Affiliation: University of Chicago
- Variants affecting exon skipping contribute to complex traitsYounghee Lee
Department of Medicine, The University of Chicago, Chicago, IL, USA
PLoS Genet 8:e1002998. 2012..We find that SNPs we would predict to affect exon skipping are enriched among the set of SNPs reported to be associated with complex human traits...
- Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseasesYounghee Lee
Center for Biomedical Informatics, The University of Chicago, Chicago, Illinois, USA
J Am Med Inform Assoc 20:619-29. 2013..Physical protein interactions have been utilized to increase our understanding of human Mendelian disease loci but have yet to be fully exploited for complex traits...
- Curation-free biomodules mechanisms in prostate cancer predict recurrent diseaseJames L Chen
Center for Biomed Informatics and Department of Medicine, The University of Chicago, Chicago, IL, USA
BMC Med Genomics 6:S4. 2013....
- Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theoryHaiquan Li
Center for Biomedical Informatics, Department of Medicine, University of Chicago, Illinois, USA
J Am Med Inform Assoc 19:295-305. 2012..The authors hypothesize that biological annotations of host genes of trait-associated SNPs may reveal the biomolecular modularity across complex-disease traits and offer insights for drug repositioning...
- Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variantsKelly Regan
Department of Medicine, University of Illinois at Chicago, Chicago, Illinois 60637, USA
J Am Med Inform Assoc 19:306-16. 2012....
- Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signaturesJames Chen
Sections of Hematology Oncology, the University of Chicago Cancer Research Center, The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA
J Biomed Inform 43:385-96. 2010..http://www.lussierlab.org/publication/networksignature/...
- Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor modelsXinan Yang
Section of Genetic Medicine, Dept, of Medicine, University of Chicago, IL, USA
BMC Bioinformatics 11:S11. 2010..Our purpose is to elucidate stromal microenvironment signals from probes on human arrays unintentionally cross-hybridizing with mouse homologous genes in xenograft tumor models...
- GO-Module: functional synthesis and improved interpretation of Gene Ontology patternsXinan Yang
Department of Medicine, Section of Genetic Medicine and Center for Biomedical Informatics, The University of Chicago, Chicago, IL, USA
Bioinformatics 27:1444-6. 2011..Altogether, the features (biomodules) of GO-Module outputs are better organized and on average four times smaller than the input GO terms list (P = 0.0005, n = 16)...
- Hidden dangers: a cryptic exon disrupts BRCA2 mRNAJames D Fackenthal
Center for Clinical Cancer Genetics and Global Health, The University of Chicago Medical Center, Chicago, IL 60637, USA
Clin Cancer Res 18:4865-7. 2012..The mutation lies deep within an intron and would not have been detected by conventional screening methods. In the future, more mutations may be discovered by direct mRNA analysis...
- Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasisYounghee Lee
Section of Genetic Medicine and Center for Biomedical Informatics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
PLoS Comput Biol 6:e1000730. 2010....