Species-specific analysis of protein sequence motifs using mutual information.

abstract：BACKGROUND:When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognosis and to identify the most influential variables for this task. In practice, this is often done fit...

journal_title：BMC bioinformatics

authors： Mayr A,Hofner B,Schmid M

更新日期：2016-07-22 00:00:00

abstract：BACKGROUND:The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the information technology (IT) advancement. This made the general public's participation in biodiversity co...

journal_title：BMC bioinformatics

authors： Paik IH,Lim J,Chun BS,Jin SD,Yu JP,Lee JW,Bhak J,Paek WK

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Time course microarray profiles examine the expression of genes over a time domain. They are necessary in order to determine the complete set of genes that are dynamically expressed under given conditions, and to determine the interaction between these genes. Because of cost and resource issues, most time se...

journal_title：BMC bioinformatics

authors： Sinha A,Markatou M

更新日期：2011-01-11 00:00:00

abstract：BACKGROUND:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...

journal_title：BMC bioinformatics

authors： Asarnow D,Singh R

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide...

journal_title：BMC bioinformatics

authors： Fernandez M,Kumagai Y,Standley DM,Sarai A,Mizuguchi K,Ahmad S

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Variation in DNA copy number, due to gains and losses of chromosome segments, is common. A first step for analyzing DNA copy number data is to identify amplified or deleted regions in individuals. To locate such regions, we propose a circular binary segmentation procedure, which is based on a sequence of nes...

journal_title：BMC bioinformatics

authors： Yang TY

更新日期：2012-10-30 00:00:00

abstract：BACKGROUND:G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical inform...

journal_title：BMC bioinformatics

authors： Bhuvaneshwar K,Belouali A,Singh V,Johnson RM,Song L,Alaoui A,Harris MA,Clarke R,Weiner LM,Gusev Y,Madhavan S

更新日期：2016-04-30 00:00:00

abstract：BACKGROUND:High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be beneficial to also integrate complementary information from different molecular levels when building...

journal_title：BMC bioinformatics

authors： Hieke S,Benner A,Schlenl RF,Schumacher M,Bullinger L,Binder H

更新日期：2016-08-30 00:00:00

abstract：BACKGROUND:The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local corre...

journal_title：BMC bioinformatics

authors： Wang WL,Yu Z,Castillo-Menendez LR,Sodroski J,Mao Y

更新日期：2019-04-03 00:00:00

abstract：BACKGROUND:Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically lin...

journal_title：BMC bioinformatics

authors： van Vliet MH,Wessels LF,Reinders MJ

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data...

journal_title：BMC bioinformatics

authors： Jones L,Goldstein DR,Hughes G,Strand AD,Collin F,Dunnett SB,Kooperberg C,Aragaki A,Olson JM,Augood SJ,Faull RL,Luthi-Carter R,Moskvina V,Hodges AK

更新日期：2006-04-19 00:00:00

abstract：BACKGROUND:Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs oft...

journal_title：BMC bioinformatics

authors： Kaltenbach HM,Wilke A,Böcker S

更新日期：2007-03-26 00:00:00

abstract：BACKGROUND:Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype s...

journal_title：BMC bioinformatics

authors： Peng J,Hui W,Shang X

更新日期：2018-04-11 00:00:00

abstract：BACKGROUND:Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each...

journal_title：BMC bioinformatics

authors： Starmer J,Magnuson T

更新日期：2016-03-24 00:00:00

abstract：BACKGROUND:Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemic...

journal_title：BMC bioinformatics

authors： Chae M,Shmookler Reis RJ,Thaden JJ

更新日期：2008-08-12 00:00:00

abstract：BACKGROUND:The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural c...

journal_title：BMC bioinformatics

authors： Zhao J,Yu H,Luo JH,Cao ZW,Li YX

更新日期：2006-08-18 00:00:00

abstract：BACKGROUND:Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order t...

journal_title：BMC bioinformatics

authors： Corradi L,Fato M,Porro I,Scaglione S,Torterolo L

更新日期：2008-11-13 00:00:00

abstract：BACKGROUND:Genetic variations predispose individuals to hereditary diseases, play important role in the development of complex diseases, and impact drug metabolism. The full information about the DNA variations in the genome of an individual is given by haplotypes, the ordered lists of single nucleotide polymorphisms (...

journal_title：BMC bioinformatics

authors： Ahn S,Vikalo H

更新日期：2015-07-16 00:00:00

abstract：BACKGROUND:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...

journal_title：BMC bioinformatics

authors： Fang Y,Gao S,Tai D,Middaugh CR,Fang J

更新日期：2013-10-28 00:00:00

abstract：BACKGROUND:Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature ...

journal_title：BMC bioinformatics

authors： Song L,Langfelder P,Horvath S

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:Analysis of expression quantitative trait loci (eQTL) aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge o...

journal_title：BMC bioinformatics

authors： Wang W,Zhang X

更新日期：2011-06-30 00:00:00

abstract：BACKGROUND:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...

journal_title：BMC bioinformatics

authors： Skums P,Dimitrova Z,Campo DS,Vaughan G,Rossi L,Forbi JC,Yokosawa J,Zelikovsky A,Khudyakov Y

更新日期：2012-06-25 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:Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We...

journal_title：BMC bioinformatics

authors： Churbanov A,Vorechovský I,Hicks C

更新日期：2010-01-12 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:Profile-based comparison of multiple sequence alignments is a powerful methodology for the detection remote protein sequence similarity, which is essential for the inference and analysis of protein structure, function, and evolution. Accurate estimation of statistical significance of detected profile similar...

journal_title：BMC bioinformatics

authors： Sadreyev RI,Wang Y,Grishin NV

更新日期：2009-12-04 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：:We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...

journal_title：BMC bioinformatics

authors： Yue Z,Wan P,Huang H,Xie Z,Chen JY

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...

journal_title：BMC bioinformatics

authors： Li C

更新日期：2008-05-08 00:00:00

abstract：BACKGROUND:Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carboh...

journal_title：BMC bioinformatics

authors： Ranzinger R,Herget S,Wetter T,von der Lieth CW

更新日期：2008-09-19 00:00:00