Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data.

abstract：BACKGROUND:Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is required to model the non-uniformity. Also, the properties of sequencing read counts can be leveraged to...

journal_title：BMC bioinformatics

authors： Cai G,Liang S,Zheng X,Xiao F

更新日期：2017-08-09 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: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: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:Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explana...

journal_title：BMC bioinformatics

authors： Samal A,Singh S,Giri V,Krishna S,Raghuram N,Jain S

更新日期：2006-03-08 00:00:00

abstract：BACKGROUND:Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting ...

journal_title：BMC bioinformatics

authors： Wang K,Nishida H

更新日期：2015-04-10 00:00:00

abstract：BACKGROUND:Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, including the processing of polycistr...

journal_title：BMC bioinformatics

authors： Smith M,Blanchette M,Papadopoulou B

更新日期：2008-03-20 00:00:00

abstract：BACKGROUND:Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engin...

journal_title：BMC bioinformatics

authors： Theys K,Deforche K,Beheydt G,Moreau Y,van Laethem K,Lemey P,Camacho RJ,Rhee SY,Shafer RW,Van Wijngaerden E,Vandamme AM

更新日期：2010-08-03 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:A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, protein functional annotation, prediction of molecular interactions, etc. These applications, however sop...

journal_title：BMC bioinformatics

authors： Vanhoutreve R,Kress A,Legrand B,Gass H,Poch O,Thompson JD

更新日期：2016-07-07 00:00:00

abstract：BACKGROUND:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...

journal_title：BMC bioinformatics

authors： Clayton EA,Pujol TA,McDonald JF,Qiu P

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA) genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complex...

journal_title：BMC bioinformatics

authors： Mori H,Maruyama F,Kurokawa K

更新日期：2010-06-18 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:Microarray technology provides the expression level of many genes. Nowadays, an important issue is to select a small number of informative differentially expressed genes that provide biological knowledge and may be key elements for a disease. With the increasing volume of data generated by modern biomedical ...

journal_title：BMC bioinformatics

authors： Martínez-Otzeta JM,Irigoien I,Sierra B,Arenas C

更新日期：2020-04-07 00:00:00

abstract：BACKGROUND:In microarray data analysis, factors such as data quality, biological variation, and the increasingly multi-layered nature of more complex biological systems complicates the modelling of regulatory networks that can represent and capture the interactions among genes. We believe that the use of multiple datas...

journal_title：BMC bioinformatics

authors： Anvar SY,'t Hoen PA,Tucker A

更新日期：2010-01-15 00:00:00

abstract：BACKGROUND:A massive amount of proteomic data is generated on a daily basis, nonetheless annotating all sequences is costly and often unfeasible. As a countermeasure, machine learning methods have been used to automatically annotate new protein functions. More specifically, many studies have investigated hierarchical m...

journal_title：BMC bioinformatics

authors： Nakano FK,Lietaert M,Vens C

更新日期：2019-09-23 00:00:00

abstract：BACKGROUND:Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classi...

journal_title：BMC bioinformatics

authors： Chen JL,Liu Y,Sam LT,Li J,Lussier YA

更新日期：2007-05-09 00:00:00

abstract：BACKGROUND:We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, ma...

journal_title：BMC bioinformatics

authors： Cherkasov A,Ho Sui SJ,Brunham RC,Jones SJ

更新日期：2004-07-26 00:00:00

abstract：BACKGROUND:One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arra...

journal_title：BMC bioinformatics

authors： Emberly E,Rajewsky N,Siggia ED

更新日期：2003-11-20 00:00:00

abstract：BACKGROUND:DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arr...

journal_title：BMC bioinformatics

authors： Yu F,Xu C,Deng HW,Shen H

更新日期：2020-12-01 00:00:00

abstract：BACKGROUND:In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with ...

journal_title：BMC bioinformatics

authors： Quest D,Dempsey K,Shafiullah M,Bastola D,Ali H

更新日期：2008-08-12 00:00:00

abstract：BACKGROUND:The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine...

journal_title：BMC bioinformatics

authors： Bujnicki JM,Feder M,Radlinska M,Rychlewski L

更新日期：2001-01-01 00:00:00

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

authors： Nahum LA,Reynolds MT,Wang ZO,Faith JJ,Jonna R,Jiang ZJ,Meyer TJ,Pollock DD

更新日期：2006-09-06 00:00:00

abstract：BACKGROUND:Determining a suitable sample size is an important step in the planning of microarray experiments. Increasing the number of arrays gives more statistical power, but adds to the total cost of the experiment. Several approaches for sample size determination have been developed for expression array studies, but...

journal_title：BMC bioinformatics

authors： Scheinin I,Ferreira JA,Knuutila S,Meijer GA,van de Wiel MA,Ylstra B

更新日期：2010-06-17 00:00:00

abstract：BACKGROUND:Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent b...

journal_title：BMC bioinformatics

authors： Cohen-Boulakia S,Chen J,Missier P,Goble C,Williams AR,Froidevaux C

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results...

journal_title：BMC bioinformatics

authors： Gautier L,Møller M,Friis-Hansen L,Knudsen S

更新日期：2004-08-14 00:00:00

abstract：BACKGROUND:GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that G...

journal_title：BMC bioinformatics

authors： Machnicka MA,Kaminska KH,Dunin-Horkawicz S,Bujnicki JM

更新日期：2015-10-23 00:00:00

abstract：BACKGROUND:In the last decade, a significant improvement in detecting remote similarity between protein sequences has been made by utilizing alignment profiles in place of amino-acid strings. Unfortunately, no analytical theory is available for estimating the significance of a gapped alignment of two profiles. Many exp...

journal_title：BMC bioinformatics

authors： Poleksic A

更新日期：2009-04-20 00:00:00

abstract：BACKGROUND:In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding...

journal_title：BMC bioinformatics

authors： Wang X,Wu D,Zheng S,Sun J,Tao L,Li Y,Cao Z

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in transcription factor databases, as well as to represent the po...

journal_title：BMC bioinformatics

authors： Kankainen M,Löytynoja A

更新日期：2007-06-08 00:00:00