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1.
Sarah D Kocher Cai Li Wei Yang Hao Tan Soojin V Yi Xingyu Yang Hopi E Hoekstra Guojie Zhang Naomi E Pierce Douglas W Yu 《Genome biology》2015,16(1)
During the type-setting of the final version of the article [1] some of the additional files were swapped, and several were completely replaced. The correct files are republished in this Erratum.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0574-0) contains supplementary material, which is available to authorized users. 相似文献2.
Andrew Schoenrock Bahram Samanfar Sylvain Pitre Mohsen Hooshyar Ke Jin Charles A Phillips Hui Wang Sadhna Phanse Katayoun Omidi Yuan Gui Md Alamgir Alex Wong Fredrik Barren?s Mohan Babu Mikael Benson Michael A Langston James R Green Frank Dehne Ashkan Golshani 《BMC bioinformatics》2014,15(1)
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 within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments.Conclusions
The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0383-1) contains supplementary material, which is available to authorized users. 相似文献3.
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A 31 year old man was referred for the evaluation of chest pain. Cardiac CT reconstruction revealed multiple calcified giant coronary aneurysms. Most likely this patient suffered from subclinical Kawasaki’s disease in his childhood.
Electronic supplementary material
The online version of this article (doi:10.1007/s12471-011-0150-0) contains supplementary material, which is available to authorized users. 相似文献5.
Introduction
Slipped capital femoral epiphysis is the most common hip disorder affecting the adolescent population, usually individuals between 8 and 15 years old. However, there are few case reports of older patients in the literature to date. It is believed that the etiology is multifactorial and may include obesity, trauma and, less frequently, endocrine pathologies comprising hypothyroidism, hypogonadism and panhypopituitarism.Case presentation
We present the case of a 28-year-old Latino woman diagnosed with hypothyroidism secondary to arachnoidocele associated with skeletal immaturity and slipped capital femoral epiphysis.Conclusions
It is important to conduct clinical and radiographic studies in these patients to rule out endocrine pathologies, especially hypothyroidism in those of sexual maturity.Electronic supplementary material
The online version of this article (doi:10.1186/1752-1947-8-336) contains supplementary material, which is available to authorized users. 相似文献6.
Vilson Mirdita Guozheng Liu Yusheng Zhao Thomas Miedaner C. Friedrich H. Longin Manje Gowda Michael Florian Mette Jochen C. Reif 《BMC genomics》2015,16(1)
Background
Fusarium head blight (FHB) and Septoria tritici blotch (STB) severely impair wheat production. With the aim to further elucidate the genetic architecture underlying FHB and STB resistance, we phenotyped 1604 European wheat hybrids and their 135 parental lines for FHB and STB disease severities and determined genotypes at 17,372 single-nucleotide polymorphic loci.Results
Cross-validated association mapping revealed the absence of large effect QTL for both traits. Genomic selection showed a three times higher prediction accuracy for FHB than STB disease severity for test sets largely unrelated to the training sets.Conclusions
Our findings suggest that the genetic architecture is less complex and, hence, can be more properly tackled to perform accurate prediction for FHB than STB disease severity. Consequently, FHB disease severity is an interesting model trait to fine-tune genomic selection models exploiting beyond relatedness also knowledge of the genetic architecture.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1628-8) contains supplementary material, which is available to authorized users. 相似文献7.
Background
Scanning force microscopy (SFM) allows direct, rapid and high-resolution visualization of single molecular complexes; irregular shapes and differences in sizes are immediately revealed by the scanning tip in three-dimensional images. However, high-throughput analysis of SFM data is limited by the lack of versatile software tools accessible to SFM users. Most existing SFM software tools are aimed at broad general use: from material-surface analysis to visualization of biomolecules.Results
We present SFMetrics as a metrology toolbox for SFM, specifically aimed at biomolecules like DNA and proteins, which features (a) semi-automatic high-throughput analysis of individual molecules; (b) ease of use working within MATLAB environment or as a stand-alone application; (c) compatibility with MultiMode (Bruker), NanoWizard (JPK instruments), Asylum (Asylum research), ASCII, and TIFF files, that can be adjusted with minor modifications to other formats.Conclusion
Assembled in a single user interface, SFMetrics serves as a semi-automatic analysis tool capable of measuring several geometrical properties (length, volume and angles) from DNA and protein complexes, but is also applicable to other samples with irregular shapes.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0457-8) contains supplementary material, which is available to authorized users. 相似文献8.
