Find your PDFs fast.
Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Databases, Genetic (2):
Recent article
Databases, Genetic
Abstract
| < More recent | Older article > |
Abstract
We screened a set of proteins from the G-protein complex using two-hybrid complementation in yeast. After deep and exhaustive interrogation, we detected 544 interactions between 434 proteins, of which 68 highly interconnected proteins form the core G-protein interactome. Within this core, over half...
|
PMID: 21952135
PDF is available here.
PDF is available here.
Abstract
We introduce a similarity-based regression method for assessing the main genetic and interaction effects of a group of markers on quantitative traits. The method uses genetic similarity to aggregate information from multiple polymorphic sites and integrates adaptive weights that depend on allele fre...
|
PMID: 21835306
PDF is available here.
PDF is available here.
Abstract
We compared the allele frequencies of antidepressant efficacy-related SNPs between the Taiwanese population and four other populations in the HapMap database. We recruited 198 Taiwanese major depression patients and 106 Taiwanese controls. A panel of possible relevant SNPs (in brain-derived neurotro...
|
PMID: 21742253
PDF is available here.
PDF is available here.
Abstract
We studied a population (OG-W-IP) that is of African-Indian origin and has resided in the western part of India for 500 years; members of this population are believed to be descendants of the Bantu-speaking population of Africa. We have carried out this study by using a set of 18,534 autosomal marke...
|
PMID: 21737057
PDF is available here.
PDF is available here.
Abstract
Abstract
The present study describes the in silico prediction of the regulatory network of Leishmania infected human macrophages. The construction of the gene regulatory network requires the identification of Transcription Factor Binding Sites (TFBSs) in the regulatory regions (promoters, enhancers) of genes...
|
PMID: 21093613
PDF is available here.
PDF is available here.
Abstract
We used gene expression data sets from the analysis of primary and metastatic melanomas to develop a molecular description of the heterogeneity that characterizes this disease. Unsupervised hierarchical clustering, gene set enrichment analyses, and pathway activity analyses were used to describe the...
|
PMID: 21641377
PDF is available here.
PDF is available here.
Abstract
We first select genes using nonnegative matrix factorization (NMF) or sparse NMF (SNMF), and then we extract features from the selected genes by virtue of NMF or SNMF. At last, we apply support vector machines (SVM) to classify the tumor samples using the extracted features. In order for a better cl...
|
PMID: 21742573
PDF is available here.
PDF is available here.
Abstract
We carried out a genome-wide association study of 7607 patients in the Electronic Medical Records and Genomics (eMERGE) network. The discovery cohort consisted of 1979 individuals from the Mayo Clinic, and the replication cohort consisted of 5628 individuals from the remaining four eMERGE sites. A n...
|
PMID: 21700265
PDF is available here.
PDF is available here.
Hereditas (Beijing) (33)6 2011
Abstract
Researches on the next generation sequencing (NGS) and the comparative genome analysis have recently been concerned. The analyses on transposable element composition and abundance are important parts for genome studies. Generally, the analyses of transposable element system were based on the complete...
|
PMID: 21684872
PDF is available here.
PDF is available here.
Abstract
We bring this 'bottom-up' approach alongside the current NGS-driven genetic study of genetic variations and disease aetiology. We describe experimental and computational techniques for assessing genetic variants and their deleterious effects on protein structure and function....
|
PMID: 21350909
PDF is available here.
PDF is available here.
Abstract
We make use of the random partial least squares regression technique (r-PLS) to trace connections between co-expressed genes in Mycobacterium tuberculosis using data downloaded from public microarray databases. We generated the overall topology of a microbial co-expression network with the exact com...
|
PMID: 21514402
PDF is available here.
PDF is available here.
Abstract
We propose to use an incremental fuzzy mining technique called incremental fuzzy mining (IFM). By transforming quantitative expression values into linguistic terms, such as highly or lowly expressed, IFM can effectively capture heterogeneity in expression data for pattern discovery. It does so using...
|
PMID: 20403777
PDF is available here.
PDF is available here.
Abstract
We describe setting up the first comprehensive human autophagy database (HADb, available at www.autophagy.lu) and the development of a companion Human Autophagy-dedicated cDNA Microarray which comprises 234 genes involved in or related to autophagy. The autophagy microarray tool used on breast adeno...
|
PMID: 21490427
PDF is available here.
PDF is available here.
Abstract
We review modern developments in genomics and systems biology that have revolutionized our understanding of the multiple means by which translation is regulated. We suggest new means to model the process of translation in a richer framework that will incorporate information about gene sequences, the...
|
PMID: 21487400
PDF is available here.
