Affiliation: Northwestern University
- Improved Statistical Analysis for Array CGH-Based DNA Copy Number AberrationsHongmei Jiang
Department of Statistics, Northwestern University, 2006 Sheridan Road, Evanston, IL 60208, USA
Cancer Inform 10:249-58. 2011..The relative strengths and weaknesses of the proposed method were demonstrated using both simulation studies and real data analysis of a liver cancer study...
- A statistical framework for accurate taxonomic assignment of metagenomic sequencing readsHongmei Jiang
Department of Statistics, Northwestern University, Evanston, Illinois, United States of America
PLoS ONE 7:e46450. 2012..It assigns reads to the low taxonomic ranks very accurately. Our statistical approach of taxonomic assignment of metagenomic reads, TAMER, is implemented in R and available at http://faculty.wcas.northwestern.edu/hji403/MetaR.htm...
- A two-step multiple comparison procedure for a large number of tests and multiple treatmentsHongmei Jiang
Northwestern University, USA
Stat Appl Genet Mol Biol 5:Article28. 2006..When compared via simulation the two-step approach has increased power over a one-step procedure, and controls the FDR at a desire significance level...
- Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitroXiao Zhang
Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
Environ Toxicol Pharmacol 34:959-68. 2012..2-fold, q-value=0.002), and some remain functionally unknown. Our results provided direct experimental evidence that diazinon may modify gene promoter DNA methylation levels, which may play a pathological role in cancer development...
- A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarraysChia Ju Lee
Computational Biology and Bioinformatics Program, Northwestemrn University, Evanston, IL 60208, USA
Int J Comput Biol Drug Des 1:396-405. 2008..In addition to the performance improvement, the general divide-and-conquer strategy can be applied to any other normalisation algorithms without modifying the underlying implementation...
- Investigating microbial co-occurrence patterns based on metagenomic compositional dataYuguang Ban
Department of Statistics, Northwestern University, Evanston, IL 60208, USA
Bioinformatics 31:3322-9. 2015..Analyzing compositional data using conventional correlation methods has been shown prone to bias that leads to artifactual correlations...
- Novel miRNA-31 and miRNA-200a-Mediated Regulation of Retinoblastoma ProliferationVanessa Montoya
Human Molecular Genetics Program, Lurie Children s Research Center, Chicago, Illinois, 60611, United States of America Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, United States of America
PLoS ONE 10:e0138366. 2015..This work has the potential to enhance the development of targeted therapeutic approaches for retinoblastoma and improve the efficacy of treatment. ..
- A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomesNaruekamol Pookhao
Department of Agricultural and Biosystems Engineering, Interdisciplinary Program in Statistics, University of Arizona, Tucson, AZ, 85721 and Department of Statistics, Northwestern University, Evanston, IL 60208, USA
Bioinformatics 31:158-65. 2015..In metagenomic studies, one main objective is to assess whether and how multiple microbial communities differ under various environmental conditions...
- Transfer of T-DNA and Vir proteins to plant cells by Agrobacterium tumefaciens induces expression of host genes involved in mediating transformation and suppresses host defense gene expression- Veena
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 1392, USA
Plant J 35:219-36. 2003..A comparison of plant responses to different strains of Agrobacterium indicates that transfer of both T-DNA and Vir proteins modulates the expression of host genes during the transformation process...
- Genomewide nonadditive gene regulation in Arabidopsis allotetraploidsJianlin Wang
Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA
Genetics 172:507-17. 2006....
- Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant developmentLu Tian
Intercollegiate Programs in Genetics and Department of Soil and Crop Sciences, Texas A and M University, College Station, Texas 77843 2474, USA
Genetics 169:337-45. 2005....