Biology subjects

Nguyen, T. H.

Publications and source records attributed to Nguyen, T. H..

3 recordsLinked to original sources

bioRxiv2018

Phylotastic: improving access to tree-of-life knowledge with flexible, on-the-fly delivery of trees

(1) A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts in research and education. This potential is limited if accessing the tree of life requires special knowledge, complex software, or long periods of training.\n\n(2) The Phylotastic project aims to use web-services technologies to lower the barrier for accessing phylogenetic knowledge, making it as easy to get a phylogeny of species as it is to get online driving directions. In prior work, we designed an open system of web services to validate and manage species names, find phylogeny resources, extract subtrees matching a users species list, calibrate them, and mash them up with images and information from online resources.\n\n(3) Here we report a publicly accessible system for on-the-fly delivery of phylogenetic knowledge, developed with user feedback on what types of functionality are considered useful by researchers and educators. The system currently consists of a web portal that implements 3 types of workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); 19 underlying web services accessible via a common registry; and toolbox code in R and Python so that others can create applications that leverage these services. These resources cover most of the use-cases identified in our analysis of user needs.\n\n(4) The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.

bioinformatics↗

bioRxiv2018

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, however, provides unrealistically small uncertainty estimates due to its neglect of dominant sources of error. Here, we present a Bayesian framework for sampling from the posterior distribution of all thermodynamic parameters and other quantities of interest from one or more ITC experiments, allowing uncertainties and correlations to be quantitatively assessed. For a series of ITC measurements on metal:chelator and protein:ligand systems, the Bayesian approach yields uncertainties which represent the variability from experiment to experiment more accurately than the standard data analysis. In some datasets, the median enthalpy of binding is shifted by as much as 1.5 kcal/mol. A Python implementation suitable for analysis of data generated by MicroCal instruments (and adaptable to other calorimeters) is freely available online.

biophysics↗

bioRxiv2017

Label-free quantitative screening of breast tissue using Spatial Light Interference Microscopy (SLIM)

Breast cancer is the most common type of cancer among women worldwide. The standard histopathology of breast tissue, the primary means of disease diagnosis, involves manual microscopic examination of stained tissue by a pathologist. Because this method relies on qualitative information, it can result in inter-observer variation. Furthermore, for difficult cases the pathologist often needs additional markers of malignancy to help in making a diagnosis. We present a quantitative method for label-free tissue screening using Spatial Light Interference Microscopy (SLIM). By extracting tissue markers of malignancy based on the nanostructure revealed by the optical path-length, our method provides an objective and potentially automatable method for rapidly flagging suspicious tissue. We demonstrated our method by imaging a tissue microarray comprising 68 different subjects - 34 with malignant and 34 with benign tissues. Three-fold cross validation results showed a sensitivity of 94% and specificity of 85% for detecting cancer. The quantitative biomarkers we extract provide a repeatable and objective basis for determining malignancy. Thus, these disease signatures can be automatically classified through machine learning packages, since our images do not vary from scan to scan or instrument to instrument, i.e., they represent intrinsic physical attributes of the sample, independent of staining quality.

pathology↗