PDF is available here.
Abstract
We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices o...
|
PMID: 21524350
PDF is available here.
PDF is available here.
Proteomics (11)7 2011
Abstract
We developed a two-step strategy for the enrichment of low-abundant soluble chloroplast proteins from Pisum sativum and their subsequent identification by MS. First, chloroplast protein extracts were depleted from the most abundant protein ribulose-1,5-bisphosphate carboxylase/oxygenase by SEC or he...
|
PMID: 21365755
PDF is available here.
PDF is available here.
Proteomics (11)7 2011
Abstract
We report the subproteome reference maps of E. coli B REL606 by analyzing cytoplasmic, periplasmic, inner and outer membrane, and extracellular proteomes based on the genome information using experimental and computational approaches. Among the total of 3487 spots, 651 proteins including 410 non-red...
|
PMID: 21337514
PDF is available here.
PDF is available here.
PLoS Genetics (7)4 2011
Abstract
We generated a catalogue of CIN genes and pathways by screening ∼ 2,000 reduction-of-function alleles for 90% of essential genes in Saccharomyces cerevisiae. Integrating this with published CIN phenotypes for other yeast genes generated a systematic CIN gene dataset comprised of 692 genes. Enriche...
|
PMID: 21552543
PDF is available here.
PDF is available here.
Abstract
We obtained genome-wide significant results at MS4A4A (rs4938933; stages 1 and 2, meta-analysis P (P(M)) = 1.7 × 10(-9), joint analysis P (P(J)) = 1.7 × 10(-9); stages 1, 2 and 3, P(M) = 8.2 × 10(-12)), CD2AP (rs9349407; stages 1, 2 and 3, P(M) = 8.6 × 10(-9)), EPHA1 (rs11767557; stages 1, 2 and...
|
PMID: 21460841
PDF is available here.
PDF is available here.
Abstract
We propose an effective approach to integrating the output of some of these tools into a unified classification; this approach is based on a weighted average of the normalized scores of the individual methods (WAS). (In this paper, the approach is illustrated for the integration of five tools.) We s...
|
PMID: 21457909
PDF is available here.
PDF is available here.
Abstract
We were able to find for these comparisons, there was a significant match between the gene expression data and sphingolipid composition (P...
|
PMID: 21415121
PDF is available here.
PDF is available here.
Abstract
We demonstrate that biologically relevant aspects of expression profiles may be captured by precision-reduced descriptions that are fully human readable, and that biologically relevant relationships may be captured by applying familiar pattern searching techniques to these precision-reduced descript...
|
PMID: 21431551
PDF is available here.
PDF is available here.
Abstract
One of the major tasks with gene expression data is to find groups of coregulated genes whose collective expression is strongly associated with sample categories. In this regard, a new clustering algorithm, termed as fuzzy-rough supervised attribute clustering (FRSAC), is proposed to find such groups...
|
PMID: 20542768
PDF is available here.
PDF is available here.
Abstract
We define the gene expression network topology of cardiac hypertrophy and failure and the extent of recapitulation of fetal gene expression programs in failing and hypertrophied adult myocardium.
We assembled all myocardial transcript data in the Gene Expression Omnibus (n=1617). Bec...
|
PMID: 21127201
PDF is available here.
PDF is available here.
Abstract
We propose a more appropriate metric and modified hierarchical clustering method to highlight those genes of interest. Use of hashing and bucket sort allows for fast clustering and the hierarchical dendrogram allows for direct comparison with easily understood meaning of the distance. The method als...
|
PMID: 21431546
PDF is available here.
PDF is available here.
Improving the accuracy of gene expression profile classification with Lorenz curves and Gini ratios.
Abstract
We show how Lorenz Curves and Gini Ratios can be modified to improve the accuracy of gene expression profile classification. Experimental results with different classification algorithms using additional techniques and strategies for improving the accuracy such as the principal component analysis, t...
|
PMID: 21431549
PDF is available here.
PDF is available here.
Abstract
We call this method Rough PCA. The proposed method is successfully applied for choosing the principal features and then applying the Upper and Lower Approximations to find the reduced set of features from a gene expression data....
|
PMID: 21431550
PDF is available here.
PDF is available here.
Abstract
We propose that using a seeded clustering algorithm, researchers can identify or verify previously unknown or doubtful normalization information. For that, we generate descriptive statistics (mean, variance, quantiles, and moments) for normalized expression data from gene chip experiments available...
|
PMID: 21431555
PDF is available here.
