Related papers: Further Thoughts on Abnormal Chromatin Configurati…
DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes, and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix…
We will briefly examine the following three issues related to the AGN synthesis models for X-ray background: 1) the possibility that absorbed AGNs evolve faster than unabsorbed ones; 2) the existence of the still debated population of…
In generic models for grand unified theories(GUT), various types of baryon number violating processes are expected when quarks and leptons propagate in the background of GUT strings. On the other hand, in models with large extra dimensions,…
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
As phenomena that necessarily emerge from the collective behavior of interacting particles, phase transitions continue to be difficult to predict using statistical thermodynamics. A recent proposal called the topological hypothesis suggests…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
Any process in which competing solutions replicate with errors and numbers of their copies depend on their respective fitnesses is the evolutionary optimization process. As during carcinogenesis mutated genomes replicate according to their…
A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in…
Recent theory progresses in (3+1)D dynamical descriptions of relativistic nuclear collisions at finite baryon density are reviewed. Heavy-ion collisions at different collision energies produce strongly coupled nuclear matter to probe the…
Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task…
The discovery of neutrino masses makes leptogenesis a very attractive scenario for explaining the puzzle of the baryon asymmetry of the Universe. We present the basic ingredients of leptogenesis, explain the predictive power of this…
We present a self-consistent theory for the description of the spectroscopic properties of odd nuclei which includes exact blocking, particle-number and angular-momentum projection and configuration mixing. In our theory the pairing…
Topological defects (e.g. pentagons, heptagons and pentagon-heptagon pairs) have been widely observed in large scale graphene and have been recognized to play important roles in tailoring the mechanical and physical properties of…
The Structural theory of chemistry introduces chemical/molecular structure as a combination of relative arrangement and bonding patterns of atoms in molecule. Nowadays, the structure of atoms in molecules is derived from the topological…
Recent cosmological observations, such as the measurement of the primordial 4He abundance, CMB, and large scale structure, give preference to the existence of extra radiation component, Delta N_nu > 0. The extra radiation may be accounted…
The study of graphene, since its discovery around 2004, is possibly the largest and fastest growing field of research in material science, because of its exotic mechanical, thermal, electronic, optical and chemical properties. The studies…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…