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https://www.readbyqxmd.com/read/27312410/argon-fast-whole-genome-simulation-of-the-discrete-time-wright-fisher-process
#1
Pier Francesco Palamara
MOTIVATION: Simulation under the coalescent model is ubiquitous in the analysis of genetic data. The rapid growth of real data sets from multiple human populations led to increasing interest in simulating very large sample sizes at whole-chromosome scales. When the sample size is large, the coalescent model becomes an increasingly inaccurate approximation of the discrete time Wright-Fisher model (DTWF). Analytical and computational treatment of the DTWF, however, is generally harder. RESULTS: We present a simulator (ARGON) for the DTWF process that scales up to hundreds of thousands of samples and whole-chromosome lengths, with a time/memory performance comparable or superior to currently available methods for coalescent simulation...
October 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26449931/cpgfilter-model-based-cpg-probe-filtering-with-replicates-for-epigenome-wide-association-studies
#2
Jun Chen, Allan C Just, Joel Schwartz, Lifang Hou, Nadereh Jafari, Zhifu Sun, Jean-Pierre A Kocher, Andrea Baccarelli, Xihong Lin
SUMMARY: The development of the Infinium HumanMethylation450 BeadChip enables epigenome-wide association studies at a reduced cost. One observation of the 450K data is that many CpG sites the beadchip interrogates have very large measurement errors. Including these noisy CpGs will decrease the statistical power of detecting relevant associations due to multiple testing correction. We propose to use intra-class correlation coefficient (ICC), which characterizes the relative contribution of the biological variability to the total variability, to filter CpGs when technical replicates are available...
February 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/25706019/public-health-101-nanocourse-a-condensed-educational-tool-for-non-public-health-professionals
#3
Cherie L Ramirez, Zofia K Z Gajdos, Catherine Kreatsoulas, Myriam C Afeiche, Morteza Asgarzadeh, Candace C Nelson, Usheer Kanjee, Alberto J Caban-Martinez
Graduate students and postdoctoral fellows-including those at the Harvard School of Public Health (HSPH)-have somewhat limited opportunities outside of traditional coursework to learn holistically about public health. Because this lack of familiarity could be a barrier to fruitful collaboration across disciplines, HSPH postdocs sought to address this challenge. In response, the Public Health 101 Nanocourse was developed to provide an overview of five core areas of public health (biostatistics, environmental health sciences, epidemiology, health policy and management, and social and behavioral sciences) in a two half-day course format...
March 2015: American Journal of Public Health
https://www.readbyqxmd.com/read/25519381/a-comparative-analysis-of-family-based-and-population-based-association-tests-using-whole-genome-sequence-data
#4
Jin J Zhou, Wai-Ki Yip, Michael H Cho, Dandi Qiao, Merry-Lynn N McDonald, Nan M Laird
The revolution in next-generation sequencing has made obtaining both common and rare high-quality sequence variants across the entire genome feasible. Because researchers are now faced with the analytical challenges of handling a massive amount of genetic variant information from sequencing studies, numerous methods have been developed to assess the impact of both common and rare variants on disease traits. In this report, whole genome sequencing data from Genetic Analysis Workshop 18 was used to compare the power of several methods, considering both family-based and population-based designs, to detect association with variants in the MAP4 gene region and on chromosome 3 with blood pressure...
2014: BMC Proceedings
https://www.readbyqxmd.com/read/25426672/au99-sph-42-nanomolecules-aromatic-thiolate-ligand-induced-conversion-of-au144-sch2ch2ph-60
#5
Praneeth Reddy Nimmala, Amala Dass
A new aromatic thiolate protected gold nanomolecule Au99(SPh)42 has been synthesized by reacting the highly stable Au144(SCH2CH2Ph)60 with thiophenol, HSPh. The ubiquitous Au144(SR)60 is known for its high stability even at elevated temperature and in the presence of excess thiol. This report demonstrates for the first time the reactivity of the Au144(SCH2CH2Ph)60 with thiophenol to form a different 99-Au atom species. The resulting Au99(SPh)42 compound, however, is unreactive and highly stable in the presence of excess aromatic thiol...
