Methods

Analysis of Microarray Data

Significance analysis of microarrays (SAM) (software) Prediction analysis for microarrays (PAM) (software)

Tusher V, Tibshirani R & Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121, 2001

Tibshirani R, Hastie T, Narasimhan B, Chu G: Multi-class diagnosis of cancers using shrunken centroids of gene expression. Proc Natl Acad Sci USA 99: 6567-6572, 2002

Rieger K, Chu G: Portrait of transcriptional responses to ultraviolet and ionizing radiation in human cells. Nuc Acids Res 32(16): 4786-4803, 2004

Rieger K, Hong WJ, Tusher VG, Tang J, Tibshirani R, Chu G: Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage. Proc Natl Acad Sci USA 101: 6635-6640, 2004

Hong WJ, Warnke R, Chu G: Immune signatures in follicular lymphoma (Letter). N Engl J Med 352: 1496-1497, 2005

Hong WJ, Tibshirani R, Chu G: Local false discovery rate facilitates comparison of different microarray experiments. Nuc Acids Res 37: 7483-7497, 2009

Pulsed Field Electrophoresis

Chu G, Vollrath D, Davis RW: Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science 234: 1582-1585, l986

Chu G: Pulsed field electrophoresis for the resolution of DNA by size or topology. Electrophoresis 10: 290-295, 1989

Chu G: Pulsed-field gel electrophoresis: theory and practice. Methods 1: 129-142, 1990

Chu G: Apparatus for contour-clamped homogeneous electric fields. Methods 1: 212-214, 1990

Chu G, Gunderson K: Separation of large DNA by a variable-angle contour-clamped homogeneous electric field apparatus. Anal Biochem 194: 439-446, 1991

Gunderson K, Chu G: Pulsed-field electrophoresis of megabase-sized DNA. Mol Cell Biol 11: 3348-3354, 1991

Chu G: Bag model for DNA migrating in a pulsed electric field. Proc Natl Acad Sci USA 88: 11071-11075, 1991

Electrophoretic Mobility Shift Assays for DNA Repair Proteins

Chu G, Chang E: Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA. Science 242: 564-567, 1988

Hwang B, Chu G: Purification and characterization of a human protein that binds to damaged DNA. Biochemistry 32: 1657-1666, 1993

Rathmell WK, Chu G: A DNA-end-binding factor involved in double-strand break repair and V(D)J recombination. Mol Cell Biol 14: 4741-4748, 1994

Tsai C, Smider V, Hwang BJ, Chu G: Electrophoretic mobility shift assays for protein-DNA complexes involved in DNA repair. Methods Mol Biol 920: 53-78, 2012

Other Methods

Chu G, Tam K: Three dimensional imaging in the positron camera using Fourier techniques. Phys Med Biol 22: 245-265, l977

Chu G: The kinetics of target cell lysis by cytotoxic T lymphocytes: a description by Poisson statistics. J Immunol l20: l26l-1267, l978

Chu G, Sharp PA: SV40 DNA transfection of cells in suspension: analysis of the efficiency of transcription and translation of T antigen. Gene l3: l97-202, l98l

Chu G, Berg P: Rapid assay for detection of Escherichia coli xanthine-guanine phosphoribosyltransferase activity in transduced animal cells. Nuc Acids Res l3: 292l-2930, l985

Chu G, Hayakawa H, Berg P: Electroporation for the efficient transfection of mammalian cells with DNA. Nuc Acids Res 15: 1311-1325, l987

Hwang BJ, Chu G: Trichloroacetic acid precipitation by ultracentrifugation to concentrate dilute protein in viscous solution. Biotechniques 20: 982-983, 1996

Hwang BJ, Smith A, Chu G: Internal sequence analysis of proteins eluted from polyacrylamide gels. J. Chromatog B: Biomed Applic 686: 165-175, 1996

Budman J, Chu G: Assays for nonhomologous end-joining in extracts. Methods Enzymol 408: 430-444, 2006