Search and clustering orders of magnitude faster than BLAST
Abstract Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAS...
Publications
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891 publications
GRADE: an emerging consensus on rating quality of evidence and strength of recommendations
Guidelines are inconsistent in how they rate the quality of evidence and the strength of recommendations. This article explores the advantages of the GRADE system, which is incr...
Very high resolution interpolated climate surfaces for global land areas
We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The c...
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biologica...
Compressed sensing
Suppose x is an unknown vector in Ropfm (a digital image or signal); we plan to measure n general linear functionals of x and then reconstruct. If x is known to be compressible ...
Cancer statistics, 2018
Abstract Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States and compiles the most recent data on ca...
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction metho...
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...
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...
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 ...
Nonlinear Dimensionality Reduction by Locally Linear Embedding
Many areas of science depend on exploratory data analysis and visualization. The need to analyze large amounts of multivariate data raises the fundamental problem of dimensional...