Program in Bioinformatics & Proteomics/Genomics : Recent Publications

Publications co-authored by, or citing BPG faculty/staff:

Mruk, Iwona, Preeti, Rajesh, Blumenthal, R.M. Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system. Nucleic Acids Res. 2007 doi: 10.1093/nar/gkm837.

Paul, L., Mishra, P.K., Blumenthal, R.M., and Matthews, R.G. Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR. BMC Microbiol. 2007 7:2, 1471-2180.

Knowle, D., Lintner, R.E., Touma, Y.M., Blumenthal, R.M. Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems. J. Bacteriol. 2005 87:488-497.

Schubert, H.L., Blumenthal, R.M., and Cheng, X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 2003 28: 329-335.

Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., et al. (47 authors total). A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids 2003 Res. 31:1805-1812.

Tani, T.H., Khodursky, A., Blumenthal, R.M., Brown, P.O., and Matthews, R.G. Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. 2002 USA 99:13471-13476.

Bujnicki, J.M., Feder, M., Radlinska, M., Blumenthal, R.M. Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m6A methyltransferase. J. Molec. Evol. 2002 55:431-444.

Naderer, M., Brust, J.R., Knowle, D., Blumenthal, R.M. Mobility of a restriction-modification system revealed by its genetic contexts in three hosts. J. Bacteriol., 2002 184:2411-2419.

Cheng, X., Blumenthal, R.M. Cytosines do it, thymines do it, even pseudouridines do it _ base flipping by an enzyme that acts on RNA. Structure, 2002 10:127-129.

Bujnicki, J.M., Blumenthal, R.M. and Rychlewski, L. Sequence analysis and structure prediction of 23S rRNA: m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. J. Mol. Microbiol. Biotechnol. 2002 4:93-99.

Paul, L., Blumenthal, R.M. and Matthews, R.G. Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF. J. Bacteriol. 2001 183:3910-3918.

Blumenthal, R.M. and Cheng, X. A Taq attack displaces bases. Nature Struct. Biol. 2001 8:101-103.

Rice, M.R., and Blumenthal, R.M. Recognition of native DNA methylation by the PvuII restriction endonuclease. Nucleic Acids Res.2000 28:3143-3150.

Vijesurier, R.M., Carlock, L., Blumenthal, R.M. and Dunbar, J.C. Role and Mechanism of Action of C.PvuII, a Regulatory Protein Conserved among Restriction-Modification Systems. J. Bact. 2000 182:477-487.

Rice, M.R., Koons, M.D. and Blumenthal, R.M. Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG sites. Nucleic Acids Res. 1999 27:1032-1038.

VanBogelen, R.A., Greis, K.D., Blumenthal, R.M., Tani, T.M. and Matthews, R.G. Mapping regulatory networks in microbial cells. Trends Microbiol. 1999 7:320-328.

Bhagwat, S.P., Rice, M.R., Matthews, R.G., and Blumenthal, R.M. Use of an inducible regulatory protein to identify members of a regulon: application to the regulon controlled by the leucine-responsive regulatory protein (Lrp) in Escherichia coli. J of Bacteriology 1997 179:6254-6263.

Wiese II, D.E., Ernsting, B.R., Blumenthal, R.M. and Matthews, R.G. A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli. J. Molec. Biol. 1997 270:152-168.

Adams, G.M. and Blumenthal, R.M. The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsindefined domains, each of which binds a molecule of S-adenosyl-L-methionine. Biochemistry 1997 36:8284-8292.

Gong, W., O'Gara, M., Blumenthal, R.M. and Cheng, X. Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 1997 25: 2702-2715 (cover article). cover image - PDF article

Master, S.S. and Blumenthal, R.M. A genetic and functional analysis of the unusually large variable region in the M•.AAluI DNA-(cytosine C5)-methyltransferase. Mol. Gen. Genet. 1997 257:14-22.

O'Gara, M., Adams, G.M., Gong, W., Kobayashi, R., Blumenthal, R.M., Cheng, X. Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). European J. Biochem. 1997 247:1009-1018.

Blumenthal, R.M., Borst, D.W., Matthews, R.G. Experimental analysis of global gene regulation in Escherichia coli [review]. Progress in Nucl. Acid Res. & Molec. Bio. 1996 55:1-86.

