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Full-Text Articles in Physical Sciences and Mathematics
Broadcasting With Prediction And Selective Forwarding In Vehicular Networks, Jainjun Yang, Zongming Fei
Broadcasting With Prediction And Selective Forwarding In Vehicular Networks, Jainjun Yang, Zongming Fei
Computer Science Faculty Publications
Broadcasting in vehicular networks has attracted great interest in research community and industry. Broadcasting on disseminating information to individual vehicle beyond the transmission range is based on inter-vehicle communication systems. It is crucial to broadcast messages to other vehicles as fast as possible because the messages in vehicle communication systems are often emergency messages such as accident warning or alarm. In many current approaches, the message initiator or sender selects the node among its neighbors that is farthest away from it in the broadcasting direction and then assigns the node to rebroadcast the message once the node gets out of …
Blackops: Increasing Confidence In Variant Detection Through Mappability Filtering, Christopher R. Cabanski, Matthew D. Wilkerson, Matthew Soloway, Joel S. Parker, Jinze Liu, Jan F. Prins, J. S. Marron, Charles M. Perou, D. Neil Hayes
Blackops: Increasing Confidence In Variant Detection Through Mappability Filtering, Christopher R. Cabanski, Matthew D. Wilkerson, Matthew Soloway, Joel S. Parker, Jinze Liu, Jan F. Prins, J. S. Marron, Charles M. Perou, D. Neil Hayes
Computer Science Faculty Publications
Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, …
Diffsplice: The Genome-Wide Detection Of Differential Splicing Events With Rna-Seq, Yin Hu, Yan Huang, Ying Du, Christian F. Orellana, Darshan Singh, Amy R. Johnson, Anaïs Monroy, Pei-Fen Kuan, Scott M. Hammond, Liza M. Hammond, Scott H. Randell, Derek Y. Chiang, D. Neil Hayes, Corbin Jones, Yufeng Liu, Jan F. Prins, Jinze Liu
Diffsplice: The Genome-Wide Detection Of Differential Splicing Events With Rna-Seq, Yin Hu, Yan Huang, Ying Du, Christian F. Orellana, Darshan Singh, Amy R. Johnson, Anaïs Monroy, Pei-Fen Kuan, Scott M. Hammond, Liza M. Hammond, Scott H. Randell, Derek Y. Chiang, D. Neil Hayes, Corbin Jones, Yufeng Liu, Jan F. Prins, Jinze Liu
Computer Science Faculty Publications
The RNA transcriptome varies in response to cellular differentiation as well as environmental factors, and can be characterized by the diversity and abundance of transcript isoforms. Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve understanding of cell differentiation and development and enable the identification of biomarkers that classify disease types. The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, making it possible to accurately detect the differences between transcriptomes. In this article, we present a new method for the detection and visualization of differential transcription. Our approach does …