Related papers: A statistical framework for SNP calling, mutation …
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Next-generation sequencing technology enables routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens.…
Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…
Studying the effects of groups of Single Nucleotide Polymorphisms (SNPs), as in a gene, genetic pathway, or network, can provide novel insight into complex diseases, above that which can be gleaned from studying SNPs individually. Common…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
The aim of this Lecture Note is to introduce the Signal Processing (SP) community to a powerful yet still under-utilised tool: the semiparametric statistics. In short, the semiparametric framework allows us to estimate or perform hypothesis…
Recent advances in next-generation sequencing technologies have facilitated the use of deoxyribonucleic acid (DNA) as a novel covert channels in steganography. There are various methods that exist in other domains to detect hidden messages…
For the vast majority of genome wide association studies (GWAS) published so far, statistical analysis was performed by testing markers individually. In this article we present some elementary statistical considerations which clearly show…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…
The reliability of the results of network meta-analysis (NMA) lies in the plausibility of key assumption of transitivity. This assumption implies that the effect modifiers' distribution is similar across treatment comparisons. Transitivity…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big…
We present a novel strategy to uncover indirect signs of new physics in collider data using the Standard Model Effective Field Theory (SMEFT) framework, offering notably improved sensitivity compared to traditional global analyses. Our…
Motivation: Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in…
Census and Household Travel Survey datasets are regularly collected from households and individuals and provide information on their daily travel behavior with demographic and economic characteristics. These datasets have important…
Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i)…
Thousands of person-years have been invested in searches for New Physics (NP), the majority of them motivated by theoretical considerations. Yet, no evidence of beyond the Standard Model (BSM) physics has been found. This suggests that…
A wide variety of application domains are concerned with data consisting of entities and their relationships or connections, formally represented as graphs. Within these diverse application areas, a common problem of interest is the…
The rapid proliferation of high-quality synthetic data -- generated by advanced AI models or collected as auxiliary data from related tasks -- presents both opportunities and challenges for statistical inference. This paper introduces a…
The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…