Borst, D.W., Blumenthal, R.M., Matthews, R.G. Use of an in vivo titration method to study a global regulator: effect of varying Lrp levels on expression of gltBDF in Escherichia coli. J. Bacteriology 1996 178:6904-6912.

Cheng, X. and Blumenthal, R.M. Finding a basis for flipping bases. Structure 1996 4:639-645.

Thole, J.E., Dessens-Kroon, M.W., van Embden, J.D., and Hermans, P.W. (1996) Host-mediated modification of PvuII restriction in mycobacterium tuberculosis. J. Bacteriology 178:78-84.

Adams, G.M. and Blumenthal, R.M. Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association. Gene 1995157:193-199.

Koons, C.,and Blumenthal, R.M. Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system. Gene 1995 157:78-79.

Ferrario, M., Ernsting, B.R., Borst, D.W., Wiese, D.E. II, Blumenthal, R.M., Matthews, R.G. The leucineresponsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF. J. Bacteriology 1995 177:103-113.

Malone, T., Blumenthal, R.M. and Cheng, X. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Molec. Biol. 1995 253:618-632.

Drummond, J.T., Huang, S., Blumenthal, R.M., and Matthews, R.G. Assignment of enzymatic function to specific protein regions of cobalamin-dependent methionine synthase from Escherichia coli. Biochemistry 1993 32:9290-9295.

Ernsting, B.R., Denninger, J.W., Blumenthal, R.M., and Matthews, R.G. Regulation of the gitBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein? J. Bacteriology 1993 175:7160-7169.

Zhang, B., Tao, T., Wilson, G.G., Blumenthal, R.M. The M. AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region. Nucl. Acids Res. 1993 21:905-911.

Guan, L., Blumenthal, R.M., and Burnham, J.C. Analysis of macromolecular biosynthesis to define the quinoloneinduced postantibiotic effect in Escherichia coli. Antimicrobial Agents & Chemotherapy 1992 36:2118-2124.

Bazeley PS, Shepelev V, Talebizadeh Z, Butler MG, Fedorova L, Filatov V, Fedorov A. snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene. 2008 Jan 31;408(1-2):172-9.

Havlioglu N, Wang J, Fushimi K, Vibranovski MD, Kan Z, Gish W, Fedorov A, Long M, Wu JY. An intronic signal for alternative splicing in the human genome. PLoS ONE. 2007 Nov 28;2(11):e1246.

Douglas JF, Iwasawa H, Sun Z, Fedorov AV, Ishikado M, Saitoh T, Eisaki H, Bando H, Iwase T, Ino A, Arita M, Shimada K, Namatame H, Taniguchi M, Masui T, Tajima S, Fujita K, Uchida S, Aiura Y, Dessau DS. Superconductors: unusual oxygen isotope effects in cuprates? Nature. 2007 Mar 15;446(7133):E5.

Colakerol L, Veal TD, Jeong HK, Plucinski L, Demasi A, Learmonth T, Glans PA, Wang S, Zhang Y, Piper LF, Jefferson PH, Fedorov A, Chen TC, Moustakas TD, McConville CF, Smith KE. Quantized electron accumulation States in indium nitride studied by angle-resolved photoemission spectroscopy. Phys Rev Lett. 2006 Dec 8; 97(23):237601.

Shepelev V, Fedorov A. Advances in the Exon-Intron Database (EID). Brief Bioinform. 2006 Jun;7(2):178-85.

Shao X, Shepelev V, Fedorov A. Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics. 2006 Mar 15;22(6):692-8.

Fedorov A, Fedorova L. Where is the difference between the genomes of humans and annelids? Genome Biol. 2006;7(1):203.

Fedorov A, Stombaugh J, Harr MW, Yu S, Nasalean L, Shepelev V. Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucleic Acids Res. 2005 Aug 10;33(14):4578-83.

Fedorov A, Fedorova L. Introns: mighty elements from the RNA world. J Mol Evol. 2004 Nov;59(5):718-21.

Fedorov A, Hartman H. What does the microsporidian E. cuniculi tell us about the origin of the eukaryotic cell? J Mol Evol. 2004 Nov;59(5):695-702.

Fedorov A, Roy S, Fedorova L, Gilbert W. Mystery of intron gain. Genome Res. 2003 Oct;13(10):2236-41.

