

abstract：BACKGROUND:Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context, computational models and computer simulations are one of the available research tools that epidemi...

journal_title：BMC bioinformatics

authors： Castagno P,Pernice S,Ghetti G,Povero M,Pradelli L,Paolotti D,Balbo G,Sereno M,Beccuti M

更新日期：2020-09-16 00:00:00

abstract：BACKGROUND:Wise et al. introduced a rank-based statistical technique for meta-analysis of genome scans, the Genome Scan Meta-Analysis (GSMA) method. Levinson et al. recently described two generalizations of the GSMA statistic: (i) a weighted version of the GSMA statistic, so that different studies could be ascribed dif...

journal_title：BMC bioinformatics

authors： Koziol JA,Feng AC

更新日期：2005-02-17 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:Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene...

journal_title：BMC bioinformatics

authors： Noureen M,Tada I,Kawashima T,Arita M

更新日期：2019-12-27 00:00:00

abstract：BACKGROUND:In omics data integration studies, it is common, for a variety of reasons, for some individuals to not be present in all data tables. Missing row values are challenging to deal with because most statistical methods cannot be directly applied to incomplete datasets. To overcome this issue, we propose a multip...

journal_title：BMC bioinformatics

authors： Voillet V,Besse P,Liaubet L,San Cristobal M,González I

更新日期：2016-10-03 00:00:00

abstract：BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...

journal_title：BMC bioinformatics

authors： Bui VK,Wei C

更新日期：2020-10-20 00:00:00

abstract：BACKGROUND:Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint ...

journal_title：BMC bioinformatics

authors： Bozdag S,Close TJ,Lonardi S

更新日期：2009-07-15 00:00:00

abstract：BACKGROUND:Analyses of molecular high-throughput data often lack in robustness, i.e. results are very sensitive to the addition or removal of a single observation. Therefore, the identification of extreme observations is an important step of quality control before doing further data analysis. Standard outlier detection...

journal_title：BMC bioinformatics

authors： Kruppa J,Jung K

更新日期：2017-05-02 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

abstract：BACKGROUND:Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific ...

journal_title：BMC bioinformatics

authors： Allhoff M,Schönhuth A,Martin M,Costa IG,Rahmann S,Marschall T

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The binding of regulatory proteins to their specific DNA targets determines the accurate expression of the neighboring genes. The in silico prediction of new binding sites in completely sequenced genomes is a key aspect in the deeper understanding of gene regulatory networks. Several algorithms have been des...

journal_title：BMC bioinformatics

authors： Oberto J

更新日期：2010-11-11 00:00:00

abstract：BACKGROUND:In many biomedical applications, there is a need for developing classification models based on noisy annotations. Recently, various methods addressed this scenario by relaying on unreliable annotations obtained from multiple sources. RESULTS:We proposed a probabilistic classification algorithm based on labe...

journal_title：BMC bioinformatics

authors： Zhang P,Cao W,Obradovic Z

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Automated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of limited utility for fungal protein annotation. They are often trained only to one species, are not a...

journal_title：BMC bioinformatics

authors： Jung J,Yi G,Sukno SA,Thon MR

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. ...

journal_title：BMC bioinformatics

authors： Wu X,Wei Z,Chen K,Zhang Q,Su J,Liu H,Zhang L,Meng J

更新日期：2019-05-02 00:00:00

abstract：BACKGROUND:RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of dif...

journal_title：BMC bioinformatics

authors： Bi R,Liu P

更新日期：2016-03-31 00:00:00

abstract：BACKGROUND:With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or i...

journal_title：BMC bioinformatics

authors： Weinberg Z,Breaker RR

更新日期：2011-01-04 00:00:00

abstract：:Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large a...

journal_title：BMC bioinformatics

authors： Kakaradov B,Xiong HY,Lee LJ,Jojic N,Frey BJ

更新日期：2012-04-19 00:00:00

abstract：BACKGROUND:Population stratification is a systematic difference in allele frequencies between subpopulations. This can lead to spurious association findings in the case-control genome wide association studies (GWASs) used to identify single nucleotide polymorphisms (SNPs) associated with disease-linked phenotypes. Meth...

journal_title：BMC bioinformatics

authors： Hajiloo M,Sapkota Y,Mackey JR,Robson P,Greiner R,Damaraju S

更新日期：2013-02-22 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:The nonparametric trend test (NPT) is well suitable for identifying the genetic variants associated with quantitative traits when the trait values do not satisfy the normal distribution assumption. If the genetic model, defined according to the mode of inheritance, is known, the NPT derived under the given g...

journal_title：BMC bioinformatics

authors： Zhang W,Li H,Li Z,Li Q

更新日期：2016-01-28 00:00:00

abstract：BACKGROUND:Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and hel...

journal_title：BMC bioinformatics

authors： Chen R,Chen W,Yang S,Wu D,Wang Y,Tian Y,Shi Y

更新日期：2011-07-29 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:Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. RESULTS:OpWise estimates the amount of systematic e...

journal_title：BMC bioinformatics

authors： Price MN,Arkin AP,Alm EJ

更新日期：2006-01-13 00:00:00

abstract：BACKGROUND:Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained. RESULTS:We present an R/Bioconductor port of a fast novel algorithm for...

journal_title：BMC bioinformatics

authors： Savage RS,Heller K,Xu Y,Ghahramani Z,Truman WM,Grant M,Denby KJ,Wild DL

更新日期：2009-08-06 00:00:00