December 10, 2014: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/25252224/interlab-comparison-of-elemental-analysis-for-low-ambient-urban-pm2-5-levels
#6
COMPARATIVE STUDY
Choong-Min Kang, Souzana Achilleos, Joy Lawrence, Jack M Wolfson, Petros Koutrakis
There is growing concern about the accuracy of trace elemental analysis of ambient particulate matter (PM) samples. This has become important because ambient PM concentrations have decreased over the years, and the lower filter loadings result in difficulties in accurate analysis. The performance of energy-dispersive X-ray reflectance spectrometry was evaluated at Harvard School of Public Health using several methodologies, including intercomparison between two other laboratories. In reanalysis of standard films as unknown samples following calibration, the HSPH ED XRF measurements represented good performance: 2% errors in precision and 4% errors in accuracy...
October 21, 2014: Environmental Science & Technology
https://www.readbyqxmd.com/read/24990607/fast-and-accurate-imputation-of-summary-statistics-enhances-evidence-of-functional-enrichment
#7
Bogdan Pasaniuc, Noah Zaitlen, Huwenbo Shi, Gaurav Bhatia, Alexander Gusev, Joseph Pickrell, Joel Hirschhorn, David P Strachan, Nick Patterson, Alkes L Price
MOTIVATION: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. RESULTS: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1-5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics...
October 15, 2014: Bioinformatics
https://www.readbyqxmd.com/read/24596661/hospitals-safety-from-disasters-in-i-r-iran-the-results-from-assessment-of-224-hospitals
#8
Ali Ardalan, Maryam Kandi, Mohammad Taghi Talebian, Hamidreza Khankeh, Gholamreza Masoumi, Reza Mohammadi, Samaneh Maleknia, Jafar Miadfar, Atieh Mobini, Sara Mehranamin
BACKGROUND AND OBJECTIVE: Iran's hospitals have been considerably affected by disasters during last decade. To address this, health system of I.R.Iran has taken an initiative to assess disaster safety of the hospitals using an adopted version of Hospital Safety Index (HSI). This article presents the results of disaster safety assessment in 224 Iran's hospitals. METHODS: A self-assessment approach was applied to assess the disaster safety in 145 items categorized in 3 components including structural, non-structural and functional capacity...
2014: PLoS Currents
https://www.readbyqxmd.com/read/23990415/a-clustering-a-novel-method-for-the-detection-of-co-regulated-methylation-regions-and-regions-associated-with-exposure
#9
Tamar Sofer, Elizabeth D Schifano, Jane A Hoppin, Lifang Hou, Andrea A Baccarelli
MOTIVATION: DNA methylation is a heritable modifiable chemical process that affects gene transcription and is associated with other molecular markers (e.g. gene expression) and biomarkers (e.g. cancer or other diseases). Current technology measures methylation in hundred of thousands, or millions of CpG sites throughout the genome. It is evident that neighboring CpG sites are often highly correlated with each other, and current literature suggests that clusters of adjacent CpG sites are co-regulated...
November 15, 2013: Bioinformatics
https://www.readbyqxmd.com/read/23904097/dnajb6-is-a-peptide-binding-chaperone-which-can-suppress-amyloid-fibrillation-of-polyglutamine-peptides-at-substoichiometric-molar-ratios
#10
Cecilia Månsson, Vaishali Kakkar, Elodie Monsellier, Yannick Sourigues, Johan Härmark, Harm H Kampinga, Ronald Melki, Cecilia Emanuelsson
Expanded polyglutamine (polyQ) stretches lead to protein aggregation and severe neurodegenerative diseases. A highly efficient suppressor of polyQ aggregation was identified, the DNAJB6, when molecular chaperones from the HSPH, HSPA, and DNAJ families were screened for huntingtin exon 1 aggregation in cells (Hageman et al. in Mol Cell 37(3):355-369, 2010). Furthermore, also aggregation of polyQ peptides expressed in cells was recently found to be efficiently suppressed by co-expression of DNAJB6 (Gillis et al...
March 2014: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/23608769/the-chi-linh-health-and-demographic-surveillance-system-chililab-hdss
#11
Bich Huu Tran, Ha Thanh Nguyen, Hien Thi Ho, Cuong Viet Pham, Vui Thi Le, Anh Vu Le
The Chi Linh Health and Demographic Surveillance System (CHILILAB HDSS) is the only health and demographic surveillance system (HDSS) in an urbanizing area of the Chi Linh district of Hai Duong, a northern province of Vietnam. It is one of the few field laboratories in the world that links operational research and health interventions with field training. The CHILILAB HDSS provides longitudinal data on demographic and health indicators for the community of Chi Linh. In 2012, when the CHILILAB HDSS included 57,561 people from 17 993 households in 3 towns and 4 communes, it used structured questionnaires to collect information on population changes (birth, death, migration, marriage, and pregnancy) in the community...
