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Breast cancer is one of the common cancers that endanger the health of women globally. Accurate target lesion segmentation is essential for early clinical intervention and postoperative follow-up. Recently, many convolutional neural…
Identifying the genes and mutations that drive the emergence of tumors is a major step to improve understanding of cancer and identify new directions for disease diagnosis and treatment. Despite the large volume of genomics data, the…
Tomasetti and Vogelstein recently proposed that the majority of variation in cancer risk among tissues is due to "bad luck," that is, random mutations arising during DNA replication in normal noncancerous stem cells. They generalize this…
Metastatic prostate cancer is one of the most common cancers in men. In the advanced stages of prostate cancer, tumours can metastasise to other tissues in the body, which is fatal. In this thesis, we performed a genetic analysis of…
Accurate classification of breast cancer subtypes from gene expression data is critical for diagnosis and treatment selection. However, such datasets are characterized by high dimensionality and limited sample size, posing challenges for…
Tumor protein P53 is believed to be involved in over half of human cancers cases, the prediction of malignancies plays essential roles not only in advance detection for cancer, but also in discovering effective prevention and treatment of…
The human body is able to generate a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design…
The influence of DNA cis-regulatory elements on a gene's expression has been intensively studied. However, little is known about expressions driven by trans-acting DNA hotspots. DNA hotspots harboring copy number aberrations are recognized…
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…
The dysregulation of transcripts is characterized as one of the main mechanisms in tumor pathogenesis. The recent discovery developed a new hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other RNA transcripts via…
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of…
An important part of breast cancer staging is the assessment of the sentinel axillary node for early signs of tumor spreading. However, this assessment by pathologists is not always easy and retrospective surveys often requalify the status…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires prior knowledge of change-point locations on the phylogeny or…
Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for comparative analyses of RNA levels at…
Cancer forms a robust system and progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to…
Somatic mutations, or alterations in DNA of a somatic cell, are key markers of cancer. In recent years, mutational signature analysis has become a prominent field of study within cancer research, commonly with Nonnegative Matrix…
The current picture of bacterial evolution is based largely on studies of 16S rRNA. However, this is just one gene. It is known that horizontal gene transfer can occur between bacterial species, although the frequency and implications of…
Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…