EM for phylogenetic topology reconstruction on nonhomogeneous data

Persistent topology for cryo-EM data analysis.

In this work, we introduce persistent homology for the analysis of cryo-electron microscopy (cryo-EM) density maps. We identify the topological fingerprint or topological signature of noise, which is widespread in cryo-EM data. For low signal-to-noise ratio (SNR) volumetric data, intrinsic topological features of biomolecular structures are indistinguishable from noise. To remove noise, we empl...

Topology-Guided Sampling of Nonhomogeneous Random Fields

Topological measurements are increasingly being accepted as an important tool for quantifying complex structures. In many applications these structures can be expressed as nodal domains of real-valued functions and are obtained only through experimental observation or numerical simulations. In both cases, the data on which the topological measurements are based are derived via some form of fini...

Phylogenetic Reconstruction from Genome Order Data

Phylogenetic reconstruction from non-genomic data

MOTIVATION Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic ...

Toward a More Reliable Morphological Data Set for Phylogenetic Reconstruction

For decades, the relationships between different species have been discerned by way of a set of observable characteristics. Based on the similarity of certain observables, two species could be grouped together, along with other organisms that shared the same features. By these methods, scientists constructed a hierarchy of life. Taxonomy is the name given to the study and organization of differ...