Quantiprot - a Python package for quantitative analysis of protein sequences.

abstract：BACKGROUND:The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relations...

journal_title：BMC bioinformatics

authors： Gutiérrez FI,Rodriguez-Valenzuela F,Ibarra IL,Devos DP,Melo F

更新日期：2016-01-05 00:00:00

abstract：BACKGROUND:Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions. RESULTS:We present a computational pipeline for detecting novel lncRNAs fro...

journal_title：BMC bioinformatics

authors： Sun L,Zhang Z,Bailey TL,Perkins AC,Tallack MR,Xu Z,Liu H

更新日期：2012-12-13 00:00:00

abstract：BACKGROUND:De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence dif...

journal_title：BMC bioinformatics

authors： Steyaert A,Audenaert P,Fostier J

更新日期：2020-09-14 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:Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, ...

journal_title：BMC bioinformatics

authors： Li Z,Lin J,Sibley AB,Truong T,Chua KC,Jiang Y,McCarthy J,Kroetz DL,Allen A,Owzar K

更新日期：2019-05-28 00:00:00

abstract：:Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time se...

journal_title：BMC bioinformatics

authors： Neretti N,Remondini D,Tatar M,Sedivy JM,Pierini M,Mazzatti D,Powell J,Franceschi C,Castellani GC

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:While biomedical text mining is emerging as an important research area, practical results have proven difficult to achieve. We believe that an important first step towards more accurate text-mining lies in the ability to identify and characterize text that satisfies various types of information needs. We rep...

journal_title：BMC bioinformatics

authors： Wilbur WJ,Rzhetsky A,Shatkay H

更新日期：2006-07-25 00:00:00

abstract：BACKGROUND:Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of alignment methods use sequence profiles that only represent conservation. There is no general way to represent correlated mutation and incorporat...

journal_title：BMC bioinformatics

authors： Jeong CS,Kim D

更新日期：2010-04-16 00:00:00

abstract：BACKGROUND:Conservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other. RESULTS:We applied 25 conservation and v...

journal_title：BMC bioinformatics

authors： Johansson F,Toh H

更新日期：2010-07-21 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:Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the im...

journal_title：BMC bioinformatics

authors： Liu K,He L,Liu Z,Xu J,Liu Y,Kuang Q,Wen Z,Li M

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...

journal_title：BMC bioinformatics

authors： Kong W,Mou X,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by ...

journal_title：BMC bioinformatics

authors： Huang FW,Li LY,Reidys CM

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. Howeve...

journal_title：BMC bioinformatics

authors： Guerra-Assunção JA,Enright AJ

更新日期：2010-03-16 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:Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detec...

journal_title：BMC bioinformatics

authors： Clote P,Lou F,Lorenz WA

更新日期：2012-04-12 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:Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionall...

journal_title：BMC bioinformatics

authors： Weeratunga S,Hu NJ,Simon A,Hofmann A

更新日期：2012-08-14 00:00:00

abstract：BACKGROUND:Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-based prediction method...

journal_title：BMC bioinformatics

authors： Tung CW,Ho SY

更新日期：2008-07-15 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:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...

journal_title：BMC bioinformatics

authors： Heberle H,Meirelles GV,da Silva FR,Telles GP,Minghim R

更新日期：2015-05-22 00:00:00

abstract：BACKGROUND:High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise ...

journal_title：BMC bioinformatics

authors： Lawless C,Wilkinson DJ,Young A,Addinall SG,Lydall DA

更新日期：2010-05-28 00:00:00

abstract：BACKGROUND:Clustering techniques are routinely used in gene expression data analysis to organize the massive data. Clustering techniques arrange a large number of genes or assays into a few clusters while maximizing the intra-cluster similarity and inter-cluster separation. While clustering of genes facilitates learnin...

journal_title：BMC bioinformatics

authors： Jonnalagadda S,Srinivasan R

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are markers of special interest in genome comparison, expression profiling, and genetic engineering. Relat...

journal_title：BMC bioinformatics

authors： Herold J,Kurtz S,Giegerich R

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D (YF-17D) immunized human subjects. Different experimental and analysis conditions were likely contr...

journal_title：BMC bioinformatics

authors： Ong E,Sun P,Berke K,Zheng J,Wu G,He Y

更新日期：2019-12-23 00:00:00

abstract：BACKGROUND:Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmann's recent review, we compared statistical performance of three methods, namely Global Tes...

journal_title：BMC bioinformatics

authors： Liu Q,Dinu I,Adewale AJ,Potter JD,Yasui Y

更新日期：2007-11-07 00:00:00

abstract：BACKGROUND:Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules. In this investigation the performance of LLM in classifying patients with cancer was evaluated using a set of eight publicly available gene expression databases f...

journal_title：BMC bioinformatics

authors： Verda D,Parodi S,Ferrari E,Muselli M

更新日期：2019-11-22 00:00:00

abstract：BACKGROUND:Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its ...

journal_title：BMC bioinformatics

authors： Kracke F,Krömer JO

更新日期：2014-12-30 00:00:00

abstract：BACKGROUND:One approach to improving the personalized treatment of cancer is to understand the cellular signaling transduction pathways that cause cancer at the level of the individual patient. In this study, we used unsupervised deep learning to learn the hierarchical structure within cancer gene expression data. Deep...

journal_title：BMC bioinformatics

authors： Young JD,Cai C,Lu X

更新日期：2017-10-03 00:00:00

abstract：BACKGROUND:Periodic phenomena are widespread in biology. The problem of finding periodicity in biological time series can be viewed as a multiple hypothesis testing of the spectral content of a given time series. The exact noise characteristics are unknown in many bioinformatics applications. Furthermore, the observed ...

journal_title：BMC bioinformatics

authors： Ahdesmäki M,Lähdesmäki H,Pearson R,Huttunen H,Yli-Harja O

更新日期：2005-05-13 00:00:00