Related papers: Gene targeting in disease networks
With the advent of Information technology, the Bioinformatics research field is becoming increasingly attractive to researchers and academicians. The recent development of various Bioinformatics toolkits has facilitated the rapid processing…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
Gene network information is believed to be beneficial for disease module and pathway identification, but has not been explicitly utilized in the standard random forest (RF) algorithm for gene expression data analysis. We investigate the…
In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
Cancer disease occurs because of a disorder in the cellular regulatory mechanism, Which causes cellular malformation. The genes that start the malformation are called Cancer driver genes (CDGs) . Numerous computational methods have been…
We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
In cancer genomics, it is of great importance to distinguish driver mutations, which contribute to cancer progression, from causally neutral passenger mutations. We propose a random-effect regression approach to estimate the effects of…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
Graph network science is becoming increasingly popular, notably in big-data perspective where understanding individual entities for individual functional roles is complex and time consuming. It is likely when a set of genes are regulated by…
Identifying phenotypes plays an important role in furthering our understanding of disease biology through practical applications within healthcare and the life sciences. The challenge of dealing with the complexities and noise within…
Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Cancer is a complex disease driven by dynamic regulatory shifts that cannot be fully captured by individual molecular profiling. We employ a data-driven approach to construct a coarse-grained dynamic network model based on hallmark…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…