Background
The power of the genome wide association studies starts to go down when the minor allele frequency (MAF) is below 0.05. Here, we proposed the use of Cohen’s h in detecting disease associated rare variants. The variance stabilizing effect based on the arcsine square root transformation of MAFs to generate Cohen’s h contributed to the statistical power for rare variants analysis. We re-analyzed published datasets, one microarray and one sequencing based, and used simulation to compare the performance of Cohen’s h with the risk difference (RD) and odds ratio (OR).Results
The analysis showed that the type 1 error rate of Cohen’s h was as expected and Cohen’s h and RD were both less biased and had higher power than OR. The advantage of Cohen’s h was more obvious when MAF was less than 0.01.Conclusions
Cohen’s h can increase the power to find genetic association of rare variants and diseases, especially when MAF is less than 0.01.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-875) contains supplementary material, which is available to authorized users. 相似文献9.
Background
Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions.Results
A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing genetic association studies. Demonstrations on synthetic and real data reveal they are able to efficiently and accurately determine which variants are involved in determining case-control status. By using graphics processing units (GPUs) the time needed to build these models is decreased by several orders of magnitude. In comparison with commonly used approaches for detecting interactions, Bayesian neural networks perform very well across a broad spectrum of possible genetic relationships.Conclusions
The proposed framework is shown to be a powerful method for detecting causal SNPs while being computationally efficient enough to handle large datasets.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0368-0) contains supplementary material, which is available to authorized users. 相似文献10.
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Background
Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female.Results
The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant.Conclusions
Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-377) contains supplementary material, which is available to authorized users. 相似文献13.
Jonah D. Hocum Logan R. Battrell Ryan Maynard Jennifer E. Adair Brian C. Beard David J. Rawlings Hans-Peter Kiem Daniel G. Miller Grant D. Trobridge 《BMC bioinformatics》2015,16(1)
Background
Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens.Results
We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads.Conclusions
VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0653-6) contains supplementary material, which is available to authorized users. 相似文献14.
Lloyd T Lam Haichao Zhang John Xue Joel D Leverson Anahita Bhathena 《Cancer cell international》2015,15(1)
Background
Evasion of apoptosis is a hallmark of cancer cells. One mechanism to deregulate the apoptotic pathway is by upregulation of the anti-apoptotic Bcl-2 family members. Navitoclax (ABT-263) is a Bcl-2/Bcl-xL inhibitor that restores the ability of cancer cells to undergo apoptosis.Methods
In this study we performed a high-throughput screen with 640 FDA-approved drugs to identify potential therapeutic combinations with navitoclax in a non-small cell lung cancer (NSCLC) cell line.Results
Other than a panel of cancer compounds such as doxorubicin, camptothecin, and docetaxel, four antihelminthic compounds (benzimidazoles) potentiated navitoclax activity. Treatment with benzimidazoles led to induction of the pro-apoptotic protein Noxa at the mRNA and protein level. Noxa binds and antagonizes antiapoptotic protein Mcl-1. siRNA-mediated knock-down of Noxa completely rescued benzimidazole-potentiated navitoclax activity. In addition, inhibiting caspase 3 and 9 partially rescued benzimidazole-potentiated navitoclax activity.Conclusions
We have identified compounds and mechanisms which potentiate navitoclax activity in lung cancer cell lines. Further validation of the benzimidazole-potentiated navitoclax effect in vivo is required to evaluate the potential for translating this observation into clinical benefit.Electronic supplementary material
The online version of this article (doi:10.1186/s12935-014-0151-3) contains supplementary material, which is available to authorized users. 相似文献15.
