Publications

A new optimizer using particle swarm theory

The optimization of nonlinear functions using particle swarm methodology is described. Implementations of two paradigms are discussed and compared, including a recently develope...

Raman Spectrum of Graphene and Graphene Layers

Graphene is the two-dimensional building block for carbon allotropes of every other dimensionality. We show that its electronic structure is captured in its Raman spectrum that ...

Evolutionary trees from DNA sequences: A maximum likelihood approach

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Single-layer MoS2 transistors

An Integrative Model Of Organizational Trust

Scholars in various disciplines have considered the causes, nature, and effects of trust. Prior approaches to studying trust are considered, including characteristics of the tru...

Evaluating the Effectiveness of Large Language Models in Representing Textual Descriptions of Geometry and Spatial Relations (Short Paper)

This research focuses on assessing the ability of large language models (LLMs) in representing geometries and their spatial relations. We utilize LLMs including GPT-2 and BERT t...

Mapping and quantifying mammalian transcriptomes by RNA-Seq

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood....

Reflecting on reflexive thematic analysis

Since initially writing on thematic analysis in 2006, the popularity of the method we outlined has exploded, the variety of TA approaches have expanded, and, not least, our thin...

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Integrating single-cell transcriptomic data across different conditions, technologies, and species