Publications

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 ...

Embryonic Stem Cell Lines Derived from Human Blastocysts

Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that cha...

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...

Parallel Distributed Processing

What makes people smarter than computers? These volumes by a pioneering neurocomputing group suggest that the answer lies in the massively parallel architecture of the human min...

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...

Risk, Return, and Equilibrium: Empirical Tests

This paper tests the relationship between average return and risk for New York Stock Exchange common stocks. The theoretical basis of the tests is the "two-parameter" portfolio ...

Evolutionary trees from DNA sequences: A maximum likelihood approach

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...

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...