Related papers: Numerical modeling of inhomogeneous DNA replicatio…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Recent studies of cancer somatic mutation profiles seek to identify mutations for targeted therapy in personalized medicine. Analysis of profiles, however, is not trivial, as each profile is heterogeneous and there are multiple confounding…
A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
This paper presents two different efficiency-enhancement techniques for probabilistic model building genetic algorithms. The first technique proposes the use of a mutation operator which performs local search in the sub-solution…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…
The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Population genomic studies have shown that genetic draft and background selection can profoundly affect the genome-wide patterns of molecular variation. We performed forward simulations under realistic gene-structure and selection scenarios…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…