Publications

Note: Students I supervised are underlined.

2016
2015
2014
2013
2012
2011
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
Chapters in Books

2016

  1. Smith ML, Lopez MF, Archer KJ, Wolen AR, Becker HC, Miles MF. Time-course analysis of brain regional expression network responses to chronic intermittent ethanol and withdrawal: Implications for mechanisms underlying excessive ethanol consumption. PLoS One, 11(1):e0146257, 2016.
  2. Ding B, Parmigiani A, Divakaruni AS, Archer K, Murphy AN, Budanov AV. Sestrin2 is induced by glucose starvation via the unfolded protein response and protects cells from non-canonical necroptotic cell death. Scientific Reports, in press.
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2015

  1. Jiayi Hou and Kellie J. Archer. Regularization method for predicting an ordinal response using longitudinal high-dimensional genomic data. Statistical Applications in Genetics and Molecular Biology 14(1):93-111, 2015.
  2. Kyle Ferber and Kellie J. Archer. Modeling discrete survival time using genomic feature data. Cancer Informatics, Mar 2;14(Suppl 2):37-43, 2015.
  3. Li W, Tang W, Teves ME, Zhang Z, Zhang L, Li H, Archer KJ, Peterson DL, Williams DC Jr, Strauss JF 3rd, Zhang Z.A MEIG1/PACRG complex in the manchette is essential for building the sperm flagella. Development, Mar 1;142(5):921-30, 2015
  4. Mateusz Makowski and Kellie J. Archer. Generalized monotone incremental forward stagewise method for modeling count data: Application predicting micronuclei frequency. Cancer Informatics, Apr 29;14(Suppl 2):97-105, 2015.
  5. Wheeler DC, Archer KJ, Burstyn I, Yu K, Stewart PA, Colt JS, Baris D, Karagas MR, Schwenn M, Johnson A, Armenti K, Silverman DT, Friesen MC. Comparison of Ordinal and Nominal Classification Trees to Predict Ordinal Expert-Based Occupational Exposure Estimates in a Case-Control Study. Ann Occup Hyg. Apr;59(3):324-35, 2015.
  6. Amanda Elswick Gentry, Colleen Jackson-Cook, Debra Lyon, Kellie J. Archer. Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces. Cancer Informatics, May 27;14(Suppl 2):201-8, 2015.
  7. Qing Zhou, Colleen Jackson-Cook, Debra Lyon, Robert Perera, Kellie J. Archer. Identifying molecular features associated with psychoneurological symptoms in women with breast cancer using multivariate mixed models. Cancer Informatics, May 7;14(Suppl 2):139-45, 2015.
  8. Chen W, Ren C, Qin H, Archer KJ, Ouyang W, Liu N, Luo X, Zhu Z, Sun S, Gao G. (2015) A generalized sequential Bonferroni procedures for GWAS in admixed populations incorporating admixture mapping information into association tests. Human Heredity, 79:80-92, 2015.
  9. Johnson RM, Vu NT, Griffin BP, Gentry AE, Archer KJ, Chalfant CE, Park MA. The Alternative Splicing of Cytoplasmic Polyadenylation Element Binding Protein 2 Drives Anoikis Resistance and the Metastasis of Triple Negative Breast Cancer. J Biol Chem. 290(42):25717-27, 2015.
  10. Siangphoe U, Archer KJ. Gene Expression in HIV-Associated Neurocognitive Disorders: A Meta-Analysis. J Acquir Immune Defic Syndr 70:479–488, 2015
  11. Archer KJ, Dobbin K, Biswas S, Day RS, Wheeler DC, Wu H. Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes. Cancer Informatics 14(Suppl 2):247-51, 2015.
  12. Sperlazza J, Rahmani M, Beckta J, Aust M, Hawkins E, Wang SZ, Zu Zhu S, Podder S, Dumur C, Archer K, Grant S, Ginder GD. Depletion of the chromatin remodeler CHD4 sensitizes AML blasts to genotoxic agents and reduces tumor formation. Blood 126(12):1462-72, 2015.
  13. Bjornsen CA, Archer KJ. Relations Between College Students' Cell Phone Use During Class and Grades. Scholarship of Teaching and Learning in Psychology Online First Publication, October 5, 2015.
  14. Mas V, Archer KJ, Maluf D. The High-Risk Age Window After Pediatric Liver Transplantation: Modeling Allograft Loss Using Mathematical Tools. Transplantation, in press
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2014

