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Displaying 1-7 out of 7 total
Invited: Multiclass RNA function classification using next-generation sequencing
Found in: 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
By P Ryvkin, Yuk Yee Leung, Li-San Wang,B D Gregory
Issue Date:February 2011
pp. 10
RNA-seq produces detailed information including length, strand and pairing states, which can be leveraged to characterize RNA functional categories using machine-learning approaches. Using fruit fly small-RNA-seq data, we demonstrate that by combining read...
 
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Li-San Wang, Jim Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, Tandy Warnow
Issue Date:July 2011
pp. 1108-1119
Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have b...
 
Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Jijun Tang, Li-San Wang
Issue Date:October 2005
pp. 137-144
The study of genome rearrangements, the evolutionary events that change the order and strandedness of genes within genomes, presents new opportunities for discoveries about deep evolutionary events. The best software so far, GRAPPA, solves breakpoint and i...
 
Toward New Software for Computational Phylogenetics
Found in: Computer
By Bernard M.E. Moret, Li-San Wang, Tandy Warnow
Issue Date:July 2002
pp. 55-64
<p>Systematists study how a group of genes or organisms evolved. These biologists now have set their sights on the Tree of Life challenge: to reconstruct the evolutionary history of all knownliving organisms.</p><p>A typical phylogenetic ...
 
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Claude W. dePamphilis, Jim Leebens-Mack, Kevin Beckmann, Li-San Wang, P. Kerr Wall, Tandy Warnow
Issue Date:July 2011
pp. 1108-1119
Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have b...
     
Weighted isotonic regression under the L1 norm
Found in: Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm (SODA '06)
By Boulos Harb, Li-San Wang, Sampath Kannan, Stanislav Angelov
Issue Date:January 2006
pp. 783-791
Isotonic regression, the problem of finding values that best fit given observations and conform to specific ordering constraints, has found many applications in biomedical research and other fields. When the constraints form a partial ordering, solving the...
     
Estimating true evolutionary distances between genomes
Found in: Proceedings of the thirty-third annual ACM symposium on Theory of computing (STOC '01)
By Li-San Wang, Tandy Warnow
Issue Date:July 2001
pp. 637-646
Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events, provided that sufficiently accu...
     
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