Fedorova L, Fedorov A. Introns in gene evolution. Genetica. 2003 Jul;118(2-3):123-31.

Roy SW, Fedorov A, Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7158-62.

Fedorov A, Roy S, Cao X, Gilbert W. Phylogenetically older introns strongly correlate with module boundaries in ancient proteins. Genome Res. 2003 Jun;13(6A):1155-7.

Fedorov A, Merican AF, Gilbert W. Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16128-33.

Roy SW, Fedorov A, Gilbert W. The signal of ancient introns is obscured by intron density and homolog number. Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15513-7.

Endo T, Fedorov A, de Souza SJ, Gilbert W. Do introns favor or avoid regions of amino acid conservation? Mol Biol Evol. 2002 Apr;19(4):521-252.

Fedorov A, Saxonov S, Gilbert W. Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 2002 Mar 1;30(5):1192-7.

Hartman H, Fedorov A. The origin of the eukaryotic cell: a genomic investigation. Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1420-5.

Khuder S, Milz SA, Bisesi M, Vincent R, McNulty W, Czajkowski K. Health survey of residents living near farm fields permitted to receive biosolids. Arch Environ Occup Health. 2007 Jan-Feb;62(1):5-11.

Kleshinski J, Khuder SA, Shapiro JI, Gold JP. Impact of preadmission variables on USMLE step 1 and step 2 performance. Adv Health Sci Educ Theory Pract. 2007 Nov 7

Akbar-Khanzadeh F, Milz S, Ames A, Susi PP, Bisesi M, Khuder SA, Akbar-Khanzadeh M. Crystalline silica dust and respirable particulate matter during indoor concrete grinding - wet grinding and ventilated grinding compared with uncontrolled conventional grinding. J Occup Environ Hyg. 2007 Oct;4(10):770-9.

Tietjen GE, Peterlin BL, Brandes JL, Hafeez F, Hutchinson S, Martin VT, Dafer RM, Aurora SK, Stein MR, Herial NA, Utley C, White L, Khuder SA. Depression and anxiety: effect on the migraine-obesity relationship. Headache. 2007 Jun;47(6):866-75.

Khuder SA, Milz S, Jordan T, Price J, Silvestri K, Butler P. The impact of a smoking ban on hospital admissions for coronary heart disease. Prev Med. 2007 Jul;45(1):3-8.

Kennedy DJ, Burket MW, Khuder SA, Shapiro JI, Topp RV, Cooper CJ. Quality of life improves after renal artery stenting. Biol Res Nurs. 2006 Oct;8(2):129-37.

Pirzada Y, Khuder S, Donabedian H. Predicting AIDS-related events using CD4 percentage or CD4 absolute counts. AIDS Res Ther. 2006 Aug 17;3:20.

Shriner AK, Smithson SL, Rabquer B, Khuder S, Westerink MA. Analysis of the young and elderly variable gene repertoire in response to pneumococcal polysaccharides using a reconstituted SCID mouse model. Vaccine. 2006 Nov 30;24(49-50):7159-66.

Shriner AK, Smithson SL, Prinz DM, Rabquer B, Khuder S, Goomber R, Westerink MA. Comparison of the human immune response to conjugate and polysaccharide pneumococcal vaccination using a reconstituted SCID mouse model. Vaccine. 2006 Nov 30;24(49-50):7197-203.

Akpunonu BE, Mutgi AB, Khuder SA. Trends in racial disparities in care. N Engl J Med. 2005 Nov 10;353(19):2081-5; author reply 2081-5. No abstract available.

Mullins DN, Crawford EL, Khuder SA, Hernandez DA, Yoon Y, Willey JC. CEBPG transcription factor correlates with antioxidant and DNA repair genes in normal bronchial epithelial cells but not in individuals with bronchogenic carcinoma. BMC Cancer. 2005 Oct 29;5:141.

Walker PR, Khuder SA, Quan WD Jr. Continuous infusion interleukin-2 and antihistamines in metastatic kidney cancer. Cancer Biother Radiopharm. 2005 Oct;20(5):487-90.

Smithson SL, Kolibab K, Shriner AK, Srivastava N, Khuder S, Westerink MA. Immune response to pneumococcal polysaccharides 4 and 14 in elderly and young adults: analysis of the variable light chain repertoire. Infect Immun. 2005 Nov;73(11):7477-84.

