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Viruses preserved in ancient materials provide snapshots of past viral diversity and a means to trace viral evolution through time. Here, we use a metagenomics approach to identify filterable and nuclease-resistant nucleic acids preserved in 700-y-old caribou feces frozen in a permanent ice patch. We were able to recover and characterize two viruses in(More)
We hypothesized that DNA methylation distributes into specific patterns in cancer cells, which reflect critical biological differences. We therefore examined the methylation profiles of 344 patients with acute myeloid leukemia (AML). Clustering of these patients by methylation data segregated patients into 16 groups. Five of these groups defined new AML(More)
Using viral metagenomics of brain tissue from a young adult crossbreed steer with acute onset of neurologic disease, we sequenced the complete genome of a novel astrovirus (BoAstV-NeuroS1) that was phylogenetically related to an ovine astrovirus. In a retrospective analysis of 32 cases of bovine encephalitides of unknown etiology, 3 other infected animals(More)
Reverse-engineering of gene networks using linear models often results in an underdetermined system because of excessive unknown parameters. In addition, the practical utility of linear models has remained unclear. We address these problems by developing an improved method, EXpression Array MINing Engine (EXAMINE), to infer gene regulatory networks from(More)
Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel(More)
Hidden Markov models (HMMs) have demonstrated great successes in modeling noisy sequential data sets in the area of speech recognition and protein sequence profiling. Results from association test showed significant Markov dependency in time-series gene expression data, and therefore HMMs would be especially appropriate for modeling gene expressions. In(More)
We present a new method, link-test, to select prostate cancer biomarkers from SELDI mass spectrometry and microarray data sets. Biomarkers selected by link-test are supported by data sets from both mRNA and protein levels, and therefore results in improved robustness. Link-test determines the level of significance of the association between a microarray(More)
An asynchronous Boolean network with N nodes whose states at each time point are determined by certain parent nodes is considered. We make use of the models developed by Matache and Heidel [Matache, M.T., Heidel, J., 2005. Asynchronous random Boolean network model based on elementary cellular automata rule 126. Phys. Rev. E 71, 026232] for a constant number(More)
In this paper, we proposed a new clustering algorithm that employs the concept of message passing to describe parallel and spontaneous biological processes. Inspired by real-life situations in which people in large gatherings form groups by exchanging messages, message passing clustering (MPC) allows data objects to communicate with each other and produces(More)
Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae,(More)