  1. Jennings C, Cassel B, Fletcher D, Wang A, Archer KJ, Skoro N, Yanni L, Del Fabbro E. Response to pain management among patients with active cancer, no evidence of disease, or chronic nonmalignant pain in an outpatient palliative care clinic. J Palliat Med. Sep;17(9):990-4, 2014.
  2. Kellie J. Archer, Jiayi Hou, Andre A.A. Williams. Classifying Normal, Nevus, and Malignant Melanoma Skin Samples using Penalized Ordinal Regression. Invited chapter in monograph, New Frontiers of Multidisciplinary Research in STEAM-H (Science, Technology, Engineering, Agriculture, Mathematics and Health) Springer Proceedings in Mathematics & Statistics, edited by Bourama Toni, pp. 111-133, 2014.
  3. Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne, Amanda Elswick Gentry. ordinalgmifs: An R package for ordinal regression in high-dimensional data settings. Cancer Informatics 13:187-95, 2014.
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2013

  1. Meier J, Roberts C, Avent K, Hazlett A, Berrie J, Payne K, Hamm D, Desmarais C, Sanders C, Hogan KT, Archer KJ, Manjili MH, Toor AA. Fractal organization of the human T cell repertoire in health and following stem cell transplantation. Biology of Blood and Marrow Transplantation, 9(3):366-77, 2013.
  2. Chen W, Chen X, Archer KJ, Liu N, Li Q, Zhao Z, Sun S, Gao G. A rapid association test procedure robust under different genetic models accounting for population stratification. Human Heredity, 75:23-33, 2013.
  3. Simon S, Archer K, Mericle R. Multi-Center Registry of Liquid Embolic Treatment of Cerebral Aneurysms. World Neurosurgery, Mar 30, pp:S1878-8750(13)00566-4, 2013.
  4. Hossein A Hamed, Adly Yacoub, Margaret A Park, Kellie Archer, Swadesh K Das, Devanand Sarkar, Steven Grant, Paul B Fisher, Paul Dent. Histone deacetylase inhibitors interact with MDA-7/IL-24 to kill primary human glioblastoma cells. Molecular Pharmacology, 84(2):171-81, 2013.
  5. Reese SE, Archer KJ, Therneau TM, Atkinson EJ, Vachon CM, de Andrade M, Kocher JP, Eckel-Passow JE. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinformatics 29(22):2877-83, 2013.
  6. Hamed HA, Das SK, Sokhi UK, Park MA, Cruickshanks N, Archer K, Ogretmen B, Grant S, Sarkar D, Fisher PB, Dent P. Combining histone deacetylase inhibitors with MDA-7/IL-24 enhances killing of renal carcinoma cells. Cancer Biol Ther., 14(11):1039-49, 2013.
  7. Menzies V, Lyon DE, Archer KJ, Zhou Q, Brumelle J, Jones KH, Gao G, York TP, Jackson-Cook C. Epigenetic alterations and an increased frequency of micronuclei in women with fibromyalgia. Nurs Res Pract., 2013:795784, 2013.
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2012

