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Our research group focuses on the development of bioinformatics methods for the analysis of next generation sequencing data. It consists of faculty and students from the department of Computer Science both at the University of Kentucky and at the University of North Carolina at Chapel Hill. Our work is largely driven by RNA-seq applications at the Cancer Genome Atlas project at the University of North Carolina at Chapel Hill and by the equine genome annotation project at the MacLeod Lab in the Gluck Equine center at the University of Kentucky. Our tools are designed to be widely applicable, depending only on a reference genome, and not on any further annotations.

Software and Publications


Yin Hu, Yan Huang, Ying Du, Christian Orellana, Darshan Singh, Amy Johnson, Anais Monroy, Pei-Fen Kuan, Scott Hammond, Liza Makowski, Scott Randell, Derek Chiang, David Hayes, Corbin Jones, Yufeng Liu, Jan Prins and Jinze Liu
Nucleic Acids Research 2012; doi: 10.1093/nar/gks1026

Yan Huang, Yin Hu, Corbin Jones, James N. MacLeod, Derek Chiang, Yufeng Liu, Jan F. Prins, and Jinze Liu
16th Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2012
[Abstract[Full Text] [PDF] [Software Download]

Darshan Singh, Christian Orellana, Yin Hu, Corbin Jones, Yufeng Liu, Derek Chiang, Jinze Liu and Jan Prins
Bioinformatics 2011 Aug 8; doi: 10.1093/bioinformatics/btr458 
[Abstract[Full Text] [PDF] [Software Download]

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
Kai Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang, Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M. Perou, James N. MacLeod, Derek Y. Chiang, Jan F. Prins and Jinze Liu
Nucleic Acids Research 2010; doi: 10.1093/nar/gkq622

A probabilistic framework for aligning paired-end RNA-seq data
Yin Hu, Kai Wang, Xiaping He, Derek Y. Chiang, Jan F. Prins and Jinze Liu
Bioinformatics 2010 26: 1950-1957  


Contact


Email:  mapsplice@netlab.uky.edu

 

Acknowledgement


Our research is supported in part by

                KBRIN