Related papers: Systematic Target Function Annotation of Human Tra…
Using brain imaging quantitative traits (QTs) to identify the genetic risk factors is an important research topic in imaging genetics. Many efforts have been made via building linear models, e.g. linear regression (LR), to extract the…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively. We show through analytic…
Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level.…
We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…
Genome-wide association studies (GWAS) have successfully identified a large number of genetic variants associated with traits and diseases. However, it still remains challenging to fully understand functional mechanisms underlying many…
Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human traits or diseases in the past decade. Nevertheless, much of the heritability of many traits is still unaccounted for. Commonly used…
Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in…
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…
Transcriptome-wide association studies (TWAS) link genetic variation to complex traits by leveraging expression quantitative trait loci (eQTL) data. However, most implementations are typically limited to local (cis-acting) effects and fail…
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence…
Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription…
Gene expression represents a fundamental interface between genes and environment in the development and ongoing plasticity of the human organism. Individual differences in gene expression are likely to underpin much of human diversity,…
Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes.…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…
To date, most genetic analyses of phenotypes have focused on analyzing single traits or, analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power, and hold…
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms…
We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif,…
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or…