  1. Simon SD, Reig AS, Archer KJ, Mericle RA. Biomechanical attributes of microcatheters used in liquid embolization of intracranial aneurysms. J Neurointerv Surg., 4(3):211-4, 2012.
  2. Gao G, Kang G, Wang J, Chen W, Qin H, Jiang B, Li Q, Sun C, Liu N, Archer KJ, Allison DB. A generalized sequential Bonferroni procedure using smoothed weights for genome-wide association studies incorporating information on Hardy-Weinberg disequilibrium among cases. Human Heredity, 73(1):1-13, 2012.
  3. Asomaning N, Archer KJ. High-throughput DNA methylation datasets for evaluating false discovery rate methodologies. Computational Statistics and Data Analysis, 56(6):1748-1756, 2012.
  4. Mas VR, Archer KJ, Dumur CI, Scian MJ, Suh JL, King AL, Wardius ME, Straub JA, Posner MP, Brayman K, Maluf DG. Reduced expression of inflammatory genes in deceased donor kidneys undergoing pulsatile pump preservation. PLoS One, 7(4):e35526, 2012.
  5. Pang CJ, Lemsaddek W, Alhashem YN, Bondzi C, Redmond LC, Ahson N, Dumur CI, Archer KJ, Haar JL, Lloyd JA, Trudel M. KLF1, KLF2 and Myc control a regulatory network essential for embryonic erythropoiesis. Mol Cell Biol. 32(13):2628-2644, 2012.
  6. Archer KJ, Williams AAA. L1 penalized continuation ratio models for ordinal response prediction using high-dimensional datasets. Statistics in Medicine, 31(14):1464-74, 2012.
  7. Mousa AA, Archer KJ, Cappello R, Estrada-Gutierrez G, Isaacs CR, Strauss JF, Walsh SW. DNA methylation is altered in maternal blood vessels of preeclamptic women. Reproductive Sciences, Aug 17. [Epub ahead of print] .
  8. Wan W, Deng X, Archer KJ, Sun SS. Pubertal pathways and the relationship to anthropometric changes in childhood: The Fels Longitudinal Study. Open Journal of Pediatrics, 2(2):118-126, 2012.
  9. Gehrau RC, Archer KJ, Mas VR, Maluf DG.Molecular profiles of HCV cirrhotic tissues derived in a panel of markers with clinical utility for hepatocellular carcinoma surveillance. PLoS One, 7(7):e40275, 2012.
  10. Kaur S, Archer KJ, Devi MG, Kriplani A, Strauss JF, Singh R. Differential gene expression in granulosa cells from polycystic ovary syndrome patients with and without insulin resistance: Identification of susceptibility gene sets through network analysis. Journal of Clinical Endocrinology and Metabolism, 97(10):E2016-21, 2012.
  11. Scian MJ, Maluf DG, Archer KJ, Turner SD, Suh JL, David KG, King AL, Posner MP, Brayman KL, Mas VR. Identi cation of Biomarkers toAssess Organ Quality and Predict Posttransplantation Outcomes. Transplantation. 2012 Sep 18. [Epub ahead of print].
  12. Wang S, Chen W, Chen X, Hu F, Archer KJ, Liu N, Sun SS, Gao G. Double genomic control is not effective to correct for population stratification in Meta-analysis for genome-wide association studies. Frontiers in Applied Genetic Epidemiology, 3:300, 2012.
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2011

  1. Mas VR, Mueller TF, Archer KJ, Maluf DG. Identifying biomarkers as diagnostic tools in kidney transplantation. Expert Rev Mol Diagn, Mar;11(2):183-96, 2011.
  2. Mas V, Maluf D, Archer KJ, Potter A, Suh J, Gehrau R, Descaizi V, Villamil. Transcriptome at the time of Hepatitic C Virus recurrence may predict the severity of fibrosis progression after liver transplantation. Liver Transplantation, 17(7):824-35, 2011.
  3. Gehrau R, Maluf D, Archer K, Stravitz R, Suh J, Le N, Mas V. Molecular pathways differentiate HCV recurrence from acute cellular rejection in HCV liver recipients. Molecular Medicine, 17(7-8):824-33, 2011
  4. Scian MJ, Maluf DG, Archer KJ, Suh JL, Massey D, Fassnacht RC, Whitehill B, Sharma A, King A, Gehr T, Cotterell A, Posner MP, Mas V. Gene expression changes are associated with loss of kidney graft function and interstitial fibrosis and tubular atrophy: diagnosis versus prediction. Transplantation Mar 27;91(6):657-65, 2011.
  5. Redmond LC, Dumur CI, Archer KJ, Grayson DR, Haar JL, Lloyd JA. Kruppel-like factor 2 regulated gene expression in mouse embryonic yolk sac erythroid cells. Blood Cells, Molecules, and Diseases, Jun 15;47(1):1-11, 2011.
  6. Scian MJ, Maluf DG, David KG, Archer KJ, Suh JL, Wolen AR, Mba MU, Massey HD, King AL, Gehr T, Cotterell A, Posner M, Mas V. MicroRNA Profiles in Allograft Tissues and Paired Urines Associate With Chronic Allograft Dysfunction With IF/TA. American Journal of Transplantation, 11(10):2110-22, 2011.
  7. Gehrau R, Mas V, Archer KJ, Maluf D. Molecular classification and clonal differentiation of hepatocellular carcinoma: the step forward for patient selection for liver transplantation. Expert Rev Gastroenterol Hepatol. 2011 Aug;5(4):539-52.
  8. Wolstenholme JT, Warner JA, Capparuccini MI, Archer KJ, Shelton KL, Miles MF. Genomic analysis of individual differences in ethanol drinking: evidence for non-genetic factors in C57BL/6 mice. PLoS One 2011;6(6):e21100. Epub 2011.
  9. Kopec A, D’Souza M, Mets B, Burgoon L, Reese S, Archer K, Potter D, Tashiro C, Sharratt B, Harkema J, Zacharewski T. Non-additive hepatic gene expression elicited by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 2,2',4,4',5,5'-hexachlorobiphenyl (PCB153) co-treatment in C57BL/6 mice. Toxicology and Applied Pharmacology, 256(2):154-67, 2011.
  10. Mas VR, Scian MJ, Archer KJ, Suh JL, David KG, Ren Q, Gehr TW, King AL, Posner MP, Mueller TF, Maluf DG. Pretransplant transcriptome profiles identify among kidneys with delayed graft function those with poorer quality and outcome. Molecular Medicine, 2011 Sep 6. doi: 10.2119/molmed.2011.00159. [Epub ahead of print].
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2010

