Related papers: Quantitative transcriptional analysis of aging C. …
Gene expression (GE) data capture valuable condition-specific information ("condition" can mean a biological process, disease stage, age, patient, etc.) However, GE analyses ignore physical interactions between gene products, i.e.,…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
In a complex network, different groups of nodes may have existed for different amounts of time. To detect the evolutionary history of a network is of great importance. We present a general method based on spectral analysis to address this…
In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Aging, the process of growing old or maturing, is one of the most widely seen natural phenomena in the world. For the stochastic processes, sometimes the influence of aging can not be ignored. For example, in this paper, by analyzing the…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
Aging is a universal consequence of life, yet researchers have identified no universal theme. This manuscript considers aging from the perspective of entropy, wherein things fall apart. We first examine biological information change as a…
In many systems we can describe emergent macroscopic behaviors, quantitatively, using models that are much simpler than the underlying microscopic interactions; we understand the success of this simplification through the renormalization…
A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses…