Genomics
Electrophoretic separations of proteins are widely used in proteomic analyses, and rely heavily on SDS electrophoresis. This mode of separation is almost exclusively used when a single dimension separation is performed, and generally…
We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data…
Background: We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce…
Sequence organizations are viewed from two points: one is from informational redundancy or informational correlation (IC) and another is from k-mer frequency statistics. Two problems are investigated. The first is how the ICs exceed the…
Complex, non-additive genetic interactions are common and can be critical in determining phenotypes. Genome-wide association studies (GWAS) and similar statistical studies of linkage data, however, assume additive models of gene…
The development of cancer is largely driven by the gain or loss of subsets of the genome, promoting uncontrolled growth or disabling defenses against it. Identifying genomic regions whose DNA copy number deviates from the normal is…
Dr. Hatchwell [2010] has proposed that the BAK1 gene variants were likely due to sequencing of a processed gene on chromosome 20. However, in response, Dr. Gottlieb and co-authors [2010] have argued that "some but not all of the sequence…
The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
Gene-gene interactions have long been recognized to be fundamentally important to understand genetic causes of complex disease traits. At present, identifying gene-gene interactions from genome-wide case-control studies is computationally…
A new method for determining whether or not a mitrochondrial DNA (mtDNA) sequence belongs to a vertebrate is described and tested. This method only needs the mtDNA sequence of the organism in question, and unlike alignment based methods, it…
Huge numbers of short reads are being generated for mapping back to the genome to discover the frequency of transcripts, miRNAs, DNAase hypersensitive sites, FAIRE regions, nucleosome occupancy, etc. Since these reads are typically short…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
On the basis of the physico-chemical principles underlying silver-staining of proteins, which are recalled in this paper, several methods of silver-staining of proteins after SDS electrophoresis in polyacrylamide gels or isoelectric…
The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by…
We present an Evolutionary Placement Algorithm (EPA) for the rapid assignment of sequence fragments (short reads) to branches of a given phylogenetic tree under the Maximum Likelihood (ML) model. The accuracy of the algorithm is evaluated…
In this work we analyze the possibility that soliton dynamics in a simple nonlinear model allows functionally relevant predictions of the behaviour of DNA. This suggestion was first put forward by Salerno [Phys. Rev. A, vol. 44, p. 5292…
Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array…
The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…