Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model.

abstract：BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...

journal_title：BMC bioinformatics

authors： Chelaru F,Corrada Bravo H

更新日期：2015-01-01 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:In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaus...

journal_title：BMC bioinformatics

authors： Lee J,Lee K,Joung I,Joo K,Brooks BR,Lee J

更新日期：2015-03-21 00:00:00

abstract：BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...

journal_title：BMC bioinformatics

authors： Jing X,Dong Q

更新日期：2017-05-25 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...

journal_title：BMC bioinformatics

authors： Kong W,Mou X,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of ...

journal_title：BMC bioinformatics

authors： Rahmatallah Y,Emmert-Streib F,Glazko G

更新日期：2014-12-05 00:00:00

abstract：BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...

journal_title：BMC bioinformatics

authors： Peng ZL,Yang JY,Chen X

更新日期：2010-08-09 00:00:00

abstract：BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

journal_title：BMC bioinformatics

authors： Choo KH,Tan TW,Ranganathan S

更新日期：2005-10-13 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:Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as...

journal_title：BMC bioinformatics

authors： Eller RJ,Janga SC,Walsh S

更新日期：2019-06-28 00:00:00

abstract：BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...

journal_title：BMC bioinformatics

authors： Wu X,Zhu L,Guo J,Fu C,Zhou H,Dong D,Li Z,Zhang DY,Lin K

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathol...

journal_title：BMC bioinformatics

authors： Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer U

更新日期：2009-10-15 00:00:00

abstract：BACKGROUND:One of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to th...

journal_title：BMC bioinformatics

authors： Scheeff ED,Bourne PE

更新日期：2006-09-14 00:00:00

abstract：BACKGROUND:Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to save lives. In this paper, a comparative analysis of different classifiers was performed for the classi...

journal_title：BMC bioinformatics

authors： Almustafa KM

更新日期：2020-07-02 00:00:00

abstract：BACKGROUND:Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for th...

journal_title：BMC bioinformatics

authors： Vinayagam A,del Val C,Schubert F,Eils R,Glatting KH,Suhai S,König R

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized c...

journal_title：BMC bioinformatics

authors： Bajcsy P,Yoon S,Florczyk SJ,Hotaling NA,Simon M,Szczypinski PM,Schaub NJ,Simon CG Jr,Brady M,Sriram RD

更新日期：2017-11-28 00:00:00

abstract：BACKGROUND:Microarray has been widely used to measure the gene expression level on the genome scale in the current decade. Many algorithms have been developed to reconstruct gene regulatory networks based on microarray data. Unfortunately, most of these models and algorithms focus on global properties of the expression...

journal_title：BMC bioinformatics

authors： Liu W,Li D,Liu Q,Zhu Y,He F

更新日期：2010-12-14 00:00:00

abstract：BACKGROUND:Joint and individual variation explained (JIVE), distinct and common simultaneous component analysis (DISCO) and O2-PLS, a two-block (X-Y) latent variable regression method with an integral OSC filter can all be used for the integrated analysis of multiple data sets and decompose them in three terms: a low(e...

journal_title：BMC bioinformatics

authors： van der Kloet FM,Sebastián-León P,Conesa A,Smilde AK,Westerhuis JA

更新日期：2016-06-06 00:00:00

abstract：BACKGROUND:The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...

journal_title：BMC bioinformatics

authors： Nazarov VI,Pogorelyy MV,Komech EA,Zvyagin IV,Bolotin DA,Shugay M,Chudakov DM,Lebedev YB,Mamedov IZ

更新日期：2015-05-28 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:Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as p...

journal_title：BMC bioinformatics

authors： Nagar A,Hahsler M

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...

journal_title：BMC bioinformatics

authors： Nashta-Ali D,Aliyari A,Ahmadian Moghadam A,Edrisi MA,Motahari SA,Hossein Khalaj B

更新日期：2017-02-23 00:00:00

abstract：BACKGROUND:Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules. In this investigation the performance of LLM in classifying patients with cancer was evaluated using a set of eight publicly available gene expression databases f...

journal_title：BMC bioinformatics

authors： Verda D,Parodi S,Ferrari E,Muselli M

更新日期：2019-11-22 00:00:00

abstract：BACKGROUND:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...

journal_title：BMC bioinformatics

authors： Cokus S,Mizutani S,Pellegrini M

更新日期：2007-05-22 00:00:00

abstract：BACKGROUND:Analyzing Variance heterogeneity in genome wide association studies (vGWAS) is an emerging approach for detecting genetic loci involved in gene-gene and gene-environment interactions. vGWAS analysis detects variability in phenotype values across genotypes, as opposed to typical GWAS analysis, which detects v...

journal_title：BMC bioinformatics

authors： Al Kawam A,Alshawaqfeh M,Cai JJ,Serpedin E,Datta A

更新日期：2018-03-21 00:00:00

abstract：BACKGROUND:Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields ...

journal_title：BMC bioinformatics

authors： Muncey HJ,Jones R,De Iorio M,Ebbels TM

更新日期：2010-10-06 00:00:00

abstract：BACKGROUNDS:Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgentl...

journal_title：BMC bioinformatics

authors： Joo T,Choi JH,Lee JH,Park SE,Jeon Y,Jung SH,Woo HG

更新日期：2019-02-20 00:00:00

abstract：BACKGROUND:Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly ass...

journal_title：BMC bioinformatics

authors： Gai X,Perin JC,Murphy K,O'Hara R,D'arcy M,Wenocur A,Xie HM,Rappaport EF,Shaikh TH,White PS

更新日期：2010-02-04 00:00:00

abstract：BACKGROUND:The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The main network reconstruction approaches are either based on Bayesian scores, which enable the ranking...

journal_title：BMC bioinformatics

authors： Affeldt S,Verny L,Isambert H

更新日期：2016-01-20 00:00:00