Related papers: Phylogenetics and the human microbiome
The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…
In the modern world, technology is at its peak. Different avenues in programming and technology have been explored for data analysis, automation, and robotics. Machine learning is key to optimize data analysis, make accurate predictions,…
For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to over-oxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal…
Phages are one of the most present groups of organisms in the biosphere. Their identification continues and their taxonomies are divergent. However, due to their evolution mode and the complexity of their species ecosystem, their…
The genome is software because it a set of verbal instructions for a programmable computer, the ribosome. The theory of evolution now reads: evolution is the software developer responsible for the existence of the genome. We claim that this…
Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow,…
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…