Kolibab K, Smithson SL, Rabquer B, Khuder S, Westerink MA. Immune response to pneumococcal polysaccharides 4 and 14 in elderly and young adults: analysis of the variable heavy chain repertoire. Infect Immun. 2005 Nov;73(11):7465-76.

Kolibab K, Smithson SL, Shriner AK, Khuder S, Romero-Steiner S, Carlone GM, Westerink MA. Immune response to pneumococcal polysaccharides 4 and 14 in elderly and young adults. I. Antibody concentrations, avidity and functional activity. Immun Ageing. 2005 Jun 27;2:10.

Tietjen GE, Athanas K, Utley C, Herial NA, Khuder SA. The combination of naratriptan and prochlorperazine in migraine treatment. Headache. 2005 Jun;45(6):751-3. No abstract available.

Weaver DA, Crawford EL, Warner KA, Elkhairi F, Khuder SA, Willey JC. ABCC5, ERCC2, XPA and XRCC1 transcript abundance levels correlate with cisplatin hemoresistance in non-small cell lung cancer cell lines. Mol Cancer. 2005 May 9;4(1):18.

Cipriani D, Fox C, Khuder S, Boudreau N. Comparing Rasch analyses probability estimates to sensitivity, specificity and likelihood ratios when examining the utility of medical diagnostic tests. J Appl Meas. 2005;6(2):180-201.

Khuder SA, Herial NA, Mutgi AB, Federman DJ. Nonsteroidal antiinflammatory drug use and lung cancer: a metaanalysis. Chest. 2005 Mar;127(3):748-54.

Werning JW, Downey NM, Brinker RA, Khuder SA, Davis WJ, Rubin AM, Elsamaloty HM. The impact of osteoporosis on patients with maxillofacial trauma. Arch Otolaryngol Head Neck Surg. 2004 Mar;130(3):353-6.

Kennedy DJ, Colyer WR, Brewster PS, Ankenbrandt M, Burket MW, Nemeth AS, Khuder SA, Thomas WJ, Shapiro JI, Cooper CJ. Renal insufficiency as a predictor of adverse events and mortality after renal artery stent placement. Am J Kidney Dis. 2003 Nov;42(5):926-35.

Fitzgerald K, Chakraborty J, Shah T, Khuder S, Duggan J. HIV/AIDS knowledge among female migrant farm workers in the midwest. J Immigr Health. 2003 Jan;5(1):29-36.

Reddy BK, Kennedy DJ, Colyer WR, Burket MW, Thomas WJ, Khuder SA, Shapiro JI, Topp RV, Cooper CJ. Compliance with antihypertensive therapy after renal artery stenting. Biol Res Nurs. 2003 Jul;5(1):37-46.

Mauro VF, Mauro LS, Kleshinski JF, Khuder SA, Wang Y, Erhardt PW. Impact of ginkgo biloba on the pharmacokinetics of digoxin. Am J Ther. 2003 Jul-Aug;10(4):247-51.

Duggan J, Khuder S, Sinha N, Chakraborty J. Survey of physician attitudes toward HIV testing in pregnant women in Ohio. AIDS Patient Care STDS. 2003 Mar;17(3):121-7.

Kleshinski JF, Crews C, Fry E, Stewart B, Reinhart C, Tolliver J, Khuder S. A survey of herbal product use in a dialysis population in Northwest Ohio. J Ren Nutr. 2003 Apr;13(2):93-7.

Khuder SA, Peshimam AZ, Agraharam S. Environmental risk factors for rheumatoid arthritis. Rev Environ Health. 2002 Oct-Dec;17(4):307-15.

Werning JW, Heard D, Pagano C, Khuder S. Elective management of the clinically negative neck by otolaryngologists in patients with oral tongue cancer. Arch Otolaryngol Head Neck Surg. 2003 Jan;129(1):83-8.

Topp R, Woolley S, Hornyak J 3rd, Khuder S, Kahaleh B. The effect of dynamic versus isometric resistance training on pain and functioning among adults with osteoarthritis of the knee. Arch Phys Med Rehabil. 2002 Sep;83(9):1187-95.

Curtin WM, Shehata BM, Khuder SA, Robinson HB, Brost BC. The feasibility of using histologic placental sections to predict newborn nucleated red blood cell counts. Obstet Gynecol. 2002 Aug;100(2):305-10.