June 2013: International Journal of Epidemiology
https://www.readbyqxmd.com/read/23539302/improved-ancestry-inference-using-weights-from-external-reference-panels
#12
Chia-Yen Chen, Samuela Pollack, David J Hunter, Joel N Hirschhorn, Peter Kraft, Alkes L Price
MOTIVATION: Inference of ancestry using genetic data is motivated by applications in genetic association studies, population genetics and personal genomics. Here, we provide methods and software for improved ancestry inference using genome-wide single nucleotide polymorphism (SNP) weights from external reference panels. This approach makes it possible to leverage the rich ancestry information that is available from large external reference panels, without the administrative and computational complexities of re-analyzing the raw genotype data from the reference panel in subsequent studies...
June 1, 2013: Bioinformatics
https://www.readbyqxmd.com/read/22989357/reactions-of-the-unsaturated-hydroxo-complex-w2cp2-oh-%C3%AE-pph2-2-co-bf4-with-mono-and-bidentate-ligands-having-e-h-bonds-e-o-s-n
#13
Fernanda Cimadevilla, M Esther García, Daniel García-Vivó, Miguel A Ruiz, Claudia Graiff, Antonio Tiripicchio
The title compound reacted with CO at room temperature in the presence of excess HBF(4)·OEt(2) to yield a mixture of the electron-precise complexes [W(2)Cp(2)(μ-PPh(2))(2)(CO)(4)](BF(4))(2) and [W(2)Cp(2)(μ-PPh(2))(2)(CO)(3)(OH(2))](BF(4))(2), with the aquo ligand in the latter complex being easily displaced by simple donors such as acetonitrile. Reaction of the title complex with simple acidic molecules such as HSPh or HBr took place rapidly with elimination of H(2)O to give the 32-electron cations [W(2)Cp(2)(Z)(μ-PPh(2))(2)(CO)](+) [Z = Br, SPh (W-W = 2...
October 1, 2012: Inorganic Chemistry
https://www.readbyqxmd.com/read/22800118/synthesis-and-the-thermal-and-catalytic-dehydrogenation-reactions-of-amine-thioboranes
#14
Alasdair P M Robertson, Mairi F Haddow, Ian Manners
A series of trimethylamine-thioborane adducts, Me(3)N·BH(2)SR (R = tBu [2a], nBu [2b], iPr [2c], Ph [2d], C(6)F(5) [2e]) have been prepared and characterized. Attempts to access secondary and primary amine adducts of thioboranes via amine-exchange reactions involving these species proved unsuccessful, with the thiolate moiety shown to be vulnerable to displacement by free amine. However, treatment of the arylthioboranes, [BH(2)-SPh](3) (9) and C(6)F(5)SBH(2)·SMe(2) (10) with Me(2)NH and iPr(2)NH successfully yielded the adducts Me(2)NH·BH(2)SR (R = Ph [11a], C(6)F(5) [12a]) and iPr(2)NH·BH(2)SR (R = Ph [11b], C(6)F(5) [12b]) in high yield...
August 6, 2012: Inorganic Chemistry
https://www.readbyqxmd.com/read/22715993/reactions-of-the-tetrafluoroborate-complex-mo2cp2-%C3%AE%C2%BA-2-f2bf2-%C3%AE-pph2-2-co-bf4-with-mono-and-bidentate-ligands-having-e-h-bonds-e-o-s-se-n-p
#15
Fernanda Cimadevilla, M Esther García, Daniel García-Vivó, Miguel A Ruiz, Claudia Graiff, Antonio Tiripicchio
The title compound reacted rapidly with CN(t)Bu at room temperature by displacing the BF(4)(-) ligand and incorporating three molecules of isocyanide to yield the electron-precise complex [Mo(2)Cp(2)(μ-PPh(2))(2)(CN(t)Bu)(3)(CO)](BF(4))(2), which was obtained as a mixture of cis and trans isomers. Reaction with several HER(n) molecules (HER(n) = HSPh, HSePh, H(2)PCy) took place with formal elimination of HBF(4) and spontaneous carbonylation to give the electron-precise cations [Mo(2)Cp(2)(μ-ER(n))(μ-PPh(2))(2)(CO)(2)](+)...
