A semi-parametric statistical model for integrating gene expression profiles across different platforms.

abstract：BACKGROUND:Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleo...

journal_title：BMC bioinformatics

authors： Wang Y,Wu H,Cai Y

更新日期：2018-12-31 00:00:00

abstract：:After publication of this supplement article. ...

journal_title：BMC bioinformatics

authors： Pan B,Kusko R,Xiao W,Zheng Y,Liu Z,Xiao C,Sakkiah S,Guo W,Gong P,Zhang C,Ge W,Shi L,Tong W,Hong H

更新日期：2019-05-15 00:00:00

abstract：BACKGROUND:Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations acco...

journal_title：BMC bioinformatics

authors： Lloyd S,Snell QO

更新日期：2011-12-07 00:00:00

abstract：BACKGROUND:We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Simila...

journal_title：BMC bioinformatics

authors： Barthel D,Hirst JD,Błazewicz J,Burke EK,Krasnogor N

更新日期：2007-10-26 00:00:00

abstract：BACKGROUND:Pseudouridylation is the most prevalent type of posttranscriptional modification in various stable RNAs of all organisms, which significantly affects many cellular processes that are regulated by RNA. Thus, accurate identification of pseudouridine (Ψ) sites in RNA will be of great benefit for understanding t...

journal_title：BMC bioinformatics

authors： He J,Fang T,Zhang Z,Huang B,Zhu X,Xiong Y

更新日期：2018-08-29 00:00:00

abstract：BACKGROUND:The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, w...

journal_title：BMC bioinformatics

authors： Smith AM,Walsh JR,Long J,Davis CB,Henstock P,Hodge MR,Maciejewski M,Mu XJ,Ra S,Zhao S,Ziemek D,Fisher CK

更新日期：2020-03-20 00:00:00

abstract：BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...

journal_title：BMC bioinformatics

authors： Zengin T,Önal-Süzek T

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and...

journal_title：BMC bioinformatics

authors： Liu Q,Crammer K,Pereira FC,Roos DS

更新日期：2008-10-14 00:00:00

abstract：BACKGROUND:Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replica...

journal_title：BMC bioinformatics

authors： Zynda GJ,Song J,Concia L,Wear EE,Hanley-Bowdoin L,Thompson WF,Vaughn MW

更新日期：2017-08-07 00:00:00

abstract：BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...

journal_title：BMC bioinformatics

authors： Khan A,Liu Q,Wang K

更新日期：2018-12-28 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:Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other rele...

journal_title：BMC bioinformatics

authors： Thielen B,Heinen S,Schomburg D

更新日期：2009-07-22 00:00:00

abstract：BACKGROUND:Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD...

journal_title：BMC bioinformatics

authors： Shen J,Vasaikar S,Zhang B

更新日期：2018-12-28 00:00:00

abstract：BACKGROUND:Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a pauci...

journal_title：BMC bioinformatics

authors： MacLean D,Moulton V,Studholme DJ

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that ...

journal_title：BMC bioinformatics

authors： Forman JJ,Clemons PA,Schreiber SL,Haggarty SJ

更新日期：2005-10-19 00:00:00

abstract：BACKGROUND:Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, ...

journal_title：BMC bioinformatics

authors： Thakur S,Guttman DS

更新日期：2016-06-30 00:00:00

abstract：BACKGROUND:Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology all...

journal_title：BMC bioinformatics

authors： Aubry M,Monnier A,Chicault C,de Tayrac M,Galibert MD,Burgun A,Mosser J

更新日期：2006-05-04 00:00:00

abstract：BACKGROUND:With the development of sequencing technologies, more and more sequence variants are available for investigation. Different classes of variants in the human genome have been identified, including single nucleotide substitutions, insertion and deletion, and large structural variations such as duplications and...

journal_title：BMC bioinformatics

authors： Liu M,Watson LT,Zhang L

更新日期：2014-01-09 00:00:00

abstract：BACKGROUND:Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical e...

journal_title：BMC bioinformatics

authors： Li H,Chen Q,Tang B,Wang X,Xu H,Wang B,Huang D

更新日期：2017-10-03 00:00:00

abstract：BACKGROUND:Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the...

journal_title：BMC bioinformatics

authors： Baumbach J

更新日期：2007-11-06 00:00:00

abstract：BACKGROUND:Viral zoonosis, the transmission of a virus from its primary vertebrate reservoir species to humans, requires ubiquitous cellular proteins known as receptor proteins. Zoonosis can occur not only through direct transmission from vertebrates to humans, but also through intermediate reservoirs or other environm...

journal_title：BMC bioinformatics

authors： Bae SE,Son HS

更新日期：2011-04-13 00:00:00

abstract：BACKGROUND:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...

journal_title：BMC bioinformatics

authors： Lucas JM,Muffato M,Roest Crollius H

更新日期：2014-08-08 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:Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain uncharted. Thus, in-depth study of the epi-transcriptomic patterns of m6A may provide insights into ...

journal_title：BMC bioinformatics

authors： Zhang L,Chen S,Zhu J,Meng J,Liu H

更新日期：2020-10-09 00:00:00

abstract：BACKGROUND:Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an interest in these antibacterial peptides. In our recent study we analyzed 999 antibacterial peptides, whi...

journal_title：BMC bioinformatics

authors： Lata S,Mishra NK,Raghava GP

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...

journal_title：BMC bioinformatics

authors： Sievers F,Hughes GM,Higgins DG

更新日期：2014-10-04 00:00:00

abstract：BACKGROUND:Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open que...

journal_title：BMC bioinformatics

authors： Yan Y,Huang SY

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary...

journal_title：BMC bioinformatics

authors： Solares EA,Tao Y,Long AD,Gaut BS

更新日期：2021-01-06 00:00:00

abstract：BACKGROUND:Differences in cell-type composition across subjects and conditions often carry biological significance. Recent advancements in single cell sequencing technologies enable cell-types to be identified at the single cell level, and as a result, cell-type composition of tissues can now be studied in exquisite de...

journal_title：BMC bioinformatics

authors： Cao Y,Lin Y,Ormerod JT,Yang P,Yang JYH,Lo KK

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Molecular biology (MB) is a dynamic research domain that benefits greatly from the use of modern software technology in preparing experiments, analyzing acquired data, and even performing "in-silico" analyses. As ever new findings change the face of this domain, software for MB has to be sufficiently flexibl...

journal_title：BMC bioinformatics

authors： Busch N,Wedemann G

更新日期：2009-03-27 00:00:00