Search results for " Applications"
showing 10 items of 4541 documents
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
2020
Motivation Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of…
Quantitative characterization of antigens using monoclonal antibody reactivities
1993
A multipurpose program that empirically relates antigenic reactivities with monoclonal antibodies (MAbs) to genetic distances is presented. The program uses a set of known genetic pairwise distances to weigh each MAb depending on its capacity to define groups of taxonomically related antigens. This allows highly accurate identification and classification of unknown antigens. Also, the weights obtained constitute a quantitative measure of epitope conservation and can be used for improved vaccine design. © 1993 Oxford University Press.
Expert-based versus citation-based ranking of scholarly and scientific publication channels
2016
Abstract The Finnish publication channel quality ranking system was established in 2010. The system is expert-based, where separate panels decide and update the rankings of a set of publications channels allocated to them. The aggregated rankings have a notable role in the allocation of public resources into universities. The purpose of this article is to analyze this national ranking system. The analysis is mainly based on two publicly available databases containing the publication source information and the actual national publication activity information. Using citation-based indicators and other available information with association rule mining, decision trees, and confusion matrices, …
Correcting for non-ignorable missingness in smoking trends
2015
Data missing not at random (MNAR) is a major challenge in survey sampling. We propose an approach based on registry data to deal with non-ignorable missingness in health examination surveys. The approach relies on follow-up data available from administrative registers several years after the survey. For illustration we use data on smoking prevalence in Finnish National FINRISK study conducted in 1972-1997. The data consist of measured survey information including missingness indicators, register-based background information and register-based time-to-disease survival data. The parameters of missingness mechanism are estimable with these data although the original survey data are MNAR. The u…
TiFoSi: an efficient tool for mechanobiology simulations of epithelia
2020
[Motivation]: Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks between gene expression and cell biomechanics. In that context, in silico experiments are a powerful tool to understand fundamental mechanisms and to formulate and test hypotheses.
Consensus among preference rankings: a new weighted correlation coefficient for linear and weak orderings
2021
AbstractPreference data are a particular type of ranking data where some subjects (voters, judges,...) express their preferences over a set of alternatives (items). In most real life cases, some items receive the same preference by a judge, thus giving rise to a ranking with ties. An important issue involving rankings concerns the aggregation of the preferences into a “consensus”. The purpose of this paper is to investigate the consensus between rankings with ties, taking into account the importance of swapping elements belonging to the top (or to the bottom) of the ordering (position weights). By combining the structure of $$\tau _x$$ τ x proposed by Emond and Mason (J Multi-Criteria Decis…
Pathway analysis of high-throughput biological data within a Bayesian network framework
2011
Abstract Motivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network. Results: Proposed method takes into account the connectivity and relatedness between nodes of the p…
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
2014
Abstract Motivation: Protein–protein interaction (PPI) networks are powerful models to represent the pairwise protein interactions of the organisms. Clustering PPI networks can be useful for isolating groups of interacting proteins that participate in the same biological processes or that perform together specific biological functions. Evolutionary orthologies can be inferred this way, as well as functions and properties of yet uncharacterized proteins. Results: We present an overview of the main state-of-the-art clustering methods that have been applied to PPI networks over the past decade. We distinguish five specific categories of approaches, describe and compare their main features and …
mRNAStab—a web application for mRNA stability analysis
2013
Abstract Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at h…
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
2014
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20 for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.