Algebraic Dynamic Programming over general data structures.

abstract：BACKGROUND:Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD...

journal_title：BMC bioinformatics

authors： Shen J,Vasaikar S,Zhang B

更新日期：2018-12-28 00:00:00

abstract：BACKGROUND:Isocitrate Dehydrogenases (IDHs) are important enzymes present in all living cells. Three subfamilies of functionally dimeric IDHs (subfamilies I, II, III) are known. Subfamily I are well-studied bacterial IDHs, like that of Escherischia coli. Subfamily II has predominantly eukaryotic members, but it also ha...

journal_title：BMC bioinformatics

authors： Vinekar R,Verma C,Ghosh I

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplicat...

journal_title：BMC bioinformatics

authors： Thierry-Mieg N

更新日期：2006-01-19 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:Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., conti...

journal_title：BMC bioinformatics

authors： Taskesen E,Beekman R,de Ridder J,Wouters BJ,Peeters JK,Touw IP,Reinders MJ,Delwel R

更新日期：2010-05-21 00:00:00

abstract：BACKGROUND:Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection pro...

journal_title：BMC bioinformatics

authors： Zheng Y,Anton BP,Roberts RJ,Kasif S

更新日期：2005-10-03 00:00:00

abstract：BACKGROUND:Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native...

journal_title：BMC bioinformatics

authors： Corona RI,Sudarshan S,Aluru S,Guo JT

更新日期：2018-12-21 00:00:00

abstract：BACKGROUND:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

journal_title：BMC bioinformatics

authors： Haskins WE,Petritis K,Zhang J

更新日期：2011-03-15 00:00:00

abstract：BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...

journal_title：BMC bioinformatics

authors： Lee M,Jeong CS,Kim D

更新日期：2007-12-03 00:00:00

abstract：BACKGROUND:Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS:We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Wa...

journal_title：BMC bioinformatics

authors： Hughes T,Hyun Y,Liberles DA

更新日期：2004-04-29 00:00:00

abstract：BACKGROUND:Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attrib...

journal_title：BMC bioinformatics

authors： Van Landeghem S,Björne J,Abeel T,De Baets B,Salakoski T,Van de Peer Y

更新日期：2012-06-26 00:00:00

abstract：BACKGROUND:Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance...

journal_title：BMC bioinformatics

authors： Giri AV,Anishetty S,Gautam P

更新日期：2004-09-09 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:Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that ...

journal_title：BMC bioinformatics

authors： Dadzie AS,Burger A

更新日期：2005-03-24 00:00:00

abstract：BACKGROUND:Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations i...

journal_title：BMC bioinformatics

authors： Meinicke P,Tech M,Morgenstern B,Merkl R

更新日期：2004-10-28 00:00:00

abstract：BACKGROUND AND GOAL:The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing with logistic regression in many innovation-friendly scientific fields. RESULTS:In this conte...

journal_title：BMC bioinformatics

authors： Couronné R,Probst P,Boulesteix AL

更新日期：2018-07-17 00:00:00

abstract：BACKGROUND:Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Di...

journal_title：BMC bioinformatics

authors： Datta S,Rodriguez A,Prado R

更新日期：2012-10-30 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: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:Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like ...

journal_title：BMC bioinformatics

authors： Stoma S,Fröhlich M,Gerber S,Klipp E

更新日期：2011-04-28 00:00:00

abstract：BACKGROUND:Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evo...

journal_title：BMC bioinformatics

authors： Ndhlovu A,Hazelhurst S,Durand PM

更新日期：2015-08-14 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

authors： Lei Z,Dai Y

更新日期：2005-12-07 00:00:00

abstract：BACKGROUND:Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled...

journal_title：BMC bioinformatics

authors： Wu SH,Rodrigo AG

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for ...

journal_title：BMC bioinformatics

authors： Aberer AJ,Stamatakis A

更新日期：2013-07-09 00:00:00

abstract：BACKGROUND:Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional natur...

journal_title：BMC bioinformatics

authors： Arakawa K,Tamaki S,Kono N,Kido N,Ikegami K,Ogawa R,Tomita M

更新日期：2009-01-23 00:00:00

abstract：:In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...

journal_title：BMC bioinformatics

authors： Aganezov S Jr,Alekseyev MA

更新日期：2012-01-01 00:00:00

abstract：:DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancer...

journal_title：BMC bioinformatics

authors： Qiu P,Zhang L

更新日期：2012-01-01 00:00:00

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:Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms. RESULTS:In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architectur...

journal_title：BMC bioinformatics

authors： Peng S,Cheng M,Huang K,Cui Y,Zhang Z,Guo R,Zhang X,Yang S,Liao X,Lu Y,Zou Q,Shi B

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular level, the adaptations of the immune system in host defense and its dysregulation in pathological condi...

journal_title：BMC bioinformatics

authors： Liu H,Liu J,Toups M,Soos T,Arendt C

更新日期：2016-04-18 00:00:00