  1. Archer KJ, Mas VR, Maluf DG, Fisher RA. High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Molecular Genetics and Genomics, 283(4): 341-349, 2010.
  2. Mas VR, Archer KJ, Scian M, Maluf DG. Molecular pathways involved in loss of kidney graft function with tubular atrophy and interstitial fibrosis in kidney transplant recipients. Expert Reviews in Molecular Diagnostics, 10(3):269-84, 2010.
  3. Archer KJ. rpartOrdinal: An R Package for Deriving a Classification Tree for Predicting an Ordinal Response, Journal of Statistical Software, 34(7):1-17, 2010.
  4. Kightlinger RS, Irvin WP, Archer KJ, Huang NW, Wilson RA, Doran JR, Quigley NB, Pinkerton JV. Prevalence of cervical cancer and human papillomavirus in indigenous Guyanese women. American Journal of Obstetrics and Gynecology, Jun;202(6):626.e1-7, 2010.
  5. Mas VR, Fassnacht R, Archer KJ, Posner M, Maluf D. Molecular mechansims involved in the interaction effects of alcohol and HCV in liver cirrhosis. Molecular Medicine, Jul-Aug;16(7-8):287-97, 2010.
  6. Kong X, Archer KJ, Moulton LH, Gray RH, Wang M.Parametric Frailty Models for Clustered Data with Arbitrary Censoring: Application to Effect of Male Circumcision on HPV Clearance. BMC Medical Research Methodology,10(1):40, 2010.
  7. Archer KJ, Lemeshow S, Litchner MI. st0099_1: Goodness-of-fit test for logistic regression fitted using survey sample data. The Stata Journal, 10(2):313, 2010.
  8. Maluf DG, Archer KJ, Villamil F, Stravitz RT, Mas V. Hepatitis C virus recurrence after liver transplantation: Biomarkers of disease and fibrosis progression. Expert Rev Gastroenterol Hepatol. Aug;4(4):445-58, 2010.
  9. Archer KJ, Zhao Z, Guennel T, Maluf DG, Fisher RA, Mas VR. Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. International Journal of Computational Biology and Drug Design, 3(1), 52-67, 2010.
  10. Maluf DG, Archer KJ, Mas VR. Kidney Grafts From HCV-Positive Donors: Advantages and Disadvantages. Transplantation Proceedings, 42(7):2436-46.
  11. Edmiston JS, Archer KJ, Scian MJ, Joyce AR, Zedler BK, Murrelle EL. Gene expression profiling of peripheral blood leukocytes identifies potential novel biomarkers of chronic obstructive pulmonary disease in current and former smokers. Biomarkers, 15(8):715-30, 2010.
  12. Mas, V, Archer K, Suh J, Scian M, Posner M, Maluf D. Distinctive gene expression profiles characterize donor biopsies from HCV positive kidney donors. Transplantation, 90(11):1172-9, 2010.
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2009

