Publications

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...

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....

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

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

The Sequence of the Human Genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp ...

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...

Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

A method and server for predicting damaging missense mutations

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucle...