Related papers: Joint discovery of haplotype blocks and complex tr…
The detection of weak and rare effects in large amounts of data arises in a number of modern data analysis problems. Known results show that in this situation the potential of statistical inference is severely limited by the large-scale…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
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…
Phenomics is an emerging branch of modern biology that uses high throughput phenotyping tools to capture multiple environmental and phenotypic traits, often at massive spatial and temporal scales. The resulting high dimensional data…
One of the major challenges arising from single-cell transcriptomics experiments is the question of how to annotate the associated single-cell transcriptomic profiles. Because of the large size and the high dimensionality of the data,…
Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypothesis testing, with…
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…
Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In simple cases, single polymorphic loci explain a significant fraction of the phenotype variability. However, many traits of…
Genome-wide association studies have proven to be essential for understanding the genetic basis of disease. However, many complex traits---personality traits, facial features, disease subtyping---are inherently high-dimensional, impeding…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…
We consider the challenging problem of statistical inference for exponential-family random graph models based on a single observation of a random graph with complex dependence. To facilitate statistical inference, we consider random graphs…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the…
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially…
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing…
Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate into more complex multi-SNP haploblocks that are maintained throughout generations in…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
Patient subtyping based on temporal observations can lead to significantly nuanced subtyping that acknowledges the dynamic characteristics of diseases. Existing methods for subtyping trajectories treat the evolution of clinical observations…
Single nucleotide polymorphisms (SNPs) often appear in clusters along the length of a chromosome. This is due to variation in local coalescent times caused by,for example, selection or recombination. Here we investigate whether…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…