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Cancer arises from successive rounds of mutations which generate tumor cells with different genomic variation i.e. clones. For drug responsiveness and therapeutics, it is necessary to identify the clones in tumor sample accurately. Many…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Models have been proposed to extract temporal patterns from longitudinal electronic health records (EHR) for clinical predictive models. However, the common relations among patients (e.g., receiving the same medical treatments) were rarely…
We present a novel method for testing the hypothesis of equality of two correlation matrices using paired high-dimensional datasets. We consider test statistics based on the average of squares, maximum and sum of exceedances of Fisher…
Xenium, a new spatial transcriptomics platform, enables subcellular-resolution profiling of complex tumor tissues. Despite the rich morphological information in histology images, extracting robust cell-level features and integrating them…
Understanding how molecular changes caused by genetic variation drive disease risk is crucial for deciphering disease mechanisms. However, interpreting genome sequences is challenging because of the vast size of the human genome, and…
While model architectures and training strategies have become more generic and flexible with respect to different data modalities over the past years, a persistent limitation lies in the assumption of fixed quantities and arrangements of…
The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
An important problem in contemporary immunology studies based on single-cell protein expression data is to determine whether cellular expressions are remodeled post infection by a pathogen. One natural approach for detecting such changes is…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…
The complexities inherent to leukemia, multifaceted cancer affecting white blood cells, pose considerable diagnostic and treatment challenges, primarily due to reliance on laborious morphological analyses and expert judgment that are…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Reconstruction of the individual energies and the opening angle between the electrons emitted in neutrinoless double-beta decay can probe the nature of the beyond-the-Standard-Model exchange mechanism that underlies the process. Although it…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
Motivation. Cancer heterogeneity is observed at multiple biological levels. To improve our understanding of these differences and their relevance in medicine, approaches to link organ- and tissue-level information from diagnostic images and…
We calculate the mutual information function for each of the 24 chromosomes in the human genome. The same correlation pattern is observed regardless the individual functional features of each chromosome. Moreover, correlations of different…
Mutual exclusivity is a widely recognized property of many cancer drivers. Knowledge about these relationships can provide important insights into cancer drivers, cancer-driving pathways, and cancer subtypes. It can also be used to predict…
Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including…