July 2, 2012: Inorganic Chemistry
https://www.readbyqxmd.com/read/22556366/analysis-of-case-control-association-studies-with-known-risk-variants
#16
Noah Zaitlen, Bogdan Pasaniuc, Nick Patterson, Samuela Pollack, Benjamin Voight, Leif Groop, David Altshuler, Brian E Henderson, Laurence N Kolonel, Loic Le Marchand, Kevin Waters, Christopher A Haiman, Barbara E Stranger, Emmanouil T Dermitzakis, Peter Kraft, Alkes L Price
MOTIVATION: The question of how to best use information from known associated variants when conducting disease association studies has yet to be answered. Some studies compute a marginal P-value for each Several Nucleotide Polymorphisms independently, ignoring previously discovered variants. Other studies include known variants as covariates in logistic regression, but a weakness of this standard conditioning strategy is that it does not account for disease prevalence and non-random ascertainment, which can induce a correlation structure between candidate variants and known associated variants even if the variants lie on different chromosomes...
July 1, 2012: Bioinformatics
https://www.readbyqxmd.com/read/22458912/report-on-emerging-technologies-for-translational-bioinformatics-a-symposium-on-gene-expression-profiling-for-archival-tissues
#17
Levi Waldron, Peter Simpson, Giovanni Parmigiani, Curtis Huttenhower
BACKGROUND: With over 20 million formalin-fixed, paraffin-embedded (FFPE) tissue samples archived each year in the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of cancer. Technologies have recently been introduced for whole-transcriptome amplification and microarray analysis of degraded mRNA fragments from FFPE samples, and studies of these platforms have only recently begun to enter the published literature. RESULTS: The Emerging Technologies for Translational Bioinformatics symposium on gene expression profiling for archival tissues featured presentations of two large-scale FFPE expression profiling studies (each involving over 1,000 samples), overviews of several smaller studies, and representatives from three leading companies in the field (Illumina, Affymetrix, and NuGEN)...
2012: BMC Cancer
https://www.readbyqxmd.com/read/22300306/oxido-bridged-di-tri-and-tetra-nuclear-iron-complexes-bearing-bis-trimethylsilyl-amide-and-thiolate-ligands
#18
Shun Ohta, Saori Yokozawa, Yasuhiro Ohki, Kazuyuki Tatsumi
A series of di-, tri-, and tetra-nuclear iron-oxido clusters with bis(trimethylsilyl)amide and thiolate ligands were synthesized from the reactions of Fe{N(SiMe(3))(2)}(2) (1) with 1 equiv of thiol HSR (R = C(6)H(5) (Ph), 4-(t)BuC(6)H(4), 2,6-Ph(2)C(6)H(3) (Dpp), 2,4,6-(i)Pr(3)C(6)H(2) (Tip)) and subsequent treatment with O(2). The trinuclear clusters [{(Me(3)Si)(2)N}Fe](3)(μ(3)-O){μ-S(4-RC(6)H(4))}(3) (R = H (3a), (t)Bu (3b)) were obtained from the reactions of 1 with HSPh or HS(4-(t)BuC(6)H(4)) and O(2), while we isolated a tetranuclear cluster [{(Me(3)Si)(2)N}(2)Fe(2)(μ-SDpp)](2)(μ(3)-O)(2) (4) as crystals from an analogous reaction with HSDpp...
February 20, 2012: Inorganic Chemistry
https://www.readbyqxmd.com/read/22156367/optimized-application-of-penalized-regression-methods-to-diverse-genomic-data
#19
Levi Waldron, Melania Pintilie, Ming-Sound Tsao, Frances A Shepherd, Curtis Huttenhower, Igor Jurisica
MOTIVATION: Penalized regression methods have been adopted widely for high-dimensional feature selection and prediction in many bioinformatic and biostatistical contexts. While their theoretical properties are well-understood, specific methodology for their optimal application to genomic data has not been determined. RESULTS: Through simulation of contrasting scenarios of correlated high-dimensional survival data, we compared the LASSO, Ridge and Elastic Net penalties for prediction and variable selection...
December 15, 2011: Bioinformatics
https://www.readbyqxmd.com/read/21752800/a-novel-signal-processing-approach-for-the-detection-of-copy-number-variations-in-the-human-genome
#20
Catherine Stamoulis, Rebecca A Betensky
MOTIVATION: Human genomic variability occurs at different scales, from single nucleotide polymorphisms (SNPs) to large DNA segments. Copy number variations (CNVs) represent a significant part of our genetic heterogeneity and have also been associated with many diseases and disorders. Short, localized CNVs, which may play an important role in human disease, may be undetectable in noisy genomic data. Therefore, robust methodologies are needed for their detection. Furthermore, for meaningful identification of pathological CNVs, estimation of normal allelic aberrations is necessary...
September 1, 2011: Bioinformatics
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