Crawford EL, Warner KA, Khuder SA, Zahorchak RJ, Willey JC. Multiplex standardized RT-PCR for expression analysis of many genes in small samples. Biochem Biophys Res Commun. 2002 Apr 26;293(1):509-16.

Tietjen GE, Gottwald L, Al-Qasmi MM, Gunda P, Khuder SA. Migraine is associated with livedo reticularis: a prospective study. Headache. 2002 Apr;42(4):263-7.

Rees MA, Butler AJ, Chavez-Cartaya G, Wight DG, Casey ND, Alexander G, Khuder SA, White DJ, Friend P J. Plonged function of extracorporeal hDAF transgenic pig livers perfused with human blood. Transplantation. 2002 Apr 27;73(8):1194-202.

Werning JW, Preston TW, Khuder S. Physician specialty is associated with differences in the evaluation and management of acute bacterial rhinosinusitis. Arch Otolaryngol Head Neck Surg. 2002 Feb;128(2):123-30.

Needham PG, Trumbly RJ. In vitro characterization of the Mig1 repressor from Saccharomyces cerevisiae reveals evidence for monomeric and higher molecular weight forms. Yeast. 2006 Dec;23(16):1151-66.

Zhang Z, Varanasi U, Carrico P, Trumbly RJ. Mutations of the WD repeats that compromise Tup1 repression function maintain structural integrity of the WD domain trypsin-resistant core. Arch Biochem Biophys. 2002 Oct 1;406(1):47-54.

Zhang Z, Varanasi U, Trumbly RJ. Functional dissection of the global repressor Tup1 in yeast: dominant role of the C-terminal repression domain. Genetics. 2002 Jul;161(3):957-69.

Davie JK, Trumbly RJ, Dent SY. Histone-dependent association of Tup1-Ssn6 with repressed genes in vivo. Mol Cell Biol. 2002 Feb;22(3):693-703.

Hong, G., Trumbly, R.J., Reimann, E.M., and Schlender, K.K. Sds22p is a subunit of a stable isolatable form of protein phosphatase 1 (GLc7p) from Saccharomyces cerevisia. Arch. Biochem. Biophys. 2000 376:228-98.

S.S. Dignam, J.S. Koushik, J. Wang, R.J. Trumbly, K.K. Schlender, E.Y.C. Lee, and E.M. Reimann Purification and characterization of Type 1 protein phosphatase form Saccharomyces cerevisiae: effect of the R73C mutation. 1998 Arch. Biochem. Biophys. 357:58-66.

J.P. Wu and R.J. Trumbly Multiple regulatory proteins mediate repression and activation by interaction with the yeast Mig1 binding site. Yeast 1998 14:985-1000.

U.S. Varanasi, M. Klis, P.B. Mikesell, and R.J. Trumbly. The Cyc8(Ssn6)-Tup1 corepressor complex is composed of one Cyc8 and four Tup1 subunits. Mol. Cell. Biol. 1996 16:6707-6714.

Lee SJ, Ways JA, Barbato JC, Essig D, Pettee K, DeRaedt SJ, Yang S, Weaver DA, Koch LG, Cicila GT. Gene expression profiling of the left ventricles in a rat model of intrinsic aerobic running capacity. Physiol Genomics. 2005 Sep 21;23(1):62-71. Epub 2005 Jul 20.

Weaver DA, Crawford EL, Warner KA, Elkhairi F, Khuder SA, Willey JC. ABCC5, ERCC2, XPA and XRCC1 transcript abundance levels correlate with cisplatin chemoresistance in non-small cell lung cancer cell lines. Mol Cancer. 2005 May 9;4(1):18.

Vondracek M, Weaver DA, Sarang Z, Hedberg JJ, Willey JC, Wärngård L, Grafström RC. Transcript profiling of enzymes involved in detoxification of xenobiotics and reactive oxygen in human normal and simian virus 40 T antigen-immortalized oral keratinocytes. Int J Cancer. 2002 Jun 20;99(6):776-82.

