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Search Results: 1 - 10 of 327 matches for " Lauri Eronen "
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HaploRec: efficient and accurate large-scale reconstruction of haplotypes
Lauri Eronen, Floris Geerts, Hannu Toivonen
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-542
Abstract: We define three novel statistical models and give an efficient algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec is based on exploiting local regularities conserved in haplotypes: it reconstructs haplotypes so that they have maximal local coherence. This approach – not assuming statistical dependence for remotely located markers – has two useful properties: it is well-suited for sparse marker maps, such as those used in gene mapping, and it can actually take advantage of long maps.Our experimental results with simulated and real data show that HaploRec is a powerful method for the large scale haplotyping needed in association studies. With sample sizes large enough for gene mapping it appeared to be the best compared to all other tested methods (Phase, fastPhase, PL-EM, Snphap, Gerbil; simulated data), with small samples it was competitive with the best available methods (real data). HaploRec is several orders of magnitude faster than Phase and comparable to the other methods; the running times are roughly linear in the number of subjects and the number of markers. HaploRec is publicly available at http://www.cs.helsinki.fi/group/genetics/haplotyping.html webcite.The problem we consider is haplotype reconstruction: given the genotypes of a sample of individuals, the task is to predict the most likely haplotype pair for each individual. Computational haplotype reconstruction methods are based on statistical dependency between closely located markers, known as linkage disequilibrium. Many computational methods have been developed for the reconstruction of haplotypes. Some of these methods do not rely on the statistical modeling of the haplotypes [1-3], but most of them, like our proposed algorithm HaploRec, do [4-10]. For a review of these and other haplotyping methods we refer to [11-13]. Laboratory techniques are being developed for direct molecular haplotyping (see, e.g., [14,15]), but these techniques are not mature yet, and are currently t
Biomine: predicting links between biological entities using network models of heterogeneous databases
Lauri MA Eronen, Hannu TT Toivonen
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-119
Abstract: Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. We present Biomine and evaluate its performance in link prediction, where the goal is to predict pairs of nodes that will be connected in the future, based on current data. In particular, we formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. We consider and experiment with several such measures, and perform a parameter optimization procedure where different edge types are weighted to optimize link prediction accuracy. We also propose a novel method for disease-gene prioritization, defined as finding a subset of candidate genes that cluster together in the graph. We experimentally evaluate Biomine by predicting future annotations in the source databases and prioritizing lists of putative disease genes.The experimental results show that Biomine has strong potential for predicting links when a set of selected candidate links is available. The predictions obtained using the entire Biomine dataset are shown to clearly outperform ones obtained using any single source of data alone, when different types of links are suitably weighted. In the gene prioritization task, an established reference set of disease-associated genes is useful, but the results show that under favorable conditions, Biomine can also perform well when no such information is available.The Biomine system is a proof of concept. Its current version contains 1.1 million entities and 8.1 million relations between them, with focus on human genetics. Some of its functionalities are available in a public query interface at http://biomine.cs.helsinki.fi webcite, allowing searching
Constrained hidden Markov models for population-based haplotyping
Landwehr Niels,Mielik?inen Taneli,Eronen Lauri,Toivonen Hannu
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-s2-s9
Abstract: Background Haplotype Reconstruction is the problem of resolving the hidden phase information in genotype data obtained from laboratory measurements. Solving this problem is an important intermediate step in gene association studies, which seek to uncover the genetic basis of complex diseases. We propose a novel approach for haplotype reconstruction based on constrained hidden Markov models. Models are constructed by incrementally refining and regularizing the structure of a simple generative model for genotype data under Hardy-Weinberg equilibrium. Results The proposed method is evaluated on real-world and simulated population data. Results show that it is competitive with other recently proposed methods in terms of reconstruction accuracy, while offering a particularly good trade-off between computational costs and quality of results for large datasets. Conclusion Relatively simple probabilistic approaches for haplotype reconstruction based on structured hidden Markov models are competitive with more complex, well-established techniques in this field.
