742 citations · 748 across the 5 of their papers we have counts for
6 papers
Deep Learning for Reference-Free Geolocation for Poplar Trees
Cai W. John, Owen Queen, Wellington Muchero +1
A core task in precision agriculture is the identification of climatic and ecological conditions that are advantageous for a given crop. The most succinct approach is geolocation,…
Dynamic network analysis improves protein 3D structural classification
Khalique Newaz, Jacob Piland, Patricia L. Clark +3
Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3…
Weighted graphlets and deep neural networks for protein structure classification
Hongyu Guo, Khalique Newaz, Scott Emrich +2
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem o…
Network analysis of synonymous codon usage
Khalique Newaz, Gabriel Wright, Jacob Piland +4
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such ra…
Hot RAD: A Tool for Analysis of Next-Gen RAD Tag Data
Lauren A. Assour, Nicholas LaRosa, Scott J. Emrich
Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.) is an emerging method for analyzing an organism's genome without completely sequencing it. This can be a…
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov +88
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished g…