E.M. Zwaan A.G.M.M. Koopman C.A.J. Holtzer F. Zijlstra M.J.P.F. Ritt G. Amoroso E. Moerman M.J.M. Kofflard A.A.J. IJsselmuiden 《Netherlands heart journal》2015,23(11):514-524
Objectives
Little is known about local access-site complications and upper extremity dysfunction after transradial percutaneous coronary procedures (TR-PCP). This systematic review study aimed to summarise the current knowledge on the incidences of access-site complications and upper extremity dysfunction after TR-PCP.Methods
Two independent, trained investigators searched MEDLINE, EMBASE and CENTRAL for eligible studies published before 1 January 2015. Also, they hand-searched the conference proceedings of the annual scientific sessions of the American College of Cardiology, the American Heart Association, European Society of Cardiology, and the Trans-catheter Cardiovascular Therapeutics. Inclusion criteria were cohort studies and clinical trials discussing the incidence of access-site complications and upper extremity function after transradial percutaneous coronary intervention (TR-PCI) and/or transradial coronary angiography (TR-CAG) as endpoints.Results
176 articles described access-site complications. The incidence is up to 9.6 %. Fourteen articles described upper extremity dysfunction, with an incidence of up to 1.7 %. Upper extremity dysfunction was rarely investigated, hardly ever as primary endpoint, and if investigated not thoroughly enough.Conclusion
Upper extremity dysfunction in TR-PCP has never been properly investigated and is therefore underestimated. Further studies are needed to investigate the magnitude, prevention and best treatment of upper extremity dysfunction. Optimising TR-PCP might be achieved by using slender techniques, detection of upper extremity dysfunction and early referral to a hand rehabilitation centre.Electronic supplementary material
The online version of this article (doi: 10.1007/s12471-015-0747-9) contains supplementary material, which is available to authorized users. This supplementary file contains References 51–202. 相似文献16.
Zhongxue Chen 《BMC genomics》2014,15(1)
Background
Current robust association tests for case–control genome-wide association study (GWAS) data are mainly based on the assumption of some specific genetic models. Due to the richness of the genetic models, this assumption may not be appropriate. Therefore, robust but powerful association approaches are desirable.Results
In this paper, we propose a new approach to testing for the association between the genotype and phenotype for case–control GWAS. This method assumes a generalized genetic model and is based on the selected disease allele to obtain a p-value from the more powerful one-sided test. Through a comprehensive simulation study we assess the performance of the new test by comparing it with existing methods. Some real data applications are also used to illustrate the use of the proposed test.Conclusions
Based on the simulation results and real data application, the proposed test is powerful and robust.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-358) contains supplementary material, which is available to authorized users. 相似文献17.
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Javiera Ortiz-Severín Macarena Varas Catalina Bravo-Toncio Nicolás Guiliani Francisco P Chávez 《Biological research》2015,48(1)
Background
Pseudomonas aeruginosa is known to be a multidrug resistant opportunistic pathogen. Particularly, P. aeruginosa PAO1 polyphosphate kinase mutant (ppk1) is deficient in motility, quorum sensing, biofilm formation and virulence.Findings
By using Phenotypic Microarrays (PM) we analyzed near 2000 phenotypes of P. aeruginosa PAO1 polyP kinase mutants (ppk1 and ppk2). We found that both ppk mutants shared most of the phenotypic changes and interestingly many of them related to susceptibility toward numerous and different type of antibiotics such as Ciprofloxacin, Chloramphenicol and Rifampicin.Conclusions
Combining the fact that ppk1 mutants have reduced virulence and are more susceptible to antibiotics, polyP synthesis and particularly PPK1, is a good target for the design of molecules with anti-virulence and anti-persistence properties.Electronic supplementary material
The online version of this article (doi:10.1186/s40659-015-0012-0) contains supplementary material, which is available to authorized users. 相似文献19.
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Andrew Higham George Booth Simon Lea Thomas Southworth Jonathan Plumb Dave Singh 《Respiratory research》2015,16(1)