UIUC/MUSC at TREC 2005 Genomics Track. - ChengXiang Zhai; Xu Ling; Xin He 001; Atulya Velivelli; Xuanhui Wang; Hui Fang 001; Azadeh Shakery; Xinghua Lu 001 (TREC, 2005)

Automatically Generating Gene Summaries from Biomedical Literature. - Xu Ling; Jing Jiang 007; Xin He 001; Qiaozhu Mei; ChengXiang Zhai; Bruce R. Schatz (Pacific Symposium on Biocomputing, 2006)

Robust Pseudo Feedback Estimation and HMM Passage Extraction: UIUC at TREC 2006 Genomics Track. - Jing Jiang 007; Xin He 001; ChengXiang Zhai (TREC, 2006)

Language Models for Genomics Information Retrieval: UIUC at TREC 2007 Genomics Track. - Yue Lu 002; Jing Jiang 007; Xu Ling; Xin He 001; ChengXiang Zhai (TREC, 2007)

Generating gene summaries from biomedical literature: A study of semi-structured summarization. - Xu Ling; Jing Jiang 007; Xin He 001; Qiaozhu Mei; Chengxiang Zhai; Bruce R. Schatz (Inf. Process. Manag., 2007)

MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules. - Saurabh Sinha; Xin He 001 (PLoS Comput. Biol., 2007)

Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison. - Xu Ling; Xin He 001; Dong Xin; Jiawei Han 001 (J. Comput. Biol., 2008)

Detecting gene clusters under evolutionary constraint in a large number of genomes. - Xu Ling; Xin He 001; Dong Xin (Bioinform., 2009)

Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution. - Xin He 001; Xu Ling; Saurabh Sinha (PLoS Comput. Biol., 2009)

Computational Models of Function and Evolution of cis-Regulatory Sequences - Xin He 001 (2009)

Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. - Xin He 001; Moushumi Sen Sarma; Xu Ling; Brant W. Chee; Chengxiang Zhai; Bruce R. Schatz (BMC Bioinform., 2010)

BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects. - Xin He 001; Yanen Li; Radhika S. Khetani; Barry Sanders; Yue Lu 002; Xu Ling; ChengXiang Zhai; Bruce R. Schatz (Nucleic Acids Res., 2010)

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression. - Xin He 001; Md. Abul Hassan Samee; Charles Blatti; Saurabh Sinha (PLoS Comput. Biol., 2010)

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature. - Moushumi Sen Sarma; David Arcoleo; Radhika S. Khetani; Brant W. Chee; Xu Ling; Xin He 001; Jing Jiang 007; Qiaozhu Mei; ChengXiang Zhai; Bruce R. Schatz (Nucleic Acids Res., 2011)