Engineering topics
Krishnakumar, Raga
Publications and source records attributed to Krishnakumar, Raga.
MAPLE v.1.0
SAND2025-00659O MAPLE is a software tool that uses epigenomic data to predict gene expression. MAPLE uses a set of epigenomic modifications to determine the effect on gene expression in a specific subset of species. The algorithm can be trained on additional species and epigenomic modifications, enhancing its predictive capabilities. EAGLE employs a hybrid neural network architecture, featuring a convolutional front-end and a multi-head attention layer, to process pre-processed signal data as input. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.
Poplar
SAND2025-00683O Poplar is a software tool that generates a phylogenetic tree from input gene and genome sequences. It integrates established tools to identify genes within genomes, group sequences, construct gene trees, and infer a species tree. Poplar processes nucleotide sequences, identifies similar sequences using Nucleotide BLAST, groups them with DBSCAN, aligns sequences with MAFFT, constructs gene trees with RAxML-NG, and infers a species tree using ASTRAL-Pro3. This pipeline provides a structured approach to phylogenetic analysis, facilitating the study of evolutionary relationships among species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.