Publications

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Cluster analysis and display of genome-wide expression patterns

A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according ...

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

The Art of Case Study Research

Introduction An Intensive Study of Case Study Research Methods The Unique Case Research Questions The Nature of Qualitative Research Data Gathering Analysis and Interpretation C...

Regularization Paths for Generalized Linear Models via Coordinate Descent

We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nom...

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...

Cancer statistics, 2023

Abstract Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths in the United States and compiles the most recent data on population‐based c...

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies ...

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

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...

Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules

Two extended basis sets (termed 5–31G and 6–31G) consisting of atomic orbitals expressed as fixed linear combinations of Gaussian functions are presented for the first row atoms...