The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma.

abstract：BACKGROUND:The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don't code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to ...

journal_title：BMC bioinformatics

authors： Gao K,Miller J

更新日期：2020-02-06 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play important roles in various cellular processes. However, the low quality of current PPI data detected from high-throughput screening techniques has diminished the potential usefulness of the data. We need to develop a method to address the high data noise and incomplet...

journal_title：BMC bioinformatics

authors： Wu M,Li X,Chua HN,Kwoh CK,Ng SK

更新日期：2010-10-15 00:00:00

abstract：BACKGROUND:Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint sequenc...

journal_title：BMC bioinformatics

authors： Kracht D,Schober S

更新日期：2015-02-18 00:00:00

abstract：BACKGROUND:Time-course microarray experiments are being increasingly used to characterize dynamic biological processes. In these experiments, the goal is to identify genes differentially expressed in time-course data, measured between different biological conditions. These differentially expressed genes can reveal the ...

journal_title：BMC bioinformatics

authors： Jonnalagadda S,Srinivasan R

更新日期：2008-06-06 00:00:00

abstract：BACKGROUND:In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited...

journal_title：BMC bioinformatics

authors： Dyrka W,Nebel JC

更新日期：2009-10-08 00:00:00

abstract：BACKGROUND:Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range o...

journal_title：BMC bioinformatics

authors： Iacoangeli A,Al Khleifat A,Sproviero W,Shatunov A,Jones AR,Morgan SL,Pittman A,Dobson RJ,Newhouse SJ,Al-Chalabi A

更新日期：2019-04-27 00:00:00

abstract：BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...

journal_title：BMC bioinformatics

authors： Tan YD,Fornage M,Xu H

更新日期：2008-03-06 00:00:00

abstract：BACKGROUND:While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for ...

journal_title：BMC bioinformatics

authors： Atallah MB,Tandon V,Hiam KJ,Boyce H,Hori M,Atallah W,Spitzer MH,Engleman E,Mallick P

更新日期：2020-08-10 00:00:00

abstract：BACKGROUND:Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our motivation is inspired by label propagation algorithm and the false positive protein-protein intera...

journal_title：BMC bioinformatics

authors： Zhang Y,Liu J,Liu X,Fan X,Hong Y,Wang Y,Huang Y,Xie M

更新日期：2018-02-08 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:Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs. Various machine learning methods have been proposed...

journal_title：BMC bioinformatics

authors： Yang F,Fan K,Song D,Lin H

更新日期：2020-07-21 00:00:00

abstract：BACKGROUND:Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier pro...

journal_title：BMC bioinformatics

authors： Wang M,Abrams ZB,Kornblau SM,Coombes KR

更新日期：2018-01-08 00:00:00

abstract：BACKGROUND:Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experimen...

journal_title：BMC bioinformatics

authors： Cutillo L,Boukouvalas A,Marinopoulou E,Papalopulu N,Rattray M

更新日期：2020-08-21 00:00:00

abstract：BACKGROUND:Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging vari...

journal_title：BMC bioinformatics

authors： Masino AJ,Dechene ET,Dulik MC,Wilkens A,Spinner NB,Krantz ID,Pennington JW,Robinson PN,White PS

更新日期：2014-07-21 00:00:00

abstract：BACKGROUND:Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (Arabidopsis thaliana). However, these networks are usually constructed and analyzed in an ad hoc manner. In this study, we propose a completely...

journal_title：BMC bioinformatics

authors： Ruan J,Perez J,Hernandez B,Lei C,Sunter G,Sponsel VM

更新日期：2011-11-24 00:00:00

abstract：BACKGROUND:Although it is not difficult for state-of-the-art gene finders to identify coding regions in prokaryotic genomes, exact prediction of the corresponding translation initiation sites (TIS) is still a challenging problem. Recently a number of post-processing tools have been proposed for improving the annotation...

journal_title：BMC bioinformatics

authors： Tech M,Meinicke P

更新日期：2006-03-09 00:00:00

abstract：BACKGROUND:The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparison of multiple biological experiments is usually performed in terms of the number of DEGs in an arbi...

journal_title：BMC bioinformatics

authors： Hur B,Kang D,Lee S,Moon JH,Lee G,Kim S

更新日期：2019-12-27 00:00:00

abstract：BACKGROUND:The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable proto...

journal_title：BMC bioinformatics

authors： Eales JM,Pinney JW,Stevens RD,Robertson DL

更新日期：2008-09-01 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating ...

journal_title：BMC bioinformatics

authors： Doran AG,Creevey CJ

更新日期：2013-02-08 00:00:00

abstract：BACKGROUND:The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS) which can also be isolated and characterized. Each DIS corr...

journal_title：BMC bioinformatics

authors： Agoston V,Cemazar M,Kaján L,Pongor S

更新日期：2005-01-27 00:00:00

abstract：BACKGROUND:In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve extra effort and cost and may yield invalid EAs. Alternatively, EA can be extracted from individual ...

journal_title：BMC bioinformatics

authors： Batsch A,Noetel A,Fork C,Urban A,Lazic D,Lucas T,Pietsch J,Lazar A,Schömig E,Gründemann D

更新日期：2008-02-12 00:00:00

abstract：BACKGROUND:RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of dif...

journal_title：BMC bioinformatics

authors： Bi R,Liu P

更新日期：2016-03-31 00:00:00

abstract：BACKGROUND:Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with m...

journal_title：BMC bioinformatics

authors： Kumar CG,LeDuc R,Gong G,Roinishivili L,Lewin HA,Liu L

更新日期：2004-11-04 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:Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactio...

journal_title：BMC bioinformatics

authors： Oda K,Kim JD,Ohta T,Okanohara D,Matsuzaki T,Tateisi Y,Tsujii J

更新日期：2008-04-11 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:The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed a...

journal_title：BMC bioinformatics

authors： Stubben CJ,Challacombe JF

更新日期：2014-02-05 00:00:00

abstract：BACKGROUND:To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, which offer larger sources of data, are currently available. Several questions arise as to whether the e...

journal_title：BMC bioinformatics

authors： Shah PK,Perez-Iratxeta C,Bork P,Andrade MA

更新日期：2003-05-29 00:00:00

abstract：BACKGROUND:Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mouse models revealed delayed maturation of neuronal morphology and autonomous as well as non-cell auton...

journal_title：BMC bioinformatics

authors： Vacca M,Tripathi KP,Speranza L,Aiese Cigliano R,Scalabrì F,Marracino F,Madonna M,Sanseverino W,Perrone-Capano C,Guarracino MR,D'Esposito M

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. RESULTS:In this paper, we have proposed a Vertical...

journal_title：BMC bioinformatics

authors： Naznin F,Sarker R,Essam D

更新日期：2011-08-25 00:00:00