Crawford, E.L., Peters, G.J., Noordhuis, P., Rots, M.G., Vondracek, M., Grafström, R.C., Lieuallen, K., Lennon, G., Zahorchak, R.J., Georgeson, M.J., Wali, A., Lechner, J.F., Fan, P.S., Kahaleh, M.B., Khuder, S.A., Warner, K.A., Weaver, D.A., and Willey, J.C.Reproducible gene expression measurement among multiple laboratories obtained in a blinded study using standardized RT (StaRT)-PCR, Mol Diagn 2001 6(4), 217-225.

Crawford, E.L., Warner, K.A., Weaver, D.A., and Willey, J.C. Quantitative end-point RT-PCR gene expression measurement using the Agilent 2100 Bioanalyzer and standardized RT-PCR, Agilent Technologies Technical Application Note, 2001.

Willey, J.C., Crawford, E.L., Olson, D.E., Hammersley, J.R., Jennings, C.A., Weaver, D.A., Utell, M.J., Frampton, M.W. and Durham, S.J.Expression measurement of genes related to cancer susceptibility in human bronchial epithelial cells, In Relationships between acute and chronic effects of air pollution, (eds) U. Heinrich and U. Mohr, 2000 International Life Sciences Press, Washington, D.C., 79-96.

Crawford, E.L., Khuder, S.A., Durham, S.J., Frampton, M., Utell, M., Thilly, W.G., Weaver, D.A., Ferencak, W.J., Jennings, C.A., Hammersley, J.R., Olson, D.E. and Willey, J.C. Normal bronchial epithelial cell expression of glutathione transferase P1, glutathione transferase M3, and glutathione peroxidase is low in subjects with bronchogenic carcinoma, Cancer Res 2000, 60(6), 1609-1618, 2000.

Weaver, D.A., Hei, T.K., Hukku, B., DeMuth, J.P., Crawford, E.L., McRaven, J.A., Girgis, S. and Willey, J.C. Localization of tumor suppressor gene candidates by cytogenetic and short tandem repeat analyses in tumorigenic human bronchial epithelial cells, Carcinogenesis 2000, 21(2), 205-211.

Crawford, E.L., Weaver, D.A., DeMuth, J.P., Jackson, C.M., Khuder, S.A., Frampton, M.W., Utell, M.J., Thilly, W.G. and Willey, J.C. Measurement of cytochrome P450 2A6 and 2E1 gene expression in primary human bronchial epithelial cells, Carcinogenesis 1998, 19(10), 1867-1871.

Willey, J.C., Crawford, E.L., Jackson, C.M., Weaver, D.A., Hoban, J.C., Khuder, S.A. and DeMuth, J.P. Expression measurement of many genes simultaneously by quantitative RT-PCR using standardized mixtures of competitive templates, Am J Respir Cell Mol Biol, 1998 19(1), 6-17.

DeMuth, J.P., Jackson, C.M., Weaver, D.A., Crawford, E.L., Durzinsky, D.S., Durham, S.J., Zaher, A., Phillips, E.R., Khuder, S.A. and Willey, J.C. The gene expression index c-myc x E2F-1/p21 is highly predictive of malignant phenotype in human bronchial epithelial cells, Am J Respir Cell Mol Biol, 1998 19(1), 18-24.

DeMuth, J.P., Weaver, D.A., Crawford, E.L., Jackson, C.M. and Willey, J.C. Loss of spr1 expression measurable by quantitative RT-PCR in human bronchogenic carcinoma cell lines, Am J Respir Cell Mol Biol 1998 19(1), 25-29.

Weaver, D.A., Hei, T.K., Hukku, B., McRaven, J.A. and Willey, J.C. Cytogenetic and molecular genetic analysis of tumorigenic human bronchial epithelial cells induced by radon alpha particles, Carcinogenesis 1997 18(6), 1251-1257.

Liao JG, Chin KV. Logistic regression for disease classification using microarray data: model selection in a large p and small n case. Bioinformatics. 2007 Aug 1;23(15):1945-51. Epub 2007 May 31.

Chin KV, Alabanza L, Fujii K, Kudoh K, Kita T, Kikuchi Y, Selvanayagam ZE, Wong YF, Lin Y, Shih WC. Application of expression genomics for predicting treatment response in cancer. Ann N Y Acad Sci. 2005 Nov;1058:186-95.

Liang L, Chen J, Vittal R, Selvanayagam ZE, McAteer JA, Deng L, Tischfield J, Chin KV, Sahota A. Expression profiling of crystal-induced injury in human kidney epithelial cells. Nephron Physiol. 2006;103(1):p53-62. Epub 2005 Dec 21.

