Related papers: A unifying framework for the modelling and analysi…
A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…
The treatment of short-tandem-repeat (STR) loci on the Y chromosome presents special problems in the forensic analysis of DNA mixtures, chiefly but not exclusively relating to the linkage of Y-STR loci which precludes the use of the…
Many forensic genetic trace samples are of too low quality to obtain short tandem repeat (STR) DNA profiles as the nuclear DNA they contain is highly degraded (e.g., telogen hairs). Instead, performing shotgun DNA sequencing of such samples…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
DNA is now routinely used in criminal investigations and court cases, although DNA samples taken at crime scenes are of varying quality and therefore present challenging problems for their interpretation. We present a statistical model for…
Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
In both criminal cases and civil cases there is an increasing demand for the analysis of DNA mixtures involving relationships. The goal might be, for example, to identify the contributors to a DNA mixture where the donors may be related, or…
Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…
Revealing the functional sites of biological sequences, such as evolutionary conserved, structurally interacting or co-evolving protein sites, is a fundamental, and yet challenging task. Different frameworks and models were developed to…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Forensic examination of evidence like firearms and toolmarks, traditionally involves a visual and therefore subjective assessment of similarity of two questioned items. Statistical models are used to overcome this subjectivity and allow…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
A common task in forensic biology is to interpret and evaluate short tandem repeat DNA profiles. The first step in these interpretations is to assign a number of contributors to the profiles, a task that is most often performed manually by…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…