Publications

UCHIME improves sensitivity and speed of chimera detection

Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Interna...

Minimap2: pairwise alignment for nucleotide sequences

Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic cont...

Evolutionary trees from DNA sequences: A maximum likelihood approach

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...

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...

APACHE II

This paper presents the form and validation results of APACHE II, a severity of disease classification system. APACHE II uses a point score based upon initial values of 12 routi...

On a Method to Measure Supervised Multiclass Model’s Interpretability: Application to Degradation Diagnosis (Short Paper)

In an industrial maintenance context, degradation diagnosis is the problem of determining the current level of degradation of operating machines based on measurements. With the ...

BEAST: Bayesian evolutionary analysis by sampling trees

BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statis...

Knowledge of the Firm, Combinative Capabilities, and the Replication of Technology

How should we understand why firms exist? A prevailing view has been that they serve to keep in check the transaction costs arising from the self-interested motivations of indiv...