Morgan N. Price

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BACKGROUND We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. METHODOLOGY/PRINCIPAL FINDINGS Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution(More)
Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses(More)
Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to(More)
Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces(More)
We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83%(More)
Reading frequently involves not just looking at words on a page, but also underlining, hi&li@ing and commenting either on the text or in a separate notebook This combination of reading with critical thinking and learning is called active reading [2]. To explore the premise that computation can enhance active reading we have built the XLibris “active reading(More)
At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of(More)
Most bacterial genes were acquired by horizontal gene transfer from other bacteria instead of being inherited by continuous vertical descent from an ancient ancestor. To understand how the regulation of these acquired genes evolved, we examined the evolutionary histories of transcription factors and of regulatory interactions from the model bacterium(More)
How will we read digital library materials? This paper describes the reading practices of an on-going reading group, and how these practices changed when we introduced XLibris, a digital library reading appliance that uses a pen tablet computer to provide a paper-like interface. We interviewed group members about their reading practices, observed their(More)
User interfaces for digital libraries tend to focus on retrieval: users retrieve documents online, but then print them out and work with them on paper. One reason for printing documents is to annotate them with freeform ink while reading. Annotation can help readers to understand documents and to make them their own. In addition, annotation can reveal(More)