PseudoPipe: an automated pseudogene identification pipeline. - Zhaolei Zhang; Nicholas Carriero; Deyou Zheng; John E. Karro; Paul M. Harrison; Mark Gerstein (Bioinform., 2006)

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. - John E. Karro; Yangpan Yan; Deyou Zheng; Zhaolei Zhang; Nicholas Carriero; Philip Cayting; Paul M. Harrison; Mark Gerstein (Nucleic Acids Res., 2007)

Is there an acceleration of the CpG transition rate during the mammalian radiation? - Martin Peifer; John E. Karro; H. H. von Grünberg (Bioinform., 2008)

PEACE: Parallel Environment for Assembly and Clustering of Gene Expression. - Dhananjai Madhava Rao; J. C. Moler; Mufit Ozden; Y. Zhang; C. Liang; John E. Karro (Nucleic Acids Res., 2010)

Workshop: Transcript assembly through a d2-based MST approach. - Yuan Zhang; Dhananjai Madhava Rao; Jens Mueller; Mufit Ozden; Chun Liang; John E. Karro (ICCABS, 2011)

Poster: Sequence classification of homopolymer emissions (SCOPE). - James T. Morton; Patricia Abrudan; Chun Liang; John E. Karro (ICCABS, 2012)

Poster: De novo expression fragment assembly from Spanning Trees (EAST). - Yuan Zhang; Dhananjai Madhava Rao; Mufit Ozden; Jens Mueller; Praveen Raj Kumar; Chun Liang; John E. Karro (ICCABS, 2012)

RAIDER: Rapid Ab Initio Detection of Elementary Repeats. - Nathaniel D. Figueroa; Xiaolin Liu; Jiajun Wang; John E. Karro (BSB, 2013)

A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences. - Sutharzan Sreeskandarajan; Michelle M. Flowers; John E. Karro; Chun Liang (Bioinform., 2014)

phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats. - Carly E. Schaeffer; Nathaniel D. Figueroa; Xiaolin Liu; John E. Karro (Bioinform., 2016)