Digital Commons Network^™

Identification Of Conserved Splicing Motifs In Mutually Exclusive Exons Of 15 Insect Species, Patricia Buendia, John Tyree, Robert Laredo, Shu-Ning Hsu

School of Computing and Information Sciences

Background: During alternative splicing, the inclusion of an exon in the final mRNA molecule is determined by nuclear proteins that bind cis-regulatory sequences in a target pre-mRNA molecule. A recent study suggested that the regulatory codes of individual RNA-binding proteins may be nearly immutable between very diverse species such as mammals and insects. The model system Drosophila melanogaster therefore presents an excellent opportunity for the study of alternative splicing due to the availability of quality EST annotations in FlyBase.

Methods: In this paper, we describe an in silico analysis pipeline to extract putative exonic splicing regulatory sequences from a multiple …

Information Discovery On Electronic Health Records Using Authority Flow Techniques, Vagelis Hristidis, Ramakrishna R. Varadarajan, Paul Biondich, Michael Weiner

School of Computing and Information Sciences

Background

As the use of electronic health records (EHRs) becomes more widespread, so does the need to search and provide effective information discovery within them. Querying by keyword has emerged as one of the most effective paradigms for searching. Most work in this area is based on traditional Information Retrieval (IR) techniques, where each document is compared individually against the query. We compare the effectiveness of two fundamentally different techniques for keyword search of EHRs.

Methods

We built two ranking systems. The traditional BM25 system exploits the EHRs' content without regard to association among entities within. The Clinical ObjectRank (CO) …

Serial Evolutionary Networks Of Within-Patient Hiv-1 Sequences Reveal Patterns Of Evolution Of X4 Strains, Patrica Buendia, Giri Narasimhan

School of Computing and Information Sciences

Background

The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation …