198 citations · 210 across the 10 of their papers we have counts for
11 papers
Identifying metabolites from protein identifiers with P2M
Christine H. Chang, Bryan J. Killinger, Ryan S. Renslow +1
The identification of metabolites from complex biological samples often involves matching experimental mass spectrometry data to signatures of compounds derived from massive chemic…
AI for Chemical Space Gap Filling and Novel Compound Generation
Monee Y. McGrady, Sean M. Colby, Jamie R Nuñez +2
When considering large sets of molecules, it is helpful to place them in the context of a "chemical space" - a multidimensional space defined by a set of descriptors that can be us…
DEIMoS: an open-source tool for processing high-dimensional mass spectrometry data
Sean M. Colby, Christine H. Chang, Jessica L. Bade +9
We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass sp…
SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES
Yasemin Yesiltepe, Ryan S. Renslow, Thomas O. Metz
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or bi…
A Validated Method for Predicting Small Molecule Ionization Sites using Gibb's Free Energies
Jessica L. Bade, Sean M. Colby, Ryan S. Renslow +1
Accurate molecular identification of metabolites can unlock new areas of the molecular universe and allow greater insight into complex biological and environmental systems than cur…
Collision cross section specificity for small molecule identification workflows
Jamie Nunez, Eva Brayfindley, Sean M. Colby +4
The physical-chemical property of molecular collision cross section (CCS) is increasingly used to assist in small molecule identification; however, questions remain regarding the e…
Similarity Downselection: A Python implementation of a heuristic search algorithm for finding the set of the n most dissimilar items with an application in conformer sampling
Felicity F. Nielson, Sean M. Colby, Ryan S. Renslow +1
Finding the set of the n items most dissimilar from each other out of a larger population becomes increasingly difficult and computationally expensive as either n or the population…
Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions
Felicity F. Nielson, Sean M. Colby, Dennis G. Thomas +2
The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection o…
Advancing Standards-Free Methods for the Identification of Small Molecules in Complex Samples
Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas +7
The current gold standard for unambiguous identification in metabolomics analysis is based on comparing two or more orthogonal properties from the analysis of authentic, pure refer…
ISiCLE: A molecular collision cross section calculation pipeline for establishing large in silico reference libraries for compound identification
Sean M. Colby, Dennis G. Thomas, Jamie R. Nunez +8
Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecule…
Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data
Jamie R. Nuñez, Christopher R. Anderton, Ryan S. Renslow
Color vision deficiency (CVD) affects more than 4% of the population and leads to a different visual perception of colors. Though this has been known for decades, colormaps with ma…