  1. Mas VR, Maluf DG, Archer KJ, Yanek K, Kong X, L Kulik L, Freise CE, Olthoff KM, Ghobrial RM, McIver P, Fisher R. Genes involved in viral carcinogenesis and tumor initiation in Hepatitis C Virus-induced Hepatocellular Carcinoma. Molecular Medicine, 15(3-4):85-94, 2009.
  2. Donald F. Brophy, Bonny L. Bukaveckas, Andrea Ferreira-Gonzalez, Kellie J. Archer, Erika J. Martin, Todd W.B. Gehr. A Pilot Study of Genetic Polymorphisms and Hemodialysis Vascular Access Thrombosis. Hemodialysis International, 13(1):19-26, 2009.
  3. VR Mas, DG Maluf, KJ Archer, K Yanek, K Bornstein, RA Fisher. Proteomic analysis of HCV cirrhosis and HCV-induced HCC: Identifying biomarkers for monitoring HCV-cirrhotic patients awaiting liver transplantation. Transplantation, Jan 15;87(1):143-152, 2009.
  4. Archer KJ, Mas VR, O'Brien TR, Pfeiffer R, Lum NL, Fisher RA. Quality assessment of microarray data in a multi-center study. Diagnostic Molecular Pathology, 18(1):34-43, 2009.
  5. Elizabeth C. Prom-Wormley, Lindon J. Eaves, Debra L. Foley, Charles O. Gardener, Kellie J. Archer, Brandon K. Wormley, Hermine H. Maes, Brien P. Riley, Judy L. Silberg. Monoamine Oxidase A and Childhood Adversity as Risk Factors for Conduct Disorder in Females. Psychological Medicine, 39(4):579-90, 2009.
  6. VR Mas, RA Fisher, KJ Archer, DG Maluf. Proteomics and liver fibrosis: identifying markers of fibrogenesis. Expert Reviews Proteomics, Aug;6(4):421-31, 2009.
  7. Archer KJ and Mas VR. Ordinal response prediction using bootstrap aggregation, with application to a high-throughput methylation dataset. Statistics in Medicine, Dec 20;28(29):3597-610, 2009.
  8. KJ Archer, VR Mas, K David, DG Maluf, K Bornstein, RA Fisher. Identifying genes for establishing a multigenic test for HCC surveillance in HCV+ cirrhotic patients. Cancer, Epidemiology, Biomarkers & Prevention, Nov;18(11):2929-32, 2009
  9. KJ Archer, SE Reese. Detection Call Algorithms for High-throughput Gene Expression Microarray Data. Briefings in Bioinformatics, 2009 Nov 25. [Epub ahead of print].
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2008

  1. Archer KJ and Kimes RV. Empirical characterization of random forest variable importance estimates. Computational Statistics and Data Analysis, 52(4): 2249-2260, 2008.
  2. LC Redmond, CI Dumur, KJ Archer, JL Haar, JA Lloyd. Identification of Erythroid-Enriched Gene Expression in the Mouse Embryonic Yolk Sac using Microdissected Cells. Developmental Dynamics, 237(2):436-446, 2008.
  3. Kong X, Mas VR, Archer KJ. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy. BMC Genomics, Feb 26; 9 (1): 98, 2008.
  4. Archer KJ , CI Dumur, GS Taylor, MD Chaplin, A Guiseppi-Elie, G Buck, G Grant, A Ferreira-Gonzalez, CT Garrett, A disattenuated correlation estimate when variables are measured with error: Illustration estimating cross-platform correlations. Statistics in Medicine,Mar 30;27(7):1026-39, 2008.
  5. Maluf, DG, Mas VR, Archer KJ, Yanek K, Gibney EM, King AL, Cotterell A, Fisher RA, Posner MP. Molecular pathways involved in loss of kidney graft function with tubular atrophy and interstial fibrosis. Molecular Medicine, May-Jun;14(5-6):276-85, 2008.
  6. Mas VR, Archer KJ , Yanek K, Dumur CI, Capparuccini MI, Mangino MJ, King A, Gibney EM, Fisher R, Posner M, Maluf D. Gene expression patterns in deceased donor kidneys developing delayed graft function after kidney transplantation. Transplantation, Feb 27; 85(4):626-35, 2008. 
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2007

