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CUBIC: IDENTIFICATION OF REGULATORY BINDING SITES THROUGH DATA CLUSTERING

VICTOR OLMAN, DONG XU, YING XU
2003 Journal of Bioinformatics and Computational Biology  
We have implemented the cluster identification algorithm and the statistical significance analysis method as a computer software CUBIC. Extensive testing on CUBIC has been carried out.  ...  We have also developed a method for assessing the statistical significance of each identified cluster, which can be used to rule out accidental data clusters.  ...  We have implemented the cluster identification algorithm and the statistical significance analysis method as a computer software CUBIC. Extensive testing on CUBIC has been carried out.  ... 
doi:10.1142/s0219720003000162 pmid:15290780 fatcat:euzdxrpdungqfhsv2dj74mrin4

Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans

T. Marques-Bonet, O. Lao, R. Goertsches, M. Comabella, X. Montalban, A. Navarro
2005 Bioinformatics  
Here we present Association Cluster Detector (ACD), a simple tool aiming to ease the analysis of the results of whole genome scans.  ...  ACD facilitates correction for multiple tests using several standard procedures and implements a sliding-window heuristic method that helps in detecting potentially interesting candidate regions by exploiting  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bti1118 pmid:16204099 fatcat:cu6lkkqrnngvzg642hl7epbgne

Rigorous evaluations of evolving interventions: can we have our cake and eat it too?

Robert E Burke, Kaveh G Shojania
2018 BMJ Quality and Safety  
(about as rigorous a non-randomised design as possible) and the other a cluster RCT.  ...  Westbrook et al are not alone in struggling with this issue, which is surprisingly common among multicomponent QI interventions that are subsequently tested in large cluster RCTs. 26 Adaptive study designs  ... 
doi:10.1136/bmjqs-2017-007554 pmid:29440483 fatcat:tbtyswj74rc63ozfhnhcnwzux4

An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors

Peyman Jafari, Francisco Azuaje
2006 BMC Medical Informatics and Decision Making  
Clustering-based analysis, the t-test and ANOVA represent the most widely applied techniques in microarray data analysis.  ...  There is a need for more rigorous reporting of important experimental factors such as statistical power and sample size, as well as the correct description and justification of statistical methods applied  ...  Acknowledgements This study was conducted while PJ was a visiting researcher at the School of Computing and Mathematics, University of Ulster (UU).  ... 
doi:10.1186/1472-6947-6-27 pmid:16790051 pmcid:PMC1523197 fatcat:6bqrluwqubco7ljh27q7ioihrq

Discovering the Unexpected & Explicable: Scientific Reasoning and Research Design for Spatial Data Analysis

Julia Koschinsky
2020 Abstracts of the International Cartographic Association  
This requires a mindset and practice of rigorously testing how our explanations might be wrong (Popper, 1959) rather than confirming that they're right (Nuzzo, 2015; Kahneman, 2011).  ...  Methods for exploratory data analysis and exploratory spatial data analysis (or ESDA) are useful to identify outliers, clusters, skewed distributions and correlations (see Figure 1 for examples implemented  ...  Acknowledgements The contributions of Marcos Falcon, R.E. Stern, Atman Mehta, Mark Baker, Jizhou Wang, Felix Farb. Luc Anselin, Thomas Coleman, and Peter-Vinten Johansen are gratefully acknowledged.  ... 
doi:10.5194/ica-abs-2-11-2020 fatcat:jj6mfyi3bjaivhqjknj2isxrga

Statistically rigorous automated protein annotation

W. G. Krebs, P. E. Bourne
2004 Bioinformatics  
The number and statistical significance of these assignments remains a challenge in this era of high-throughput proteomics.  ...  Availability: PDB annotations and sample software implementation are freely accessible on the Web at  ...  National Science Foundation (NSF) National Partnership for Advanced Computational Infrastructure (NPACI) and the U.S NSF Division of Biological Infrastructure grant DBI 0111710.  ... 
doi:10.1093/bioinformatics/bth039 pmid:14764575 fatcat:qioask3quvcypgyb3zowiduzsy

Implementation errors in the GingerALE Software: Description and recommendations

Simon B. Eickhoff, Angela R. Laird, P. Mickle Fox, Jack L. Lancaster, Peter T. Fox
2016 Human Brain Mapping  
In both primary data and meta-analytic neuroimaging analyses, correction for multiple comparisons is a complex but critical step for ensuring statistical rigor.  ...  These errors have given rise to published reports with more liberal statistical inferences than were specified by the authors. The intent of this technical report is threefold.  ...  Acknowledgments The authors acknowledge funding from the US National Institute of Mental Health (RO1-MH074457 to PTF), the Helmholtz Portfolio Theme "Supercomputing and Modelling for the Human Brain" and  ... 
doi:10.1002/hbm.23342 pmid:27511454 pmcid:PMC5323082 fatcat:5oyx2yylrfgbzoopopinecp53y

Evaluation of Systems-Oriented Public Health Interventions: Alternative Research Designs

Robert W. Sanson-Fisher, Catherine A. D'Este, Mariko L. Carey, Natasha Noble, Christine L. Paul
2014 Annual Review of Public Health  
Keywords cluster randomized controlled trial, stepped wedge design, interrupted time series, multiple baseline design, controlled prepost design Abstract The need to provide sound evidence of the costs  ...  A range of alternatives to the individual randomized controlled trial (RCT) can be used for evaluating such interventions, including the cluster RCT, stepped wedge design, interrupted time series, multiple  ...  Bernstein p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 153 Mental Health Consequences of Disasters  ... 
doi:10.1146/annurev-publhealth-032013-182445 pmid:24387088 fatcat:kkhifyecw5hlff4zkkn6alyeue