Are the Typologies Determined by the Post-Critical Belief Scale Predicted Well by the Religious Attitudes and Behaviour of Maltese Undergraduate Students?  [PDF]
Mary Anne Lauri, Josef Lauri, Joseph Borg
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.25063
Abstract: Religious beliefs play an important role in the study of religious practices and behaviour. Wulff (1997) suggested that there are four basic attitudes towards religion: Literal Affirmation, Literal Disaffirmation, Reductive Interpretation and Restorative Interpretation. Building on this work, Duriez, Soenans and Hutsebaut (2005) constructed the Post-Critical Belief Scale (PCBS). In their work, Duriez at al. conducted a Principal Component Analysis of the responses to this questionnaire. It yielded two factors which partitioned 2-dimensional space into four quadrants corresponding to the four types of beliefs postulated by Wulff (1997). The research question which is addressed in this paper is whether there is an association between scores on the PCBS and religious practices and behaviour in a staunchly Catholic country like Malta where over 98% are baptized in the Roman Catholic Church. This question was addressed by administering a questionnaire to a random sample of 650 students at the University of Malta, of which 421 completed the questionnaire. Of those who answered the questionnaire, 349 were undergraduates. The questionnaire consisted of a number of questions about religious attitudes and behaviour, and also included the PCBS. The analysis of the association between membership of one of the four belief typologies and the participants’ responses to other questions related to religious beliefs, religious practice and sexual norms was carried out using Discriminant Analysis. The results indicate that, at least in this sample of Maltese university students, these three measures do a reasonably good job in identifying membership in three of Wulff’s four belief typologies.
Parabolic John-Nirenberg Spaces
Lauri Berkovits
Journal of Function Spaces and Applications , 2012, DOI: 10.1155/2012/901917
Abstract: We introduce a parabolic version of John-Nirenberg space with exponent p and show that it is contained in local weak- spaces.
Lauri Honko
M?etagused. Hüperajakiri , 1998,
Abstract: The Folklore Process. The theoretical article by L. Honko follows the changing of the notion "folklore". A thorough change have undergone attitude towards the informant, creator, needer and performer of traditions. Instead of people, there are social groups that can be defined by their social status, profession, ethnical background, religion, place of living and whatever other criteria and what makes it possible to speak about a circle of members. L. Honko treats the basic new definitions of folklore and divides the folklore process into 22 stages, the 12 first of which are part of folklore's "first life" or take place on the basis of those criteria being filled, the rest 10 stages are folklore's "second life .
Triratna Budistlik Kogukond: juhtumiuuring budistlikust kogudusest Eestis
Lauri Liiders
M?etagused. Hüperajakiri , 2013, DOI: 10.7592/mt2013.53.liiders
Abstract: This paper provides an overview of the first detailed case study of a Buddhist congregation in Estonia. The object of this study is Triratna Buddhist Community in Estonia, which was established here in 1989 and is part of international Triratna Buddhist Community (formerly known as Friends of the Western Buddhist Order) created in the United Kingdom in 1967. Mainly through oral history and participant observation methods as well as analysis of data presented by different written and oral sources the researcher strives to give an overview of various aspects of activity connected with one particular Buddhist group in Estonia, including its practice, ordination rituals, beliefs and membership characteristics. It also includes a detailed overview of the congregation’s history and its relationship with members of Triratna congregations in Finland and the UK. It presents Buddhism as an emerging new religion in Estonia through a case study of a Western Buddhist ecumenical congregation.
Stuck in the Funicular: the Deceptive Levity of Translating Poetic Stoppages of Imagery
Lauri Pilter
Interlitteraria , 2013, DOI: 10.12697/il.2012.17.23
Abstract: -
Finnish Chironomidae
Lauri Paasivirta
Chironomus Newsletter on Chironomidae Research , 2012,
The "human" statistics of terrestrial impact cratering rate
Lauri Jetsu
Physics , 1997,
Abstract: The most significant periodicities in the terrestrial impact crater record are due to the human-signal: the bias of assigning integer values for the crater ages. This bias seems to have eluded the proponents and opponents of real periodicity in the occurrence of these events, as well as the theorists searching for an extraterrestrial explanation for such periodicity. The human-signal should be seriously considered by scientists in astronomy, geology and paleontology when searching for a connection between terrestrial major comet or asteroid impacts and mass extinctions of species.
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