Hierarchical bayesian modelling

Integrating rare variation from trio family and case–control studies has successfully implicated specific genes contributing to risk of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), intellectual disability (ID), developmental disorders (DDs), and epilepsy (EPI). For schizophrenia (SCZ), however, while sets of genes have been implicated through the study of rare variation, only two risk genes have been identified.

22p vioraclene 31-03-2024 5 2   Download

Genome-wide Association Studies (GWAS) are typically designed to identify phenotype-associated single nucleotide polymorphisms (SNPs) individually using univariate analysis methods. Though providing valuable insights into genetic risks of common diseases, the genetic variants identified by GWAS generally account for only a small proportion of the total heritability for complex diseases.

11p vinarcissa 21-03-2023 3 1   Download

Cholera is a diarrheal disease caused by infection of the intestine with the gram-negative bacteria Vibrio cholera. It is caused by the ingestion of food or water and infected all age groups. This study aimed at identifying risk factors associated with cholera disease in Ethiopia using the Bayesian hierarchical model.

10p viferrari 29-10-2022 7 2   Download

We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylaseassisted bisulfite sequencing data.

22p viaristotle 29-01-2022 7 0   Download

Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means, incorporating built-in normalization and quantifying technical artifacts by borrowing information from spike-in genes.

14p viaristotle 29-01-2022 14 0   Download

Alternative splicing is a biological process during gene expression that allows a single gene to code for multiple proteins. However, splicing patterns can be altered in some conditions or diseases. Here, we present BANDITS, a R/Bioconductor package to perform differential splicing, at both gene and transcript level, based on RNA-seq data.

13p viarchimedes 26-01-2022 12 0   Download

Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) data remains a challenge due to the low depth. Furthermore, there is no method to identify the sequences of unknown HLA types not registered in HLA databases.

11p vitzuyu2711 29-09-2021 10 1   Download

The human microbiome forms very complex communities that consist of hundreds to thousands of different microorganisms that not only affect the host, but also participate in disease processes.

17p vilichoo2711 25-06-2021 17 2   Download

Time course data from microarrays and high-throughput sequencing experiments require simple, computationally efficient and powerful statistical models to extract meaningful biological signal, and for tasks such as data fusion and clustering.

12p viwyoming2711 16-12-2020 7 0   Download

One of the goals of the Systems Biology community is to have a detailed map of all biological interactions in an organism. One small yet important step in this direction is the creation of biological networks from post-genomic data.

10p vikentucky2711 24-11-2020 28 2   Download

Flow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can not render absolute measurements, hence samples can only be interpreted in relation to each other while at the same time comparisons are confounded by inter-sample variation.

16p vioklahoma2711 19-11-2020 7 1   Download

The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer.

12p vioklahoma2711 19-11-2020 12 1   Download

Group structures among genes encoded in functional relationships or biological pathways are valuable and unique features in large-scale molecular data for survival analysis. However, most of previous approaches for molecular data analysis ignore such group structures.

15p vicoachella2711 27-10-2020 13 0   Download

High-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiments, statistical methods are often too simplistic to understand the complexity of gene expression.

13p vicolorado2711 23-10-2020 11 1   Download

As the barriers to incorporating RNA sequencing (RNA-Seq) into biomedical studies continue to decrease, the complexity and size of RNA-Seq experiments are rapidly growing. Paired, longitudinal, and other correlated designs are becoming commonplace, and these studies offer immense potential for understanding how transcriptional changes within an individual over time differ depending on treatment or environmental conditions.

20p vicolorado2711 22-10-2020 12 0   Download

Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of disease loci.

25p vicolorado2711 22-10-2020 6 0   Download

A Bayesian approach with frequentist validity has been developed to support inferences derived from a BLevel A^ in vivo-in vitro correlation (IVIVC). Irrespective of whether the in vivo data reflect in vivo dissolution or absorption, the IVIVC is typically assessed using a linear regression model. Confidence intervals are generally used to describe the uncertainty around the model. While the confidence intervals can describe population-level variability, it does not address the individual-level variability.

16p caothientrangnguyen 09-05-2020 27 0   Download

In this work I address the challenge of augmenting n-gram language models according to prior linguistic intuitions. I argue that the family of hierarchical Pitman-Yor language models is an attractive vehicle through which to address the problem, and demonstrate the approach by proposing a model for German compounds. In an empirical evaluation, the model outperforms the Kneser-Ney model in terms of perplexity, and achieves preliminary improvements in English-German translation.

10p bunthai_1 06-05-2013 51 3   Download

We introduce two Bayesian models for unsupervised semantic role labeling (SRL) task. The models treat SRL as clustering of syntactic signatures of arguments with clusters corresponding to semantic roles. The first model induces these clusterings independently for each predicate, exploiting the Chinese Restaurant Process (CRP) as a prior. In a more refined hierarchical model, we inject the intuition that the clusterings are similar across different predicates, even though they are not necessarily identical.

11p bunthai_1 06-05-2013 45 3   Download

A standard form of analysis for linguistic typology is the universal implication. These implications state facts about the range of extant languages, such as “if objects come after verbs, then adjectives come after nouns.” Such implications are typically discovered by painstaking hand analysis over a small sample of languages. We propose a computational model for assisting at this process. Our model is able to discover both well-known implications as well as some novel implications that deserve further study.

8p hongvang_1 16-04-2013 38 3   Download