SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups.

abstract：BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....

journal_title：BMC bioinformatics

authors： Bayerlová M,Jung K,Kramer F,Klemm F,Bleckmann A,Beißbarth T

更新日期：2015-10-22 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:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

journal_title：BMC bioinformatics

authors： Haskins WE,Petritis K,Zhang J

更新日期：2011-03-15 00:00:00

abstract：BACKGROUND:The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across different experimental conditions or time points. Using microarray data sets, clustering algorithms have ...

journal_title：BMC bioinformatics

authors： Maulik U,Mukhopadhyay A,Bandyopadhyay S

更新日期：2009-01-20 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：BACKGROUND:The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. Whi...

journal_title：BMC bioinformatics

authors： Skvortsov D,Abdueva D,Stitzer ME,Finkel SE,Tavaré S

更新日期：2007-06-14 00:00:00

abstract：BACKGROUND:Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple ...

journal_title：BMC bioinformatics

authors： Guo Y,Korhonen A,Liakata M,Silins I,Hogberg J,Stenius U

更新日期：2011-03-08 00:00:00

abstract：BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

journal_title：BMC bioinformatics

authors： Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have bee...

journal_title：BMC bioinformatics

authors： Thomas JM,Horspool D,Brown G,Tcherepanov V,Upton C

更新日期：2007-01-23 00:00:00

abstract：BACKGROUND:High throughput sequencing technology provides us unprecedented opportunities to study transcriptome dynamics. Compared to microarray-based gene expression profiling, RNA-Seq has many advantages, such as high resolution, low background, and ability to identify novel transcripts. Moreover, for genes with mult...

journal_title：BMC bioinformatics

authors： Zheng W,Chung LM,Zhao H

更新日期：2011-07-19 00:00:00

abstract：BACKGROUND:RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and even more so transcript counting methods which avoid mapping and quantify gene and transcript expres...

journal_title：BMC bioinformatics

authors： Pérez-Rubio P,Lottaz C,Engelmann JC

更新日期：2019-05-03 00:00:00

abstract：BACKGROUND:Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly co...

journal_title：BMC bioinformatics

authors： Groza T,Hunter J,Zankl A

更新日期：2012-10-15 00:00:00

abstract：BACKGROUND:The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootst...

journal_title：BMC bioinformatics

authors： Cai B,Yang X,Tuskan GA,Cheng ZM

更新日期：2011-03-18 00:00:00

abstract：BACKGROUND:The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dyna...

journal_title：BMC bioinformatics

authors： Segal MR,Fletez-Brant K

更新日期：2020-02-24 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 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:When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognosis and to identify the most influential variables for this task. In practice, this is often done fit...

journal_title：BMC bioinformatics

authors： Mayr A,Hofner B,Schmid M

更新日期：2016-07-22 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:Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but h...

journal_title：BMC bioinformatics

authors： Robinson TJ,Dinan MA,Dewhirst M,Garcia-Blanco MA,Pearson JL

更新日期：2010-02-25 00:00:00

abstract：BACKGROUND:Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discreti...

journal_title：BMC bioinformatics

authors： Li Y,Liu L,Bai X,Cai H,Ji W,Guo D,Zhu Y

更新日期：2010-10-19 00:00:00

abstract：BACKGROUND:The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In pa...

journal_title：BMC bioinformatics

authors： Lustgarten JL,Visweswaran S,Bowser RP,Hogan WR,Gopalakrishnan V

更新日期：2009-09-17 00:00:00

abstract：BACKGROUND:Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with up to d mismatches and is mainly used to locate transcription factor binding sites in DNA sequenc...

journal_title：BMC bioinformatics

authors： Yu Q,Wei D,Huo H

更新日期：2018-06-18 00:00:00

abstract：BACKGROUND:We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model to discriminate CD8+ T cell epitopes. RESULTS:We first assembled an epitope dataset consisting of...

journal_title：BMC bioinformatics

authors： Gomez-Perosanz M,Ras-Carmona A,Lafuente EM,Reche PA

更新日期：2020-12-14 00:00:00

abstract：BACKGROUND:We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so ...

journal_title：BMC bioinformatics

authors： Saunders NF,Brinkworth RI,Huber T,Kemp BE,Kobe B

更新日期：2008-05-26 00:00:00

abstract：BACKGROUND:Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison-one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational...

journal_title：BMC bioinformatics

authors： Lu G,Zhang S,Fang X

更新日期：2008-05-28 00:00:00

abstract：BACKGROUND:It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enou...

journal_title：BMC bioinformatics

authors： Meyer F,Kurtz S,Beckstette M

更新日期：2013-07-17 00:00:00

abstract：BACKGROUND:In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of co...

journal_title：BMC bioinformatics

authors： Adhikari B,Nowotny J,Bhattacharya D,Hou J,Cheng J

更新日期：2016-12-07 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:The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running ti...

journal_title：BMC bioinformatics

authors： Meyer F,Kurtz S,Backofen R,Will S,Beckstette M

更新日期：2011-05-27 00:00:00

abstract：BACKGROUND:Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidences to enhance the quality of predicted complexes. However, it is still a challenge to integrate diffe...

journal_title：BMC bioinformatics

authors： Xu B,Li K,Zheng W,Liu X,Zhang Y,Zhao Z,He Z

更新日期：2018-12-20 00:00:00