Hou Z, Sang S, You H, Lee MJ, Hong J, Chin KV, Yang CS. Mechanism of action of (-)-epigallocatechin-3-gallate: auto-oxidation-dependent inactivation of epidermal growth factor receptor and direct effects on growth inhibition in human esophageal cancer KYSE 150 cells. Cancer Res. 2005 Sep 1; 65 (17): 8049-56.

Ravatn R, Wells V, Nelson L, Vettori D, Mallucci L, Chin KV. Circumventing multidrug resistance in cancer by beta-galactoside binding protein, an antiproliferative cytokine. Cancer Res. 2005 Mar 1;65(5):1631-4.

Hou Z, Lambert JD, Chin KV, Yang CS. Effects of tea polyphenols on signal transduction pathways related to cancer chemoprevention. Mutat Res. 2004 Nov 2;555(1-2):3-19.

Selvanayagam ZE, Cheung TH, Wei N, Vittal R, Lo KW, Yeo W, Kita T, Ravatn R, Chung TK, Wong YF, Chin KV. Prediction of chemotherapeutic response in ovarian cancer with DNA microarray expression profiling. Cancer Genet Cytogenet. 2004 Oct 1;154(1):63-6.

Vittal R, Selvanayagam ZE, Sun Y, Hong J, Liu F, Chin KV, Yang CS. Gene expression changes induced by green tea polyphenol (-)-epigallocatechin-3-gallate in human bronchial epithelial 21BES cells analyzed by DNA microarray. Mol Cancer Ther. 2004 Sep;3(9):1091-9.

Kita T, Goydos J, Reitman E, Ravatn R, Lin Y, Shih WC, Kikuchi Y, Chin KV. Extracellular cAMP-dependent protein kinase (ECPKA) in melanoma. Cancer Lett. 2004 May 28;208(2):187-91.

Yang CS, Chin KV, Lambert JD. Cancer chemoprevention by targeting proteasomal degradation: commentary re KA Dragnev et al, Specific chemopreventive agents trigger proteasomal degradation of G1 cyclins: implications for combination therapy. Clin Cancer Res, 2004;10:2570-7. Clin Cancer Res. 2004 Apr 1;10(7):2220-1. No abstract available.

Wong YF, Selvanayagam ZE, Wei N, Porter J, Vittal R, Hu R, Lin Y, Liao J, Shih JW, Cheung TH, Lo KW, Yim SF, Yip SK, Ngong DT, Siu N, Chan LK, Chan CS, Kong T, Kutlina E, McKinnon RD, Denhardt DT, Chin KV, Chung TK. Expression genomics of cervical cancer: molecular classification and prediction of radiotherapy response by DNA microarray. Clin Cancer Res. 2003 Nov 15;9(15):5486-92.

Chin KV, Kong AN. Application of DNA microarrays in pharmacogenomics and toxicogenomics. Pharm Res. 2002 Dec;19(12):1773-8.

Zheng X, Ravatn R, Lin Y, Shih WC, Rabson A, Strair R, Huberman E, Conney A, Chin KV. Gene expression of TPA induced differentiation in HL-60 cells by DNA microarray analysis. Nucleic Acids Res. 2002 Oct 15;30(20):4489-99.

Strair RK, Schaar D, Goodell L, Aisner J, Chin KV, Eid J, Senzon R, Cui XX, Han ZT, Knox B, Rabson AB, Chang R, Conney A. Administration of a phorbol ester to patients with hematological malignancies: preliminary results from a phase I clinical trial of 12-O-tetradecanoylphorbol-13-acetate. Clin Cancer Res. 2002 Aug;8(8):2512-8.

Chin KV, Yang WL, Ravatn R, Kita T, Reitman E, Vettori D, Cvijic ME, Shin M, Iacono L. Reinventing the wheel of cyclic AMP: novel mechanisms of cAMP signaling. Ann N Y Acad Sci. 2002 Jun;968:49-64.

Chin KV, Seifer DB, Feng B, Lin Y, Shih WC. DNA microarray analysis of the expression profiles of luteinized granulosa cells as a function of ovarian reserve. Fertil Steril. 2002 Jun;77(6):1214-8.