Publications

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

The cBioPortal enables integration, visualization, and analysis of multidimensional cancer genomic and clinical data.

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

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...

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

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 ...

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

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

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...

Bioconductor: open software development for computational biology and bioinformatics

Absence of Diffusion in Certain Random Lattices

This paper presents a simple model for such processes as spin diffusion or conduction in the "impurity band." These processes involve transport in a lattice which is in some sen...

bibliometrix : An R-tool for comprehensive science mapping analysis