WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

abstract：BACKGROUND:MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction speci...

journal_title：BMC bioinformatics

authors： Liu H,Yue D,Chen Y,Gao SJ,Huang Y

更新日期：2010-09-22 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:Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mouse models revealed delayed maturation of neuronal morphology and autonomous as well as non-cell auton...

journal_title：BMC bioinformatics

authors： Vacca M,Tripathi KP,Speranza L,Aiese Cigliano R,Scalabrì F,Marracino F,Madonna M,Sanseverino W,Perrone-Capano C,Guarracino MR,D'Esposito M

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional too...

journal_title：BMC bioinformatics

authors： Keller O,Odronitz F,Stanke M,Kollmar M,Waack S

更新日期：2008-06-13 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: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:Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for presence of DNA binding motifs in the promoter regions of co-regulated genes. However, this strateg...

journal_title：BMC bioinformatics

authors： Roy S,Heinrich K,Phan V,Berry MW,Homayouni R

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise ...

journal_title：BMC bioinformatics

authors： Lawless C,Wilkinson DJ,Young A,Addinall SG,Lydall DA

更新日期：2010-05-28 00:00:00

abstract：BACKGROUND:Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS:On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network ...

journal_title：BMC bioinformatics

authors： Schoenrock A,Samanfar B,Pitre S,Hooshyar M,Jin K,Phillips CA,Wang H,Phanse S,Omidi K,Gui Y,Alamgir M,Wong A,Barrenäs F,Babu M,Benson M,Langston MA,Green JR,Dehne F,Golshani A

更新日期：2014-12-10 00:00:00

abstract：BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...

journal_title：BMC bioinformatics

authors： Karwath A,King RD

更新日期：2002-04-23 00:00:00

abstract：BACKGROUND:Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis ...

journal_title：BMC bioinformatics

authors： Yu G

更新日期：2010-10-12 00:00:00

abstract：BACKGROUND:Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions...

journal_title：BMC bioinformatics

authors： Arenas M,Patricio M,Posada D,Valiente G

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:We present the algorithm PFClust (Parameter Free Clustering), which is able automatically to cluster data and identify a suitable number of clusters to group them into without requiring any parameters to be specified by the user. The algorithm partitions a dataset into a number of clusters that share some co...

journal_title：BMC bioinformatics

authors： Mavridis L,Nath N,Mitchell JB

更新日期：2013-07-03 00:00:00

abstract：BACKGROUND:Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures ca...

journal_title：BMC bioinformatics

authors： Schreiner E,Trabuco LG,Freddolino PL,Schulten K

更新日期：2011-05-23 00:00:00

abstract：BACKGROUND:Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies, new protein sequences are becoming available at an extraordinary rate. The ra...

journal_title：BMC bioinformatics

authors： Abnousi A,Broschat SL,Kalyanaraman A

更新日期：2018-03-05 00:00:00

abstract：BACKGROUND:The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying...

journal_title：BMC bioinformatics

authors： Du J,Li M,Yuan Z,Guo M,Song J,Xie X,Chen Y

更新日期：2016-10-06 00:00:00

abstract：BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...

journal_title：BMC bioinformatics

authors： Khan A,Liu Q,Wang K

更新日期：2018-12-28 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 00:00:00

abstract：BACKGROUND:The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which inten...

journal_title：BMC bioinformatics

authors： Pasche E,Gobeill J,Kreim O,Oezdemir-Zaech F,Vachon T,Lovis C,Ruch P

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be ...

journal_title：BMC bioinformatics

authors： Andrieu O,Fiston AS,Anxolabéhère D,Quesneville H

更新日期：2004-07-13 00:00:00

abstract：BACKGROUND:It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opp...

journal_title：BMC bioinformatics

authors： Borozan I,Wilson S,Blanchette P,Laflamme P,Watt SN,Krzyzanowski PM,Sircoulomb F,Rottapel R,Branton PE,Ferretti V

更新日期：2012-08-17 00:00:00

abstract：BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...

journal_title：BMC bioinformatics

authors： Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SY

更新日期：2020-12-17 00:00:00

abstract：BACKGROUND:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...

journal_title：BMC bioinformatics

authors： Sinha R,Hiller M,Pudimat R,Gausmann U,Platzer M,Backofen R

更新日期：2008-11-12 00:00:00

abstract：BACKGROUND:Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain uncharted. Thus, in-depth study of the epi-transcriptomic patterns of m6A may provide insights into ...

journal_title：BMC bioinformatics

authors： Zhang L,Chen S,Zhu J,Meng J,Liu H

更新日期：2020-10-09 00:00:00

abstract：BACKGROUND:Reproducibility of results can have a significant impact on the acceptance of new technologies in gene expression analysis. With the recent introduction of the so-called next-generation sequencing (NGS) technology and established microarrays, one is able to choose between two completely different platforms f...

journal_title：BMC bioinformatics

authors： Stiglic G,Bajgot M,Kokol P

更新日期：2010-04-08 00:00:00

abstract：BACKGROUND:Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, e...

journal_title：BMC bioinformatics

authors： Zhang F,Deng CK,Wang M,Deng B,Barber R,Huang G

更新日期：2020-12-03 00:00:00

abstract：BACKGROUND:Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the...

journal_title：BMC bioinformatics

authors： de la Grange P,Dutertre M,Correa M,Auboeuf D

更新日期：2007-06-04 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:Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities tha...

journal_title：BMC bioinformatics

authors： Moritz T,Krishnan S,Roberts D,Ingwersen P,Agosti D,Penev L,Cockerill M,Chavan V,Data Publishing Framework Task Group.

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadl...

journal_title：BMC bioinformatics

authors： Hummel J,Niemann M,Wienkoop S,Schulze W,Steinhauser D,Selbig J,Walther D,Weckwerth W

更新日期：2007-06-23 00:00:00