Publications

Inference from Iterative Simulation Using Multiple Sequences

The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, ho...

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Molecular portraits of human breast tumours

Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories

Functionality-specific vulnerabilities, which mainly occur in Application Programming Interfaces (APIs) with specific functionalities, are crucial for software developers to det...

Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift

Training Deep Neural Networks is complicated by the fact that the distribution of each layer's inputs changes during training, as the parameters of the previous layers change. T...

Comprehensive Integration of Single-Cell Data

Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new...

Normalized cuts and image segmentation

We propose a novel approach for solving the perceptual grouping problem in vision. Rather than focusing on local features and their consistencies in the image data, our approach...

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...

Energy-efficient communication protocol for wireless microsensor networks

Wireless distributed microsensor systems will enable the reliable monitoring of a variety of environments for both civil and military applications. In this paper, we look at com...

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...

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

The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for...

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

Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and defin...