Constructing patch-based ligand-binding pocket database for predicting function of proteins.

abstract：BACKGROUND:Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV da...

journal_title：BMC bioinformatics

authors： Vandeweyer G,Reyniers E,Wuyts W,Rooms L,Kooy RF

更新日期：2011-01-05 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: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:Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the development of effective statistical methods to calibrat...

journal_title：BMC bioinformatics

authors： Komorowski M,Finkenstädt B,Harper CV,Rand DA

更新日期：2009-10-19 00:00:00

abstract：BACKGROUND:Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profil...

journal_title：BMC bioinformatics

authors： Vilaprinyo E,Alves R,Sorribas A

更新日期：2006-04-03 00:00:00

abstract：BACKGROUND:High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of pr...

journal_title：BMC bioinformatics

authors： Ayub U,Haider I,Naveed H

更新日期：2020-11-04 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:Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites. RESULTS:We propose to identify and group similar profiles using tw...

journal_title：BMC bioinformatics

authors： Kielbasa SM,Gonze D,Herzel H

更新日期：2005-09-28 00:00:00

abstract：BACKGROUND:The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-d...

journal_title：BMC bioinformatics

authors： Wang Q,Tang B,Song L,Ren B,Liang Q,Xie F,Zhuo Y,Liu X,Zhang L

更新日期：2013-11-14 00:00:00

abstract：BACKGROUND:Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstrom...

journal_title：BMC bioinformatics

authors： Carugo O

更新日期：2018-02-23 00:00:00

abstract：BACKGROUND:Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but h...

journal_title：BMC bioinformatics

authors： Robinson TJ,Dinan MA,Dewhirst M,Garcia-Blanco MA,Pearson JL

更新日期：2010-02-25 00:00:00

abstract：BACKGROUND:Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. RESULTS:We introduce Accucopy, a method t...

journal_title：BMC bioinformatics

authors： Fan X,Luo G,Huang YS

更新日期：2021-01-15 00:00:00

abstract：BACKGROUND:The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune deficiency syndrome (AIDS). Development of HIV-1 protease inhibitors can help understand the specifici...

journal_title：BMC bioinformatics

authors： Singh O,Su EC

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:Observed levels of gene expression strongly depend on both activity of DNA binding transcription factors (TFs) and chromatin state through different histone modifications (HMs). In order to recover the functional relationship between local chromatin state, TF binding and observed levels of gene expression, r...

journal_title：BMC bioinformatics

authors： Aflakparast M,Geeven G,de Gunst MCM

更新日期：2020-01-02 00:00:00

abstract：BACKGROUND:The improvements of high throughput technologies have produced large amounts of multi-omics experiments datasets. Initial analysis of these data has revealed many concurrent gene alterations within single dataset or/and among multiple omics datasets. Although powerful bioinformatics pipelines have been devel...

journal_title：BMC bioinformatics

authors： Chen D,Zhang F,Zhao Q,Xu J

更新日期：2019-11-08 00:00:00

abstract：BACKGROUND:Non-coding RNAs gain more attention as their diverse roles in many cellular processes are discovered. At the same time, the need for efficient computational prediction of ncRNAs increases with the pace of sequencing technology. Existing tools are based on various approaches and techniques, but none of them p...

journal_title：BMC bioinformatics

authors： Raasch P,Schmitz U,Patenge N,Vera J,Kreikemeyer B,Wolkenhauer O

更新日期：2010-09-29 00:00:00

abstract：BACKGROUND:One of the main goals in cancer studies including high-throughput microRNA (miRNA) and mRNA data is to find and assess prognostic signatures capable of predicting clinical outcome. Both mRNA and miRNA expression changes in cancer diseases are described to reflect clinical characteristics like staging and pro...

journal_title：BMC bioinformatics

authors： Gade S,Porzelius C,Fälth M,Brase JC,Wuttig D,Kuner R,Binder H,Sültmann H,Beissbarth T

更新日期：2011-12-21 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:Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain c...

journal_title：BMC bioinformatics

authors： Mótyán JA,Bagossi P,Benkő S,Tőzsér J

更新日期：2013-09-17 00:00:00

abstract：BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...

journal_title：BMC bioinformatics

authors： Zamani N,Sundström G,Meadows JR,Höppner MP,Dainat J,Lantz H,Haas BJ,Grabherr MG

更新日期：2014-06-30 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

abstract：BACKGROUND:MicroRNAs (miRNAs) are a kind of small noncoding RNA molecules that are direct posttranscriptional regulations of mRNA targets. Studies have indicated that miRNAs play key roles in complex diseases by taking part in many biological processes, such as cell growth, cell death and so on. Therefore, in order to ...

journal_title：BMC bioinformatics

authors： Yan C,Wu FX,Wang J,Duan G

更新日期：2020-03-18 00:00:00

abstract：BACKGROUND:Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional g...

journal_title：BMC bioinformatics

authors： Raj S,Hussain F,Husein Z,Torosdagli N,Turgut D,Deo N,Pattanaik S,Chang CJ,Jha SK

更新日期：2017-06-07 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:Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On...

journal_title：BMC bioinformatics

authors： Yuan Y,Li CT,Wilson R

更新日期：2008-06-18 00:00:00

abstract：BACKGROUND:Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objectiv...

journal_title：BMC bioinformatics

authors： Zuyderduyn SD,Jones SJ

更新日期：2003-10-28 00:00:00

abstract：BACKGROUND:The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. Whi...

journal_title：BMC bioinformatics

authors： Skvortsov D,Abdueva D,Stitzer ME,Finkel SE,Tavaré S

更新日期：2007-06-14 00:00:00

abstract：BACKGROUND:The classification of cancer subtypes is of great importance to cancer disease diagnosis and therapy. Many supervised learning approaches have been applied to cancer subtype classification in the past few years, especially of deep learning based approaches. Recently, the deep forest model has been proposed a...

journal_title：BMC bioinformatics

authors： Guo Y,Liu S,Li Z,Shang X

更新日期：2018-04-11 00:00:00

abstract：BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...

journal_title：BMC bioinformatics

authors： Del Vecchio F,Gallo F,Di Marco A,Mastroiaco V,Caianiello P,Zazzeroni F,Alesse E,Tessitore A

更新日期：2015-12-10 00:00:00

abstract：BACKGROUND:The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, w...

journal_title：BMC bioinformatics

authors： Smith AM,Walsh JR,Long J,Davis CB,Henstock P,Hodge MR,Maciejewski M,Mu XJ,Ra S,Zhao S,Ziemek D,Fisher CK

更新日期：2020-03-20 00:00:00