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. RESULTS:To date, the study of epitranscriptome layer gene regulation is mostly focused on the function of mediator proteins of RNA methylation, i.e., the readers, writers and erasers. There is limited investigation of the functional relevance of individual m6A RNA methylation site. To address this, we annotated human m6A sites in large-scale based on the guilt-by-association principle from an RNA co-methylation network. It is constructed based on public human MeRIP-Seq datasets profiling the m6A epitranscriptome under 32 independent experimental conditions. By systematically examining the network characteristics obtained from the RNA methylation profiles, a total of 339,158 putative gene ontology functions associated with 1446 human m6A sites were identified. These are biological functions that may be regulated at epitranscriptome layer via reversible m6A RNA methylation. The results were further validated on a soft benchmark by comparing to a random predictor. CONCLUSIONS:An online web server m6Acomet was constructed to support direct query for the predicted biological functions of m6A sites as well as the sites exhibiting co-methylated patterns at the epitranscriptome layer. The m6Acomet web server is freely available at: www.xjtlu.edu.cn/biologicalsciences/m6acomet .
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Wu X,Wei Z,Chen K,Zhang Q,Su J,Liu H,Zhang L,Meng Jdoi
10.1186/s12859-019-2840-3subject
Has Abstractpub_date
2019-05-02 00:00:00pages
223issue
1issn
1471-2105pii
10.1186/s12859-019-2840-3journal_volume
20pub_type
杂志文章abstract:BACKGROUND:Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; http://egenbio.lsu.edu) to begin to address this....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-S2-S7
更新日期:2006-09-06 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
pub_type: 杂志文章
doi:10.1186/s12859-016-1273-5
更新日期:2016-10-03 00:00:00
abstract:BACKGROUND:We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how thi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-430
更新日期:2010-08-18 00:00:00
abstract:BACKGROUND:Patient records contain valuable information regarding explanation of diagnosis, progression of disease, prescription and/or effectiveness of treatment, and more. Automatic recognition of clinically important concepts and the identification of relationships between those concepts in patient records are preli...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S3-S3
更新日期:2011-06-09 00:00:00
abstract:BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1691-z
更新日期:2017-05-25 00:00:00
abstract:BACKGROUND:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-117
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise and contaminant peaks. It is widely accepted that a valid primary peak tends to have high intensity an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-346
更新日期:2011-08-17 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
pub_type: 杂志文章
doi:10.1186/1471-2105-8-420
更新日期:2007-10-29 00:00:00
abstract:BACKGROUND:Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies, new protein sequences are becoming available at an extraordinary rate. The ra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2080-y
更新日期:2018-03-05 00:00:00
abstract:BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-420
更新日期:2010-08-09 00:00:00
abstract:BACKGROUND:The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-386
更新日期:2006-08-18 00:00:00
abstract:BACKGROUND:A drug-drug interaction (DDI) occurs when one drug influences the level or activity of another drug. The increasing volume of the scientific literature overwhelms health care professionals trying to be kept up-to-date with all published studies on DDI. METHODS:This paper describes a hybrid linguistic approa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S2-S1
更新日期:2011-03-29 00:00:00
abstract:BACKGROUND:Non-coding RNAs gain more attention as their diverse roles in many cellular processes are discovered. At the same time, the need for efficient computational prediction of ncRNAs increases with the pace of sequencing technology. Existing tools are based on various approaches and techniques, but none of them p...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-491
更新日期:2010-09-29 00:00:00
abstract:BACKGROUND:Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional g...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1662-4
更新日期:2017-06-07 00:00:00
abstract:BACKGROUND:Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-278
更新日期:2005-11-23 00:00:00
abstract:BACKGROUND:As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consid...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-371
更新日期:2007-10-03 00:00:00
abstract:BACKGROUND:Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to improve. RESULTS:Here we expand on the common base method to develop procedures for testing linear re...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03696-y
更新日期:2020-09-29 00:00:00
abstract:BACKGROUND:The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-430
更新日期:2011-11-03 00:00:00
abstract:BACKGROUND:It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally related patterns to propose hypotheses for their behavior and the biological processes involved. T...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-101
更新日期:2014-04-10 00:00:00
abstract:BACKGROUND:Community structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a system's functional components and the impact of local structures on dynamics at a global scale. Choosing an a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-220
更新日期:2014-06-25 00:00:00
abstract:BACKGROUND:The large gap between the number of protein sequences in databases and the number of functionally characterized proteins calls for the development of a fast computational tool for the prediction of subnuclear and subcellular localizations generally applicable to protein sequences. The information on localiza...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-291
更新日期:2005-12-07 00:00:00
abstract:BACKGROUND:Several studies demonstrated the feasibility of predicting bacterial antibiotic resistance phenotypes from whole-genome sequences, the prediction process usually amounting to detecting the presence of genes involved in antibiotic resistance mechanisms, or of specific mutations, previously identified from a t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2403-z
更新日期:2018-10-17 00:00:00
abstract:BACKGROUND:The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. RESULTS:We offer BAGEL (Bayesian Analysis of Gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1015-8
更新日期:2016-04-16 00:00:00
abstract:BACKGROUND:Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-160
更新日期:2009-05-27 00:00:00
abstract:BACKGROUND:We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. RESULTS:Explicit modeling of multilabels significantly improves the capability o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S2-S12
更新日期:2007-05-03 00:00:00
abstract:BACKGROUND:Stable isotope tracing can follow individual atoms through metabolic transformations through the detection of the incorporation of stable isotope within metabolites. This resulting data can be interpreted in terms related to metabolic flux. However, detection of a stable isotope in metabolites by mass spectr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3096-7
更新日期:2019-10-28 00:00:00
abstract:BACKGROUND:During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused. METHODS:We investi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S9-S1
更新日期:2011-10-05 00:00:00
abstract:BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1493-3
更新日期:2017-02-02 00:00:00
abstract:BACKGROUND:One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1952-x
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3020-1
更新日期:2019-08-13 00:00:00