  1. Archer KJ, Lemeshow S, Hosmer DW. Goodness-of-fit tests for logistic regression models when data are collected using a complex sampling design. Computational Statistics and Data Analysis, 51, 4450-4464, 2007.
  2. Mas V, Maluf D, Archer K, Yanek K, Mas L, King A, Gibney E, Massey D, Cotterell A, Fisher R, Posner M. Establishing the molecular pathways involved in chronic allograft nephropathy (CAN) for testing new non-invasive diagnostic markers. Transplantation, Feb 27;83(4):448-57, 2007.
  3. Mas VR, Fisher RA, Archer KJ, Yanek KC, Williams B, Dumur CI, Maluf DG. Genes associated with progression and recurrence of Hepatocellular Carcinoma in Hepatitis C Patients Waiting and Undergoing Liver Transplantation: Preliminary results. Transplantation, 83(7):973-81, 2007.
  4. Kennedy RE, Yeatts SD, Archer KJ, Gennings C, Ramakrishnan V. Opportunities for biostatisticians: Training and fellowship grants from the National Institutes of Health. The American Statistician, 61(2): 120-126, 2007.
  5. Valeria R Mas, Luciana A Mas, Kellie Archer, Kenneth Yanek, Anne King, Eric Gibney, Adrian Cotterell, Robert Fisher, Marc Posner, Daniel Maluf. Evaluation of a Gene Panel mRNAs in Urine Samples of Kidney Transplant Recipients as Non-invasive Indicator of Graft Function. Molecular Medicine, 13(5-6):315-324, 2007.
  6. Mas VR, Maluf DG, Archer KJ, Yanek KC, Fisher RA. Angiogenesis soluable factors as HCC non-invasive markers for monitoring HCV cirrhotic patients. Transplantation, 84 (10): 1262-71, 2007.
  7. KJ Archer, CI Dumur, GS Taylor, MD Chaplin, A Guiseppi-Elie, G Grant, A Ferreira-Gonzalez and CT Garrett. Application of a correlation correction factor in a microarray cross-platform reproducibility study. BMC Bioinformatics, Nov 15;8:447, 2007.
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2006

  1. Archer KJ and Lemeshow S. Goodness-of-fit test for a logistic regression model estimated using survey sample data. The Stata Journal, 6(1): 97-105, 2006.
  2. Archer KJ, Dumur CI, Joel SE, Ramakrishnan V. Assessing quality of hybridized RNA in Affymetrix GeneChip experiments using mixed effects models. Biostatistics7(2):198-212, 2006.
  3. Kennedy RE, Archer KJ, Miles MF. Empirical validation of the S-score algorithm in the analysis of gene expression data. BMC Bioinformatics, Mar 17;7(1):154, 2006.
  4. Farag SS, Archer KJ, Mrózek K, Ruppert AS, Carroll AJ, Vardiman, JW, Pettenati MJ, Baer MR, Qumsiyeh MB, Koduru PR, Stamberg J, Mayer RJ, Stone RM, Larson RA, Bloomfield CD. Pretreatment Cytogenetics add to Other Prognostic Factors Predicting Complete Remission and Long-Term Outcome in Patients 60 Years of Age or Older with Acute Myeloid Leukemia: Results from Cancer and Leukemia Group B 8461. Blood, 108(1):63-73, 2006.
  5. Kennedy RE, Kerns RT, Kong X, Archer KJ, Miles MF. An R package for detecting differential gene expression without gene expression summaries. Bioinformatics, 22(10):1272-1274, 2006. [S-Score Bioconductor package]
  6. Mas VR, Maluf DG, Dumur CI, Archer KJ, Yanek K, Jackson-Cook C, Fisher RA. Molecular techniques for identifying HCC origin and biology after orthotopic liver transplantation. Diagnostic Molecular Pathology, 15(2):90-94, 2006.
  7. Hackett JL, Archer KJ, Gaigalas AK, Garrett CT, Joseph LJ, Kock WH, Kricka LJ, McGlennen RC, Van Deerlin V, Vasquez GB. Clinical and Laboratory Standards Institute (CLSI). Diagnostic Nucleic Acid Microarrays; Approved Guideline. CLSI document MM12-A (ISBN 1-56238-608-5). Clinical and Laboratory Standards Institute, 940 West Valley Road, Suite 1400, Wayne, Pennsylvania 19087-1898 USA, 2006.
  8. Mas VR, Maluf DG, Archer KJ, Yanek KC, Williams B, Fisher RA. Differentially expressed genes between early and advanced Hepatocellular Carcinoma (HCC) as a potential tool for selecting liver transplant recipients. Molecular Medicine, 12(4-6):97-104, 2006.
  9. Archer KJ and Guennel T. An application for assessing quality of RNA hybridized to Affymetrix GeneChips, Bioinformatics 22: 2699-2701, 2006. [Stand-alone application]
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2005

