Publications

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

Transforming Qualitative Information: Thematic Analysis and Code Development

The Search for the Codable Moment A Way of Seeing Developing Themes and Codes Deciding on Units of Analysis and Units of Coding as Issues of Sampling Developing Themes and a Cod...

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 ...

A Global Geometric Framework for Nonlinear Dimensionality Reduction

Scientists working with large volumes of high-dimensional data, such as global climate patterns, stellar spectra, or human gene distributions, regularly confront the problem of ...

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

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexib...

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

A method and server for predicting damaging missense mutations

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...

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...

A Simple, Positive Semi-Definite, Heteroskedasticity and AutocorrelationConsistent Covariance Matrix

This paper describes a simple method of calculating a heteroskedasticity and autocorrelation consistent covariance matrix that is positive semi-definite by construction. It also...