SNP and gene networks construction and analysis from classification of copy number variations data.

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: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:In many biomedical applications, there is a need for developing classification models based on noisy annotations. Recently, various methods addressed this scenario by relaying on unreliable annotations obtained from multiple sources. RESULTS:We proposed a probabilistic classification algorithm based on labe...

journal_title：BMC bioinformatics

authors： Zhang P,Cao W,Obradovic Z

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel Dat...

journal_title：BMC bioinformatics

authors： Li B,Gallin WJ

更新日期：2004-01-09 00:00:00

abstract：BACKGROUND:An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class prediction for problems such as the detection of a disease, disease prognosis, or for predicting treatment ...

journal_title：BMC bioinformatics

authors： Kaur P,Schlatzer D,Cooke K,Chance MR

更新日期：2012-08-07 00:00:00

abstract：BACKGROUND:Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may r...

journal_title：BMC bioinformatics

authors： Jo Y,Kim S,Lee D

更新日期：2018-06-13 00:00:00

abstract：BACKGROUND:With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceabilit...

journal_title：BMC bioinformatics

authors： Thallinger GG,Baumgartner K,Pirklbauer M,Uray M,Pauritsch E,Mehes G,Buck CR,Zatloukal K,Trajanoski Z

更新日期：2007-03-07 00:00:00

abstract：BACKGROUND:The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appea...

journal_title：BMC bioinformatics

authors： Tatusov RL,Fedorova ND,Jackson JD,Jacobs AR,Kiryutin B,Koonin EV,Krylov DM,Mazumder R,Mekhedov SL,Nikolskaya AN,Rao BS,Smirnov S,Sverdlov AV,Vasudevan S,Wolf YI,Yin JJ,Natale DA

更新日期：2003-09-11 00:00:00

abstract：BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...

journal_title：BMC bioinformatics

authors： Negre V,Grunau C

更新日期：2004-05-07 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: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: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:To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is compu...

journal_title：BMC bioinformatics

authors： Abby SS,Tannier E,Gouy M,Daubin V

更新日期：2010-06-15 00:00:00

abstract：BACKGROUND:Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden virus-receptor interactions must be discovered. However, current computational methods for predicti...

journal_title：BMC bioinformatics

authors： Yan C,Duan G,Wu FX,Wang J

更新日期：2019-12-27 00:00:00

abstract：BACKGROUND:Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic sc...

journal_title：BMC bioinformatics

authors： Falda M,Toppo S,Pescarolo A,Lavezzo E,Di Camillo B,Facchinetti A,Cilia E,Velasco R,Fontana P

更新日期：2012-03-28 00:00:00

abstract：BACKGROUND:Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) directed against genomic regions conserved between different isolates. Genetic varia...

journal_title：BMC bioinformatics

authors： Vanneste K,Garlant L,Broeders S,Van Gucht S,Roosens NH

更新日期：2018-09-04 00:00:00

abstract：BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 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:Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the m...

journal_title：BMC bioinformatics

authors： McQuisten KA,Peek AS

更新日期：2007-06-07 00:00:00

abstract：BACKGROUND:Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient's lifetime. With the development of the next-generation sequencing technology, multiple omics data, such as cancer genomic, epigenomic and transcriptomic data etc., can be measured from each indiv...

journal_title：BMC bioinformatics

authors： Wei PJ,Zhang D,Xia J,Zheng CH

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:The aberrant expression of microRNAs is closely connected to the occurrence and development of a great deal of human diseases. To study human diseases, numerous effective computational models that are valuable and meaningful have been presented by researchers. RESULTS:Here, we present a computational framew...

journal_title：BMC bioinformatics

authors： Gao Z,Wang YT,Wu QW,Ni JC,Zheng CH

更新日期：2020-02-18 00:00:00

abstract：BACKGROUND:With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. RESULTS...

journal_title：BMC bioinformatics

authors： Sykacek P,Kreil DP,Meadows LA,Auburn RP,Fischer B,Russell S,Micklem G

更新日期：2011-03-14 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:Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to select genes that change their relationships with other genes in different biological conditions (diffe...

journal_title：BMC bioinformatics

authors： Hu R,Qiu X,Glazko G,Klebanov L,Yakovlev A

更新日期：2009-01-15 00:00:00

abstract：BACKGROUND:Reliability and Reproducibility of differentially expressed genes (DEGs) are essential for the biological interpretation of microarray data. The microarray quality control (MAQC) project launched by US Food and Drug Administration (FDA) elucidated that the lists of DEGs generated by intra- and inter-platform...

journal_title：BMC bioinformatics

authors： Zhang L,Zhang J,Yang G,Wu D,Jiang L,Wen Z,Li M

更新日期：2013-04-29 00:00:00

abstract：BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...

journal_title：BMC bioinformatics

authors： McCorrison JM,Venepally P,Singh I,Fouts DE,Lasken RS,Methé BA

更新日期：2014-11-19 00:00:00

abstract：BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...

journal_title：BMC bioinformatics

authors： Che D,Guo S,Jiang Q,Chen L

更新日期：2020-07-14 00:00:00

abstract：BACKGROUND:In real-time PCR data analysis, the cycle threshold (CT) method is currently the gold standard. This method is based on an assumption of equal PCR efficiency in all reactions, and precision may suffer if this condition is not met. Nonlinear regression analysis (NLR) or curve fitting has therefore been sugges...

journal_title：BMC bioinformatics

authors： Goll R,Olsen T,Cui G,Florholmen J

更新日期：2006-03-03 00:00:00

abstract：BACKGROUND:The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. RESULTS:We offer BAGEL (Bayesian Analysis of Gene...

journal_title：BMC bioinformatics

authors： Hart T,Moffat J

更新日期：2016-04-16 00:00:00

abstract：BACKGROUND:Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing. RESULTS:We propose s...

journal_title：BMC bioinformatics

authors： Rudra P,Shi WJ,Vestal B,Russell PH,Odell A,Dowell RD,Radcliffe RA,Saba LM,Kechris K

更新日期：2017-03-02 00:00:00