198 citations · 228 across the 8 of their papers we have counts for
8 papers
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…
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…
Application and Assessment of Deep Learning for the Generation of Potential NMDA Receptor Antagonists
Katherine J. Schultz, Sean M. Colby, Yasemin Yesiltepe +3
Uncompetitive antagonists of the N-methyl D-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzhe…
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples
Sean M. Colby, Jamie R. Nuñez, Nathan O. Hodas +2
Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing a…
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…