  1. Hackett JL, Archer KJ, Gaigalas AK, Garrett CT, Joseph LJ, Kock WH, Kricka LJ, McGlennen RC, Van Deerlin V, Vasquez GB. Clinical and Laboratory Standards Institute. Diagnostic Nucleic Acid Microarrays; Proposed Guideline . CLSI document MM12-P [ISBN 1-56238- 578-X ]. Clinical and Laboratory Standards Institute, 940 West Valley Road, Suite 1400 , Wayne , Pennsylvania 19087-1898 USA , 2005.
  2. Mas VR, Maluf DG, Archer KJ, Yanek K, King A, Cotterell A, Ferreira-Gonzalez A, Rodgers C , Fisher RA, Posner M. Study of mRNA growth factors in urinary cells of kidney transplant recipients as predictors of chronic allograft nephropathy. Transplantation 80(12):1686-1691, 2005.
  3. Maluf DG, Mas VR, Archer KJ, Yanek K, King A, Ferreira-Gonzalez A, Fisher RA, Posner M. Apolipoprotein E genotypes as predictors of high-risk groups for developing hyperlipidemia in kidney transplant recipients undergoing sirolimus treatment. Transplantation 80(12):1705-1711, 2005.
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2004

  1. Dumur CI, Nasim S, Best AM, Archer KJ , Ladd AC, Mas VR, Wilkinson DS, Garrett CT , Ferreria-Gonzalez A. Evaluation of quality control parameters for microarray gene expression analysis. Clinical Chemistry, 50(11): 1994-2002, 2004.
  2. Dumur CI, Garrett CT, Archer KJ, Nasim S, Wilkinson DS, Ferreira-Gonzalez A. Evaluation of a linear amplification method for small samples used on high density oligonucleotide microarray analysis. Analytical Biochemistry 331(2):314-321, 2004.
  3. Archer KJ, Dumur CI, Ramakrishnan V. Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals. BMC Bioinformatics 5:60, 2004.
  4. Marcucci G, Mrózek K, Ruppert AS, Archer KJ, Pettenati MJ, Heerema NA, Carroll AJ, Koduru PR, Kolitz JE, Sterling LJ, Edwards CG, Anastasi J, Larson RA, Bloomfield CD. Abnormal cytogenetics at date of morphologic complete remission predicts short overall and disease-free survival, and higher relapse rate in adult acute myeloid leukemia: Results from Cancer and Leukemia Group B Study 8461. Journal of Clinical Oncology 22(12): 2410-2418, 2004.
  5. Mas VR, Fisher RA, Maluf DG, Archer KJ, Contos MJ, Mills SA, Shiffman ML, Wilkinson DS, Oliveros L, Garrett CT, Ferreira-Gonzalez A. Polymorphisms in cytokines and growth factor genes and their association with acute rejection and recurrence of hepatitis C virus disease in liver transplantation. Clinical genetics 65:191-201, 2004.
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2003

  1. Baldus CD, Tanner SM, Ruppert A, Whitman SP, Archer KJ, Marcucci G, Caligiuri MA, Carroll AJ, Vardiman JW, Powell B, Allen SL, Moore JO, Larson RA, Kolitz JE, de la Chapelle A, Bloomfield CD. BAALC expression predicts clinical outcome of de novo acute myeloid leukemia patients with normal cytogenetics: A Cancer and Leukemia Group B Study. Blood 102(5):1613-1618, 2003.
  2. Arthur DW, Koo D, Zwicker RD, Tong S, Bear HD, Kaplan BJ, Kavanagh BD, Warwicke LA, Holdford D, Amir C, Archer KJ, Schmidt-Ullrich RK. Partial breast brachytherapy following lumpectomy: a low dose rate and high dose rate experience. International Journal of Radiation Oncology, Biology, Physics 56(3):681-689, 2003.
  3. Klisovic MI, Maghraby EA, Parthun MR, Guimond M, Sklenar AR, Whitman SP, Chan KK, Murphy T, Anon J, Archer KJ, Rush LJ, Plass C, Grever MR, Byrd JC, Marcucci G. Depsipeptide (FR 901228) promotes histone acetylation, gene transcription, apoptosis and its activity is enhanced by DNA methyltransferase inhibitors in AML1/ETO-positive leukemic cells. Leukemia 17: 350-358, 2003.
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2002

