Abstract:
:Comparison of sequences that have descended from a common ancestor based on an explicit stochastic model of substitutions, insertions and deletions has risen to prominence in the last decade. Making statements about the positions of insertions-deletions (abbr. indels) is central in sequence and genome analysis and is called alignment. This statistical approach is harder conceptually and computationally, than competing approaches based on choosing an alignment according to some optimality criteria. But it has major practical advantages in terms of testing evolutionary hypotheses and parameter estimation. Basic dynamic approaches can allow the analysis of up to 4-5 sequences. MCMC techniques can bring this to about 10-15 sequences. Beyond this, different or heuristic approaches must be used. Besides the computational challenges, increasing realism in the underlying models is presently being addressed. A recent development that has been especially fruitful is combining statistical alignment with the problem of sequence annotation, making statements about the function of each nucleotide/amino acid. So far gene finding, protein secondary structure prediction and regulatory signal detection has been tackled within this framework. Much progress can be reported, but clearly major challenges remain if this approach is to be central in the analyses of large incoming sequence data sets.
journal_name
Stat Methods Med Resjournal_title
Statistical methods in medical researchauthors
Miklós I,Novák A,Satija R,Lyngsø R,Hein Jdoi
10.1177/0962280208099500subject
Has Abstractpub_date
2009-10-01 00:00:00pages
453-85issue
5eissn
0962-2802issn
1477-0334pii
0962280208099500journal_volume
18pub_type
杂志文章abstract::This article outlines the statistical developments that have taken place in the use of the EM algorithm in emission and transmission tomography during the past decade or so. We discuss the statistical aspects of the modelling of the projection data for both the emission and transmission cases and define the relevant p...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/096228029700600105
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abstract::Methods for the analysis of reliability of ordered categorical scales are discussed, focussing on the limitation of the single summary-weighted kappa coefficients. A symmetric matrix of kappa-type coefficients is suggested as an alternative. The method is proposed as being suitable for ordinal scale where there is no ...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1191/0962280205sm413oa
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abstract::We propose a flexible and computationally efficient penalized estimation method for a semi-parametric linear transformation model with current status data. To facilitate model fitting, the unknown monotone function is approximated by monotone B-splines, and a computationally efficient hybrid algorithm involving the Fi...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280218820406
更新日期:2020-01-01 00:00:00
abstract::Propensity score methods are common for estimating a binary treatment effect when treatment assignment is not randomized. When exposure is measured on an ordinal scale (i.e. low-medium-high), however, propensity score inference requires extensions which have received limited attention. Estimands of possible interest w...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280214560046
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abstract::Rapid Early Action for Coronary Treatment (REACT) was a multisite trial testing a community intervention to reduce the delay between onset of symptoms of acute myocardial infarction (MI) and patients' arrival at a hospital emergency department. The study employed a group-randomized trial design, with ten communities r...
journal_title:Statistical methods in medical research
pub_type: 临床试验,杂志文章,随机对照试验
doi:10.1177/096228020000900204
更新日期:2000-04-01 00:00:00
abstract::Improving the quality of care that patients receive is a major focus of clinical research, particularly in the setting of cardiovascular hospitalization. Quality improvement studies seek to estimate and visualize the degree of variability in dichotomous treatment patterns and outcomes across different providers, where...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280217754230
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abstract::The change-point model has drawn much attention over the past few decades. It can accommodate the jump process, which allows for changes of the effects before and after the change point. Intellectual disability is a long-term disability that impacts performance in cognitive aspects of life and usually has its onset pr...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280212463415
更新日期:2016-04-01 00:00:00
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journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/096228029700600305
更新日期:1997-09-01 00:00:00
abstract:BACKGROUND:When trials are subject to departures from randomised treatment, simple statistical methods that aim to estimate treatment efficacy, such as per protocol or as treated analyses, typically introduce selection bias. More appropriate methods to adjust for departure from randomised treatment are rarely employed,...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280217735560
更新日期:2019-03-01 00:00:00
abstract::Several epidemiological parameters have been introduced for quantifying the population impact of a certain exposure on morbidity on a population level, termed 'attributable risk' (AR). Of these definitions, the AR as suggested by Levin in 1953 or some algebraic transformations of it are most commonly used. A structure...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/096228020101000305
更新日期:2001-06-01 00:00:00
abstract::Ordinal classification scales are commonly used to define a patient's disease status in screening and diagnostic tests such as mammography. Challenges arise in agreement studies when evaluating the association between many raters' classifications of patients' disease or health status when an ordered categorical scale ...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280216643347
更新日期:2018-03-01 00:00:00
abstract::Non-parametric linkage analysis examines similarities among affected relatives in alleles of one or more genetic markers (pieces of DNA at known locations on a chromosome). The objective is to evaluate departures from the null hypothesis that the markers are not near a disease gene. Under the null hypothesis, Mendel's...
journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/096228020101000103
更新日期:2001-02-01 00:00:00
abstract::Nonlinear mixed-effects modeling is one of the most popular tools for analyzing repeated measurement data, particularly for applications in the biomedical fields. Multiple integration and nonlinear optimization are the two major challenges for likelihood-based methods in nonlinear mixed-effects modeling. To solve thes...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280220949898
更新日期:2020-08-24 00:00:00
abstract::Multilevel models were originally developed to allow linear regression or ANOVA models to be applied to observations that are not mutually independent. This lack of independence commonly arises due to clustering of the units of observations into 'higher level units' such as patients in hospitals. In linear mixed model...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/096228020101000604
更新日期:2001-12-01 00:00:00
abstract::In multi-regional trials, the underlying overall and region-specific accrual rates often do not hold constant over time and different regions could have different start-up times, which combined with initial jump in accrual within each region often leads to a discontinuous overall accrual rate, and these issues associa...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280214557581
更新日期:2017-04-01 00:00:00
abstract::Competing risks data often exist within a center in multi-center randomized clinical trials where the treatment effects or baseline risks may vary among centers. In this paper, we propose a subdistribution hazard regression model with multivariate frailty to investigate heterogeneity in treatment effects among centers...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280214526193
更新日期:2016-12-01 00:00:00
abstract::In medical experiments with the objective of testing the equality of two means, data are often partially paired by design or because of missing data. The partially paired data represent a combination of paired and unpaired observations. In this article, we review and compare nine methods for analyzing partially paired...
journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/0962280215577111
更新日期:2017-06-01 00:00:00
abstract::In the past two decades, it has become increasingly clear that genetic factors contribute to the aetiology of many common diseases including cancers, coronary disease, allergy and psychiatric disorders. While one goal of genetic epidemiological studies is to locate susceptibility genes for these complex diseases, it i...
journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/096228020000900603
更新日期:2000-12-01 00:00:00
abstract::Cancer survival trend analyses are essential to describe accurately the way medical practices impact patients' survival according to the year of diagnosis. To this end, survival models should be able to account simultaneously for non-linear and non-proportional effects and for complex interactions between continuous v...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280218779408
更新日期:2019-08-01 00:00:00
abstract::Exposure measurement error in epidemiological studies is recognized as a feature that must be considered because of the potential bias that can result in estimates of the exposure-disease association. Most of the work to date has focused on methods of analysis that adjust for the resultant bias, but the implications o...
journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/096228029500400405
更新日期:1995-12-01 00:00:00
abstract::Age-period-cohort models are a popular tool for studying population-level rates; for example, trends in cancer incidence and mortality. Age-period-cohort models decompose observed trends into age effects that correlate with natural history, period effects that reveal factors impacting all ages simultaneously (e.g. inn...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280217713033
更新日期:2019-01-01 00:00:00
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journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280211428371
更新日期:2013-10-01 00:00:00
abstract::A growing body of evidence suggests that genetic factors have an important influence on the onset and course of smoking. Here we review some of the statistical methods that have been used to test for genetic influences on smoking behaviour, with a particular focus on studies of large national twin samples. We show how...
journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/096228029800700205
更新日期:1998-06-01 00:00:00
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journal_title:Statistical methods in medical research
pub_type: 杂志文章,评审
doi:10.1177/096228029400300204
更新日期:1994-01-01 00:00:00
abstract::We consider two exact unconditional procedures to test the difference between two multinomials with ordered categorical data. Exact unconditional procedures are compared to other approaches based on the Wilcoxon mid-rank test and the proportional odds model. We use a real example from an arthritis pain study to illust...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280212450957
更新日期:2016-02-01 00:00:00
abstract::One purpose of a longitudinal study is to gain a better understanding of how an outcome of interest changes among a given population over time. In what follows, a trajectory will be taken to mean the series of measurements of the outcome variable for an individual. Group-based trajectory modelling methods seek to iden...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280215598806
更新日期:2017-08-01 00:00:00
abstract::In many experiments and especially in translational and preclinical research, sample sizes are (very) small. In addition, data designs are often high dimensional, i.e. more dependent than independent replications of the trial are observed. The present paper discusses the applicability of max t-test-type statistics (mu...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280220970228
更新日期:2020-11-24 00:00:00
abstract::In this paper, we describe a Bayesian hierarchical Poisson model for the prospective analysis of data for infectious diseases. The proposed model consists of two components. The first component describes the behavior of disease during nonepidemic periods and the second component represents the increase in disease coun...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280214527385
更新日期:2014-12-01 00:00:00
abstract::One of the main advantages of Bayesian analyses of clinical trials is their ability to formally incorporate skepticism about large treatment effects through the use of informative priors. We conducted a simulation study to assess the performance of informative normal, Student- t, and beta distributions in estimating r...
journal_title:Statistical methods in medical research
pub_type: 杂志文章
doi:10.1177/0962280215620828
更新日期:2018-01-01 00:00:00
abstract::Repeated measures and multivariate outcomes are an increasingly common feature of trials. Their joint analysis by means of random effects and latent variable models is appealing but patterns of heterogeneity in outcome profile may not conform to standard multivariate normal assumptions. In addition, there is much inte...
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更新日期:2010-06-01 00:00:00