PDF is available here.
Abstract
I alleles for SARS Corona virus (Tor2 Replicase polyprotein 1ab) has been used for training and prediction of BNB. A total of 90 datasets (nine different MHC class I alleles with tenfold cross validation) have been retrieved from IEDB database for BNB. For fixed learning rate approach, the best valu...
|
PMID: 21431562
PDF is available here.
PDF is available here.
Abstract
We apply entropic filter methods for gene selection, in combination with several off-the-shelf classifiers. The introduction of bootstrap resampling techniques permits the achievement of more stable performance estimates. Our findings show that the proposed methodology permits a drastic reduction in...
|
PMID: 21431545
PDF is available here.
PDF is available here.
Abstract
We focus on evaluating the performance of the training algorithms of the single hidden layer feedforward neural networks (SLFNs) to classify DNA microarrays. The training algorithms consist of backpropagation (BP), extreme learning machine (ELM) and regularized least squares ELM (RLS-ELM), and an ef...
|
PMID: 21431554
PDF is available here.
PDF is available here.
Abstract
We present another ensemble of decision trees called Rotation Forest and evaluate its classification performance on different microarray datasets. Rotation Forest can also be applied to different already existing ensembles of classifiers like Random Forest to improve their accuracy and robustness. T...
|
PMID: 21431561
PDF is available here.
PDF is available here.
Abstract
We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa....
|
PMID: 21431569
PDF is available here.
PDF is available here.
Abstract
There has been a deluge of biological sequence data in the public domain, which makes sequence comparison one of the most fundamental computational problems in bioinformatics. The biologists routinely use pairwise alignment programs to identify similar, or more specifically, related sequences (having...
|
PMID: 21431570
PDF is available here.
PDF is available here.
Abstract
One current challenge in biomedicine is to analyze large amounts of complex biological data for extracting domain knowledge. This work holds on the use of knowledge-based techniques such as knowledge discovery (KD) and knowledge representation (KR) in pharmacogenomics, where knowledge units represent...
|
PMID: 21431576
PDF is available here.
PDF is available here.
Clinical calcium (21)6 2011
Abstract
We created a whole-mount in situ hybridization (WISH) database, containing expression data of transcription factors, cofactors and microRNA expressed in mouse embryos a highly dynamic stage of skeletogenesis. Our approach, WISH provided us new regulators as a critical effector in a myogenic feedback...
|
PMID: 21628797
PDF is available here.
PDF is available here.
Abstract
We present Mayday SeaSight, an extension that allows to integrate data from different platforms such as deep sequencing and microarrays. It offers methods for computing expression values from mapped reads and raw microarray data, background correction and normalization and linking microarray probes...
|
PMID: 21305015
PDF is available here.
PDF is available here.
Abstract
We tested whether these CNVs were more likely to be functional than frequency-matched SNPs as trait-associated loci or as expression quantitative trait loci (eQTLs) influencing phenotype by altering gene regulation. Our study found that CNV-tagging SNPs are significantly enriched for cis eQTLs; furt...
|
PMID: 21304891
PDF is available here.
PDF is available here.
Abstract
We analyze the robustness issue existing in feature selection for high-dimensional and small-sized gene-expression data, and propose to improve robustness of feature selection algorithm by using multiple feature selection evaluation criteria. Based on this idea, a multicriterion fusion-based recursi...
|
PMID: 21566255
PDF is available here.
PDF is available here.
Abstract
We find unexpected selection pressure much further upstream, up to 200 nucleotides (nts), from the PAS than previously thought. Strikingly, close to 3,000 long (30-500 nts) non-coding conserved fragments (CFs) were discovered in the PAS-flanking region of three remotely related mammalian species, hu...
|
PMID: 21705472
PDF is available here.
PDF is available here.
Abstract
We provide an overview of strategies for target identification, and present examples of selected drug targets, ranging from proteins to nucleic acids to intermediary metabolism....
|
PMID: 21619514
PDF is available here.
PDF is available here.
Abstract
To evaluate the accuracy of the sub-classification of renal cortical neoplasms using molecular signatures.
|
PMID: 21818257
PDF is available here.
PDF is available here.
Abstract
We address these issues by studying five populations: the popular Sprague-Dawley strain, sub-strains of Long-Evans and Wistar rats, and two lines derived from crosses between the Long-Evans and Wistar sub-strains. Using three independent techniques - variance analysis, linear modelling, and unsuperv...
|
PMID: 21760882
PDF is available here.
PDF is available here.
