New challenges for text mining: mapping between text and manually curated pathways.

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:Visualization tools for deep learning models typically focus on discovering key input features without considering how such low level features are combined in intermediate layers to make decisions. Moreover, many of these methods examine a network's response to specific input examples that may be insufficien...

journal_title：BMC bioinformatics

authors： Liu G,Zeng H,Gifford DK

更新日期：2019-07-19 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:We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. RESULTS:LAVA identifies combinations of six primer regions for basic LAM...

journal_title：BMC bioinformatics

authors： Torres C,Vitalis EA,Baker BR,Gardner SN,Torres MW,Dzenitis JM

更新日期：2011-06-16 00:00:00

abstract：BACKGROUND:Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human cells into malignant cancer cells. Interrogation of cancer genomes holds the promise of understandi...

journal_title：BMC bioinformatics

authors： Sanchez-Garcia F,Akavia UD,Mozes E,Pe'er D

更新日期：2010-04-14 00:00:00

abstract：BACKGROUND:Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene e...

journal_title：BMC bioinformatics

authors： Müller HG,Chiou JM,Leng X

更新日期：2008-01-28 00:00:00

abstract：BACKGROUND:Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, int...

journal_title：BMC bioinformatics

authors： Yu C,Zavaljevski N,Desai V,Johnson S,Stevens FJ,Reifman J

更新日期：2008-01-25 00:00:00

abstract：BACKGROUND:The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D sh...

journal_title：BMC bioinformatics

authors： Heeren B,Paulus S,Goldbach H,Kuhlmann H,Mahlein AK,Rumpf M,Wirth B

更新日期：2020-07-29 00:00:00

abstract：BACKGROUND:The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is d...

journal_title：BMC bioinformatics

authors： Wang L,Stein LD

更新日期：2010-11-08 00:00:00

abstract：BACKGROUND:Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six software programs capable of high throughput and employing a wide range of prediction methods, SignalP 3....

journal_title：BMC bioinformatics

authors： Klee EW,Ellis LB

更新日期：2005-10-14 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:Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysa...

journal_title：BMC bioinformatics

authors： Kim JG,Park D,Kim BC,Cho SW,Kim YT,Park YJ,Cho HJ,Park H,Kim KB,Yoon KO,Park SJ,Lee BM,Bhak J

更新日期：2008-01-24 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:Normalization in real-time qRT-PCR is necessary to compensate for experimental variation. A popular normalization strategy employs reference gene(s), which may introduce additional variability into normalized expression levels due to innate variation (between tissues, individuals, etc). To minimize this inna...

journal_title：BMC bioinformatics

authors： Chervoneva I,Li Y,Schulz S,Croker S,Wilson C,Waldman SA,Hyslop T

更新日期：2010-05-14 00:00:00

abstract：BACKGROUND:A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging ty...

journal_title：BMC bioinformatics

authors： Dubinkina VB,Ischenko DS,Ulyantsev VI,Tyakht AV,Alexeev DG

更新日期：2016-01-16 00:00:00

abstract：BACKGROUND:Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local...

journal_title：BMC bioinformatics

authors： Koren S,Miller JR,Walenz BP,Sutton G

更新日期：2010-09-10 00:00:00

abstract：BACKGROUND:Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inferen...

journal_title：BMC bioinformatics

authors： Lu G,Jiang L,Helikar RM,Rowley TW,Zhang L,Chen X,Moriyama EN

更新日期：2006-12-12 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

authors： Attie O,Darling AE,Yancopoulos S

更新日期：2011-10-05 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:Proteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational methodologies for large-scale determina...

journal_title：BMC bioinformatics

authors： Portugaly E,Harel A,Linial N,Linial M

更新日期：2006-06-02 00:00:00

abstract：BACKGROUND:Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using v...

journal_title：BMC bioinformatics

authors： Hocking TD,Schleiermacher G,Janoueix-Lerosey I,Boeva V,Cappo J,Delattre O,Bach F,Vert JP

更新日期：2013-05-22 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: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:In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaus...

journal_title：BMC bioinformatics

authors： Lee J,Lee K,Joung I,Joo K,Brooks BR,Lee J

更新日期：2015-03-21 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:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...

journal_title：BMC bioinformatics

authors： Bullard JH,Purdom E,Hansen KD,Dudoit S

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a...

journal_title：BMC bioinformatics

authors： Puigbò P,Bravo IG,Garcia-Vallvé S

更新日期：2008-01-29 00:00:00

abstract：BACKGROUND:A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The...

journal_title：BMC bioinformatics

authors： Varón A,Wheeler WC

更新日期：2013-02-26 00:00:00

abstract：BACKGROUND:Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A 'master regulator' transcription factor often appears to control most of the regulatory activities of the other transcription factors and the assoc...

journal_title：BMC bioinformatics

authors： Sikdar S,Datta S

更新日期：2017-02-02 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