Publications

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...

Framing: Toward Clarification of a Fractured Paradigm

Journal Article Framing: Toward Clarification of a Fractured Paradigm Get access Robert M. Entman Robert M. Entman 1Robert M. Entman is an associate professor of communication s...

Neural Machine Translation by Jointly Learning to Align and Translate

Neural machine translation is a recently proposed approach to machine translation. Unlike the traditional statistical machine translation, the neural machine translation aims at...

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...

Regularization Paths for Generalized Linear Models via Coordinate Descent.

We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multinomia...

Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

Abstract We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of va...

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Abstract The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide difference...

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....

Markets and Hierarchies: Analysis and Antitrust Implications.

Journal Article Markets and Hierarchies: Analysis and Antitrust Implications Get access Markets and Hierarchies: Analysis and Antitrust Implications. By O. E. WILLIAMSON. (Londo...

Data Analysis Using Regression and Multilevel/Hierarchical Models

Data Analysis Using Regression and Multilevel/Hierarchical Models, first published in 2007, is a comprehensive manual for the applied researcher who wants to perform data analys...