Publications
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Numerical optimization
This third edition of Braun and Murdoch's bestselling textbook now includes discussion of the use and design principles of the tidyverse packages in R, including expanded covera...
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...
Integrated analysis of multimodal single-cell data
ezSingleCell is an interactive and easy-to-use application for the analysis of multiple single-cell and spatial omics data types for biologists. It combines the best-performing ...
How to Do Things With Words
Abstract This work sets out the author's conclusions in the field to which he directed his main efforts for at least the last ten years of his life. Starting from an examination...
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...
Limited-dependent and qualitative variables in econometrics
This book presents the econometric analysis of single-equation and simultaneous-equation models in which the jointly dependent variables can be continuous, categorical, or trunc...
Twelve years of SAMtools and BCFtools
Abstract Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion an...