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Displaying 1-11 out of 11 total
Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By William Arndt,Thomas M. Asbury,W. Jim Zheng,Matt Mitman,Jijun Tang
Issue Date:November 2011
pp. 936-938
New technologies permit the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is structural in nature and challenging to coordinate with existing data formats. There is an in...
Matching a Set of Patterns with Wildcards
Found in: Parallel Architectures, Algorithms and Programming, International Symposium on
By Meng Zhang,Yi Zhang,Jijun Tang
Issue Date:December 2010
pp. 169-174
Multi-pattern matching with wildcards is to find all the occurrences of a set of patterns with wildcards in a text. This problem arises in various fields, such as computational biology and network security. But the problem is not extensively studied as the...
A New Approach for Tree Alignment Based on Local Re-Optimization
Found in: BioMedical Engineering and Informatics, International Conference on
By Feng Yue, Jijun Tang
Issue Date:May 2008
pp. 34-38
Multiple sequence alignment is the most fundamentaltask in bioinformatics and computational biology. In thispaper, we present a new algorithm to conduct multiple sequencesalignment based on phylogenetic trees. It is widelyaccepted that a good phylogenetic ...
A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference
Found in: Bioinformatics and Biomedicine, IEEE International Conference on
By Feng Yue, Jijun Tang
Issue Date:November 2007
pp. 143-150
In this paper, we present an algorithm to simultaneously align three biological sequences with affine gap model and infer their common ancestral sequence. Our algorithm can be further extended to perform tree alignment for more se- quences, and eventually ...
A Fast 3D Correspondence Method for Statistical Shape Modeling
Found in: Computer Vision and Pattern Recognition, IEEE Computer Society Conference on
By Pahal Dalal, Brent C. Munsell, Song Wang, Jijun Tang, Kenton Oliver, Hiroaki Ninomiya, Xiangrong Zhou, Hiroshi Fujita
Issue Date:June 2007
pp. 1-8
Accurately identifying corresponded landmarks from a population of shape instances is the major challenge in constructing statistical shape models. In this paper, we address this landmark-based shape-correspondence problem for 3D cases by developing a high...
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...
Phylogenetic Reconstruction from Arbitrary Gene-Order Data
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Jijun Tang, Bernard M. E. Moret, Liying Cui, Claude W. dePamphilis
Issue Date:May 2004
pp. 592
Phylogenetic reconstruction from gene-order data has attracted attention from both biologists and computer scientists over the last few years. So far, our software suite GRAPPA is the most accurate approach, but it requires that all genomes have identical ...
Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Fei Hu,Jun Zhou,Lingxi Zhou,Jijun Tang
Issue Date:July 2014
pp. 667-672
Changes of gene orderings have been extensively used as a signal to reconstruct phylogenies and ancestral genomes. Inferring the gene order of an extinct species has a wide range of applications, including the potential to reveal more detailed evolutionary...
Exploring genomes with a game engine
Found in: 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
By Jeremiah J. Shepherd,Lingxi Zhou,Yan Zhang,Jim Zheng,Jijun Tang
Issue Date:December 2013
pp. 26-30
Studying genomes continues to be beneficial for evolutionary discover, and prognosticating/diagnosing many genetic disorders and diseases. Most of the these studies have used systems that view the DNA in a linear structure, but having this information is o...
Emulating Insertion and Deletion Events in Genome Rearrangement Analysis
Found in: Bioinformatics and Biomedicine, IEEE International Conference on
By William Arndt,Jijun Tang
Issue Date:November 2011
pp. 105-108
Great advancements have been achieved in phylogenetic reconstruction from genome rearrangement events but difficult problems still remain. One challenge is to deal with more complex events such as gene insertions and deletions such that we can analyze both...
Lost in the Middle Kingdom: a second language acquisition video game
Found in: Proceedings of the 49th Annual Southeast Regional Conference (ACM-SE '11)
By Jeremiah J. Shepherd, Jijun Tang, Matthew Arnold, Nancy Cheek, Renaldo J. Doe, Yun Zhu
Issue Date:March 2011
pp. 290-294
From the days of computer assisted language learning (CALL) [12], using computers as a means to acquire a new language has been a long standing research field. While typical class room strategies like memorization and drills have shown to be effective [13]...