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Articles 1 - 5 of 5
Full-Text Articles in Physical Sciences and Mathematics
Integration Of Breast Cancer Gene Signatures Based On Graph Centrality, Jianxin Wang, Gang Chen, Min Li, Yi Pan
Integration Of Breast Cancer Gene Signatures Based On Graph Centrality, Jianxin Wang, Gang Chen, Min Li, Yi Pan
Computer Science Faculty Publications
Background: Various gene-expression signatures for breast cancer are available for the prediction of clinical outcome. However due to small overlap between different signatures, it is challenging to integrate existing disjoint signatures to provide a unified insight on the association between gene expression and clinical outcome.
Results: In this paper, we propose a method to integrate different breast cancer gene signatures by using graph centrality in a context-constrained protein interaction network (PIN). The context-constrained PIN for breast cancer is built by integrating complete PIN and various gene signatures reported in literatures. Then, we use graph centralities to quantify the importance of …
Parallel Progressive Multiple Sequence Alignment On Reconfigurable Meshes, Ken Nguyen, Yi Pan, Ge Nong
Parallel Progressive Multiple Sequence Alignment On Reconfigurable Meshes, Ken Nguyen, Yi Pan, Ge Nong
Computer Science Faculty Publications
Background: One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand.
Results: We design O(1) run-time solutions …
A Comparison Of The Functional Modules Identified From Time Course And Static Ppi Network Data, Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan
A Comparison Of The Functional Modules Identified From Time Course And Static Ppi Network Data, Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan
Computer Science Faculty Publications
Background: Cellular systems are highly dynamic and responsive to cues from the environment. Cellular function and response patterns to external stimuli are regulated by biological networks. A protein-protein interaction (PPI) network with static connectivity is dynamic in the sense that the nodes implement so-called functional activities that evolve in time. The shift from static to dynamic network analysis is essential for further understanding of molecular systems.
Results: In this paper, Time Course Protein Interaction Networks (TC- PINs) are reconstructed by incorporating time series gene expression into PPI networks. Then, a clustering algorithm is used to create functional modules from three …
Inferring Viral Quasispecies Spectra From 454 Pyrosequencing Reads, Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Măndoiu, Peter Balfe, Alexander Zelikovskiy
Inferring Viral Quasispecies Spectra From 454 Pyrosequencing Reads, Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Măndoiu, Peter Balfe, Alexander Zelikovskiy
Computer Science Faculty Publications
Background: RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.
Results: In this paper, we introduce a new Viral Spectrum Assembler (ViSpA) method for quasispecies spectrum reconstruction …
Estimation Of Alternative Splicing Isoform Frequencies From Rna-Seq Data, Marius Nicolae, Serghei Mangul, Ion I. Măndoiu, Alexander Zelikovskiy
Estimation Of Alternative Splicing Isoform Frequencies From Rna-Seq Data, Marius Nicolae, Serghei Mangul, Ion I. Măndoiu, Alexander Zelikovskiy
Computer Science Faculty Publications
Background: Massively parallel whole transcriptome sequencing, commonly referred as RNA-Seq, is quickly becoming the technology of choice for gene expression profiling. However, due to the short read length delivered by current sequencing technologies, estimation of expression levels for alternative splicing gene isoforms remains challenging.
Results: In this paper we present a novel expectation-maximization algorithm for inference of isoform- and genespecific expression levels from RNA-Seq data. Our algorithm, referred to as IsoEM, is based on disambiguating information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand and read pairing information …