Abstract
Abstract
To date, nine Parkinson disease (PD) genome-wide association studies in North American, European and Asian populations have been published. The majority of studies have confirmed the association of the previously identified genetic risk factors, SNCA and MAPT, and two studies have identified three ne...
|
PMID: 21812969
PDF is available here.
PDF is available here.
Abstract
Mahalanobis class separability measure provides an effective evaluation of the discriminative power of a feature subset, and is widely used in feature selection. However, this measure is computationally intensive or even prohibitive when it is applied to gene expression data. In this...
|
PMID: 20479500
PDF is available here.
PDF is available here.
Abstract
Expression quantitative trait loci (eQTL) studies have helped identify the genetic determinants of gene expression. Understanding the potential interacting mechanisms underlying such findings, however, is challenging.
|
PMID: 21226949
PDF is available here.
PDF is available here.
Abstract
We performed chromatin immunoprecipitation-sequencing and gene expression analysis. We identified 1153 ChREBP binding sites and 783 target genes using the chromatin from HepG2, a human hepatocellular carcinoma cell line. A motif search revealed a refined consensus sequence (CABGTG-nnCnG-nGnSTG) to b...
|
PMID: 21811631
PDF is available here.
PDF is available here.
Abstract
Human biobanks, and genetic research databases, as referred to by the Organisation for Economic Co-operation and Development (OECD), are essential tools for modern biomedical research. Biobanks may consist in collections created in clinical diagnosis (such as pathology tissue samples in hospitals) o...
|
PMID: 20949382
PDF is available here.
PDF is available here.
BMC Systems Biology (5)Suppl 1 2011
Abstract
Hypoxia-inducible factors (HIFs) are transcription factors that play a crucial role in response to hypoxic stress in living organisms. The HIF pathway is activated by changes in cellular oxygen levels and has significant impacts on the regulation of gene expression patterns in cancer...
|
PMID: 21689478
PDF is available here.
PDF is available here.
Comptes Rendus Biologies (334)8-9 2011
Abstract
This short article presents an overview of tandem gene arrays (TGAs) in hemiascomycete yeasts. In silico and in vivo analyses are combined to address structural, functional and evolutionary aspects of these particular chromosomal structures. Genomic instability of TGAs is discussed....
|
PMID: 21819945
PDF is available here.
PDF is available here.
Abstract
We propose an imputation scheme based on nonlinear dependencies between genes. By simulations based on real microarray data, we show that incorporating nonlinear relationships could improve the accuracy of missing value imputation, both in terms of normalized root-mean-squared error and in terms of...
|
PMID: 20733236
PDF is available here.
PDF is available here.
Comptes Rendus Biologies (334)8-9 2011
Abstract
We report the early phase of yeast comparative genomics conducted by a group of seven French CNRS laboratories: the Génolevures Consortium. This first multispecies comparison of Hemiascomycetes (now called Saccharomycotina) opened the way to yeast evolutionary genomics. This analysis indicates that...
|
PMID: 21819937
PDF is available here.
PDF is available here.
Comptes Rendus Biologies (334)8-9 2011
Abstract
The Génolevures online database (URL: http://www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several campaigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedic...
|
PMID: 21819938
PDF is available here.
PDF is available here.
Comptes Rendus Biologies (334)8-9 2011
Abstract
We took advantage of this plethora of data to compile and assess the intron content of the protein-coding genes of 13 genomes representative of the evolution of hemiascomycetous yeasts. We first observed that intron paucity is a general rule and that the fastest evolving genomes tend to lose their i...
|
PMID: 21819948
PDF is available here.
PDF is available here.
Comptes Rendus Biologies (334)8-9 2011
Abstract
We describe the assembly of two automatic annotation pipelines, integrating publicly available tools, for homology and de novo ncRNA search in genomes. We applied both pipelines to 10 Saccharomycotina genomes and were able to find and annotate 693 ncRNA genes, corresponding to 81% of the ncRNAs expe...
|
PMID: 21819949
PDF is available here.
PDF is available here.
Biology Direct (6) 2011
Abstract
We review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. PROPOSAL: The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. T...
|
PMID: 21303550
PDF is available here.
PDF is available here.
BMC Immunology (12)1 2011
Abstract
We need to characterise the immune system of our distant relatives, the marsupials and monotremes. The recent sequencing of the genomes of two marsupials (opossum and tammar wallaby) and a monotreme (platypus) provides an opportunity to characterise the immune gene repertoires of these model organis...
|
PMID: 21854560
PDF is available here.
PDF is available here.