Oral Paper presentation:
Presenter: Jin Liu (M.S., Computer Science)
Title: Combinatorial Fusion Algorithm for Peak Finding in ChIP-Seq Histone Study
Mentors: Prof. D. Frank Hsu and Prof. Christina Schweikert
Other Co-authors:
Wei An (M.S. Candidate, Computer Science)
Samantha Yu (B.S. Candidate, Chemistry)
Dr. Stuart Brown (NYU Medical School)
Dr. Zuojian Tang (NYU Medical School)
Next generation sequencing, such as ChIP-seq, is used to analyze protein interactions
with DNA. In this project we apply Combinatorial Fusion Analysis (CFA) to various
systems for analyzing ChIP-seq data; in this case we are using a histone modification data
set. CFA is a method for analyzing the combination and fusion of multiple scoring
systems. CFA has been successfully used in several different domains including
microarray gene expression analysis, information retrieval, pattern recognition, target
tracking, virtual screening and drug discovery, and protein structure prediction. We
analyze the following five methods: TRLocator (Transcription Region Locator), MACS
(Model-based Analysis of ChIP-Seq), SISSRs (Site Identification from Short Sequence
Reads), CisGenome, and QuEST (quantitative enrichment of sequence tags). For each
method, we analyze various features which associate scores with each putative region
such as tag count, p-value, and fold enrichment; we apply CFA to analyze feature
combinations by score and rank. On the level of method combination, we merge
overlapping regions between two methods to create the intersection and union between
each pair of methods in order to evaluate their combination.
Brief Bio
Jin Liu obtained her Master’s degree in Computer Science in the Department of
Computer and Information Science at Fordham University in February 2010. She
received her Bachelor’s degree in Software Engineering from Huazhong University of
Science and Technology, China in 2007. She did research on the peer-to-peer
communication across Network Address Translators and graduated with the Outstanding
Graduate prize. In fall 2008, Jin Liu entered Fordham to start her graduate study as the
Presidential Tuition Scholarship and University Fellowship recipient. Jin Liu is currently
working on applying the combinatorial fusion algorithm for peak finding in ChIP-seq
histone study in the Informatics and Data Mining Lab in the Department of Computer and
Information Science.