Selected Publications
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Culhane AC, Quackenbush J
Confounding Effects in "A Six-Gene Signature Predicting Breast Cancer Lung Metastasis"
Cancer Research 2009. 69(18):7480-5.
Supplemental Material
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Aryee MJ, Gutiérrez-Pabello JA, Kramnik I, Maiti T, Quackenbush J
An Improved Empirical Bayes Approach to Estimating Differential Gene Expression in Microarray Time-Course Data: BETR (Bayesian Estimation of Temporal Regulation)
Submitted.
Supplemental Material: BETR R Package.
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Aryee M, Quackenbush J
An Optimized Predictive Strategy for Interactome Mapping
J Proteome Res. 2008 Sep;7(9):4089-94.
Supplemental Material. Format: zip, size: 1.6M.
The zip file contains the simulation code and the datasets used in the paper as well as a README
describing the contents.
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Djebbari A, Quackenbush J
Seeded Bayesian Networks:
constructing genetic networks from microarray data.
BMC Systems Biology. 2008 2:57.
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Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush J
Functional
classification analysis of somatically mutated genes in human breast and colorectal cancers.
Genomics. 2008 Jun;61(6):508-11.
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Cheng AS, Culhane AC, Chan MW, Venkataramu CR, Ehrich M, Nasir A,
Rodriguez BA, Liu J, Yan PS, Quackenbush J, Nephew KP, Yeatman TJ, Huang TH
Epithelial
progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.
Cancer Res. 2008 Mar 15;68(6):1786-96.
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Song, JS, Maghsoudi, K, Li, W, Fox, E, Quackenbush, J, and Shirley Liu, X.
Microarray blob-defect removal improves array analysis.
Bioinformatics 2007 Apr 15;23(8):966-71
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Danley PD, Mullen SP, Liu F, Nene V, Quackenbush J, Shaw KL
A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution.
BMC Genomics. 2007 Apr 25;8:109.
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Mar JC, Rubio R, Quackenbush J.
Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples.
Genome Biol. 2006;7(12):R119.
Additional file 1 Format: zip, size: 19MB.
A ZIP file containing the qRT-PCR data analyzed in this
manuscript, the software (as R code) used to perform the analysis and produce the figures
presented, and instructions on how to install R and perform the analysis as well as a
"README" that explicitly describes each file in the .zip archive.
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Chen T, Yang I, Irby R, Shain KH, Wang HG, Quackenbush J, Coppola D, Cheng JQ, Yeatman TJ.
Regulation of caspase expression and apoptosis by adenomatous polyposis coli
Cancer Res. Aug 1;63(15):4368-74 2003.
Supporting Materials
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Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Coppola D, Yeatman TJ.
Osteopontin Identified as Lead Marker of Colon Cancer Progression Using Expression Profiling on Pooled Samples
J Natl Cancer Inst. 2002 Apr 3;94(7):513-21.
Supporting Materials
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Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, and Quackenbush J.
Identification of tumor markers in models of human colorectal cancer using a 19,200 element cDNA microarray.
Cancer Res. Nov 1, 2001.
Supporting Materials:
TABLE
Slide Map
Protocols and Standard Operating Procedures
