Publications

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...

Tissue-based map of the human proteome

Protein expression across human tissues Sequencing the human genome gave new insights into human biology and disease. However, the ultimate goal is to understand the dynamic exp...

Improved Survival with Ipilimumab in Patients with Metastatic Melanoma

Ipilimumab, with or without a gp100 peptide vaccine, as compared with gp100 alone, improved overall survival in patients with previously treated metastatic melanoma. Adverse eve...

Evaluating Goodness-of-Fit Indexes for Testing Measurement Invariance

Abstract Measurement invariance is usually tested using Multigroup Confirmatory Factor Analysis, which examines the change in the goodness-of-fit index (GFI) when cross-group co...

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

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...

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 ...

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Exchange and Power in Social Life.

In his landmark study of exchange and power in social life, Peter M. Blau contributes to an understanding of social structure by analyzing the social processes that govern the r...

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...

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...