Effectiveness-implementation hybrid designs: implications for quality improvement science

Alice C Bernet, David E Willens, Mark S Bauer
2013 Implementation Science  
Type 2 hybrid designs simultaneously test the clinical intervention, while rigorously testing the implementation strategy.  ...  Type 1 hybrid designs rigorously test the clinical intervention and secondarily gather data to inform subsequent implementation research trials.  ... 
doi:10.1186/1748-5908-8-s1-s2 pmcid:PMC3633015 fatcat:ojrr5pjyvjgejmt3evw6a3rdo4

Outpatient Electronic Health Records and the Clinical Care and Outcomes of Patients With Diabetes Mellitus

Mary Reed, Jie Huang, Ilana Graetz, Richard Brand, John Hsu, Bruce Fireman, Marc Jaffe
2012 Annals of Internal Medicine  
Objective-To examine the association between use of a commercially available certified EHR and clinical care processes and disease control in patients with diabetes.  ...  Background-Physicians can receive federal payments for meaningful use of complete certified electronic health records (EHRs). Evidence is limited on how EHR use affects clinical care and outcomes.  ...  Acknowledgments Role of the Funding Source This study was funded by the National Institute of Diabetes and Digestive and Kidney Diseases.  ... 
doi:10.7326/0003-4819-157-7-201210020-00004 pmid:23027319 pmcid:PMC3603566 fatcat:telqymfhzrh3viodj6fttskz2y

Parallel kinetic Monte Carlo simulation of Al 3 Sc precipitation

Alfredo Moura, António Esteves
2017 Ciencia e Tecnologia dos Materiais  
The ultimate validity test for any parallel kMC algorithm is that it solves the same master equation as the sequential method rigorously.  ...  nucleation rate, and cluster size distribution.  ...  Density Based Spatial Clustering of Applications with Noise (DBSCAN) technique [M.  ... 
doi:10.1016/j.ctmat.2016.01.003 fatcat:a4ppjgnx2zfdhodobzhsa4l3jy

Impact of a multifaceted program to prevent postoperative delirium in the elderly: the CONFUCIUS stepped wedge protocol

Christelle Mouchoux, Pascal Rippert, Antoine Duclos, Thomas Fassier, Marc Bonnefoy, Brigitte Comte, Damien Heitz, Cyrille Colin, Pierre Krolak-Salmon
2011 BMC Geriatrics  
Method/Design: Study design is a stepped wedge cluster randomized trial within 3 surgical wards of three French university hospitals.  ...  Endpoints comparison between intervention and control arms of the trial will be performed by considering the cluster and time effects.  ...  Statistical analysis Univariate analyses using Student's test or non-parametric tests (quantitative data) and Khi 2 test or Fisher's exact test (qualitative data) will be performed to describe population  ... 
doi:10.1186/1471-2318-11-25 pmid:21592324 pmcid:PMC3111354 fatcat:h3uptzzua5b53e7zwhn5jxxpve

Spatiotemporal pattern of COVID-19 and government response in South Korea (as of May 31, 2020)

Sun Kim, Marcia C. Castro
2020 International Journal of Infectious Diseases  
Global Moran's I statistic was used for spatial autocorrelation analysis and retrospective space-time scan statistic was used to analyze spatiotemporal clusters of COVID-19.  ...  The spatial pattern of clusters changed and the duration of clusters became shorter over time.  ...  Conflict of interest The authors declare no conflicts of interest.  ... 
doi:10.1016/j.ijid.2020.07.004 pmid:32634584 pmcid:PMC7334954 fatcat:onnxclani5caxnifemry7xqh3y

Comparison of two survey methodologies to assess vaccination coverage

E. T Luman, A. Worku, Y. Berhane, R. Martin, L. Cairns
2007 International Journal of Epidemiology  
Chi-square tests were used to compare results from the two methodologies; relative feasibility of the sampling methodologies was assessed.  ...  Methods Thirty clusters were selected from an urban (Ambo) and a rural (Yaya-Gulelena D/Libanos) district of Ethiopia; vaccination coverage surveys were conducted using both EPI sampling and systematic  ...  Statistically rigorous sampling methodology can be used to obtain the precise and unbiased estimates of vaccination coverage needed as countries move towards elimination goals.  ... 
doi:10.1093/ije/dym025 pmid:17420165 fatcat:q3idvppsxvhapoi6f56x5e3ptq

The CRASSS plug-in for integrating annotation data with hierarchical clustering results

E. C. Buehler, J. R. Sachs, K. Shao, A. Bagchi, L. H. Ungar
2004 Bioinformatics  
We describe an algorithm for finding the most statistically significant non-overlapping subtrees of a hierarchical clustering of gene expression data with respect to a set of secondary data labels on genes  ...  The method is implemented as a Java plug-in for a commercial gene expression analysis program (GeneSpring).  ...  of Affymetrix data.  ... 
doi:10.1093/bioinformatics/bth362 pmid:15201188 fatcat:biyg5hg6pffzdjv3wo7huu4lp4
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