  1. Farag SS, Archer KJ, Mrózek K, Vardiman JW, Carroll AJ, Pettenati MJ, Moore JO, Kolitz JE, Mayer RJ, Stone RM, Larson RA, Bloomfield CD. Isolated Trisomy of Chromosomes 8, 11, 13 and 21 is an adverse prognostic factor in adults with de novo acute myeloid leukemia not treated with stem cell transplantation: Results from Cancer and Leukemia Group B 8461. International Journal of Oncology 21:1041-1051, 2002.
  2. Bloomfield CD, Archer KJ, Mrózek K, Lillington DM, Kaneko Y, Head DR, Dal Cin P and Raimondi SC. 11q23 balanced chromosome aberrations in treatment-related myelodysplastic syndromes and acute leukemia: Report from an international workshop. Genes, Chromosomes and Cancer, 33:362-378, 2002.
  3. Karrison T, Archer KJ, Espinosa R, Wen M and Huo D. Data management and statistical methods used in the analysis of balanced chromosome abnormalities in therapy-related myelodysplastic syndromes and therapy-related acute leukemia: Report from an international workshop. Genes, Chromosomes and Cancer, 33:346-361, 2002.
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2001

  1. Tanner, SM, Austin JL, Leone G, Rush LJ, Plass C, Heinonen K, Mrózek K, Sill H, Knuutila S, Kolitz JE, Archer KJ, Caligiuri MA, Bloomfield CD and de la Chapelle A. BAALC, the human member of a novel mammalian neuroectoderm gene lineage, is implicated in hematopoiesis and acute leukemia. Proc Natl Acad Sci U S A, 98:13901-13906, 2001.
  2. Marcucci G, Caligiuri MA, Döhner H, Archer KJ, Schlenk RF, Döhner K, Maghraby EA and Bloomfield CD. Quantification of CBFb/MYH11 fusion transcript by Real Time RT-PCR in patients with inv(16) acute myeloid leukemia (AML). Leukemia, 15:1072-1080, 2001.
  3. Whitman SP, Archer KJ, Feng L, Baldus C, Becknell B, Carlson BD, Carroll AJ, Mrózek K, Vardiman JW, George SL, Kolitz JE, Larson RA, Bloomfield CD and Caligiuri MA. Absence of the wild type allele predicts poor prognosis in adult de novo acute myeloid leukemia with normal cytogenetics and the internal tandem duplication of FLT3: A Cancer and Leukemia Group B study. Cancer Res, 61:7233-7239, 2001.
  4. Mrózek K, Prior TW, Edwards C, Marcucci G, Carroll AJ, Snyder PJ, Koduru PRK, Theil KS, Pettenati MJ, Archer KJ, Caligiuri MA, Vardiman JW, Kolitz JE, Larson RA and Bloomfield CD. Comparison of cytogenetic and molecular genetic detection of t(8;21) and inv(16) in a prospective series of adults with de novo acute myeloid leukemia: A Cancer and Leukemia Group B study. J Clin Oncol, 19:2482-2492, 2001.
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    Chapters in books

  1. Bloomfield CD, Archer KJ, Mrózek K, Byrd JC, Whitman SP, Dodge RK, Carroll AJ, Larson RA and Caligiuri MA. Cytogenetics for treatment stratification in de novo adult acute myeloid leukemia. In Acute Leukemias IX: Basic Research, Experimental Approaches and Novel Therapies, Eds Hiddemann W, Haferlach T, Büchner T, Ritter J, Unterhalt M, Springer-Verlag, New York, 2003.
  2. Kellie J. Archer, Jiayi Hou, Andre A.A. Williams. Classifying Normal, Nevus, and Malignant Melanoma Skin Samples using Penalized Ordinal Regression. Invited chapter in monograph, New Frontiers of Multidisciplinary Research in STEAM-H (Science, Technology, Engineering, Agriculture, Mathematics and Health) Springer Proceedings in Mathematics & Statistics, edited by Bourama Toni, pp. 111-133, 2014.