Wing-Kin Sung

TL;DR: An algorithm called LocalMotif is reported, based on a novel scoring function, called spatial confinement score, which can determine the exact interval of localization of a motif and successfully discovers biologically relevant motifs and their intervals of localization in scenarios where the motifs cannot be discovered by general motif finding tools.

TL;DR: The performance of BatVI was compared with existing methods VirusFinder and VirusSeq using both simulated and real-life datasets of liver cancer patients and it was able to predict almost twice the number of true positives compared to other methods while maintaining a false positive rate less than 1%.

TL;DR: A new, fast graph decomposition technique called a three-layer partition is introduced that may be useful for solving other graph problems in the future and the first non-trivial lower bound is presented, 2.8n-2, on the period length for the oblivious case.

TL;DR: An O(n)-space index that supports k-error matching in O(m+occ+(logn)^k^(^k ^+^1^)log logn) worst-case time is presented, which can be further compressed from O (n) words into O( n) bits with a slight increase in the time complexity.

TL;DR: This paper proposes new techniques to improve database-free non-reference transposition calling, including a realignment strategy called one-end remapping that corrects the alignments of reads in interspersed repeats and a SNV-aware filter that removes some incorrectly aligned reads.