Publications by Michael A. Newton and co-authors.

Ma, X, Kendziorski, C, and Newton, MA (2020). EBSeq: improving mixing computations for multi-group differential expression analysis. bioRxiv . doi: See code at .

Zuleger CL, Newton MA, Ma X, Ong IM, Pei Q, Albertini MR (2020). Enrichment of melanoma-associated T cells in 6-thioguanine-resistant T cells from metastatic melanoma patients. Melanoma Research. 30(1), 52-61. PMID: 31135600 . PMCID: PMC6874720 . DOI: 10.1097/CMR.0000000000000625

Zheng, Z., Mergaert, A.M., Fahmy, L.M., Bawadekar, M., Holmes, C.L., Ong, I.M., Bridges, A.J., Newton, M.A. and Shelef, M.A., 2020. Disordered Antigens and Epitope Overlap Between AntiCitrullinated Protein Antibodies and Rheumatoid Factor in Rheumatoid Arthritis. Arthritis & Rheumatology. 72(2):262-272. doi: 10.1002/art.41074 , pdf .

Patel, NJ, Hogan, KJ, Rizk, E, Stuart, K, Madrid, A, Meethal, SV, Alisch, R, Borth, L, Papale, LA, Ondoma, S, Gorges, LR, Weber, K, Lake, W, Bauer, A, Hariharan, N, Kuehn, T, Cook, T, Keles, S, Newton, MA, and Iskandar, B (2020). Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny. Molecular Neurobiology , 57: 2048-2071 doi:10.1007/s12035-019-01812-5 . pdf .

Vo, T., Ithapu, V., Singh, V. and Newton, M.A., 2019. Dimension constraints improve hypothesis testing for large-scale, graph-associated, brain-image data. arXiv:1908.07176. ; Supplementary Material .

Castro-Pérez, E., Rodríguez, C.I., Mikheil, D., Siddique, S., McCarthy, A., Newton, M.A. and Setaluri, V., 2019. Melanoma Progression Inhibits Pluripotency and Differentiation of Melanoma-Derived iPSCs Produces Cells with Neural-like Mixed Dysplastic Phenotype. Stem cell reports. Volume 13, Issue 1, 9 July 2019, Pages 177-192.

Ma, X., Korthauer, K., Kendziorski, C., and Newton, M. A. (2019). A Compositional Model To Assess Expression Changes From Single-Cell RNA-Seq Data. bioRxiv, 655795.

Stephanie L. Fricke, Susan N. Payne, Peter F. Favreau, Jeremy D. Kratz, Cheri A. Pasch, Tyler M. Foley, Alexander E. Yueh, Dana R. Van De Hey, Mitchell G. Depke, Demetra P. Korkos, Gioia Chengcheng Sha, Rebecca A. DeStefanis, Linda Clipson, Mark E. Burkard, Kayla K. Lemmon, Benjamin M. Parsons, Paraic A. Kenny, Kristina A. Matkowskyj, Michael A. Newton, Melissa C. Skala and Dustin A. Deming (2019). MTORC1/2 Inhibition as a Therapeutic Strategy for PIK3CA Mutant Cancers Mol Cancer Therapeutics February 1 2019 (18) (2) 346-355; DOI: 10.1158/1535-7163.MCT-18-0510

Predicting kinase inhibitors using bioactivity matrix derived informer sets. Huikun Zhang, Spencer S Ericksen, Ching-pei Lee, Gene E Ananiev, Nathan Wlodarchak, Julie C. Mitchell, Anthony Gitter, Stephen J Wright, F. Michael Hoffmann, Scott A. Wildman, and Michael A Newton. PLoS Computational Biology 15 (8), e1006813. Also, bioRxiv 532762

Mikheil, D.M., Prabhakar, K., Arshad, A., Rodriguez, C., Newton, M.A. and Setaluri, V., 2019. Notch Signaling Activation Induces Cell Death in MAPK resistant Melanoma Cells. Pigment cell and melanoma research .

Pleiman, J.K., Irving, A.A., Wang, Z., Toraason, E., Clipson, L., Dove, W.F., Deming, D.A. and Newton, M.A., 2018. The conserved protective cyclic AMP-phosphodiesterase function PDE4B is expressed in the adenoma and adjacent normal colonic epithelium of mammals and silenced in colorectal cancer. PLoS genetics, 14(9), p.e1007611.

Anding, A.L., Jones, J.D., Newton, M.A., CURLEY, R.W. and Clagett-Dame, M., 2018. 4-HPR Is an Endoplasmic Reticulum Stress Aggravator and Sensitizes Breast Cancer Cells Resistant to TRAIL/Apo2L. Anticancer research, 38(8), pp.4403-4416.

Newton MA, Polson NG, and Xu J (2018). Weighted Bayesian Bootstrap for Scalable Bayes. arXiv preprint. arXiv:1803.04559

Reinhart JM, Rose W, Panyard DJ, Newton MA, Liebenstein TK, Yee J, and Trepanier LA (2018). RNA expression profiling in sulfamethoxazole-treated patients with a range of in vitro lymphocyte cytotoxicity phenotypes. Pharmacol Res Perspect. e00388 ; pdf

Newton MA (2017). Discussion of, `Statistical contributions to bioinformatics` by Morris and Baladandayuthapani. Statistical Modeling 17, 300-304.

Zuleger CL, Kang C, Ranheim EA, Kurzman ID, Macklin MD, Newton MA, Wolchok JD, Vail DM, Eriksson E, Albertini MR (2017). Pilot study of safety and feasibility of DNA microseeding for treatment of spontaneous canine melanoma . Veterinary Medicine and Science , 3, 134-145.

Zheng, L., Kim, H.J., Adluru, N., Newton, M.A. and Singh, V., 2017, July. Riemannian Variance Filtering: An Independent Filtering Scheme for Statistical Tests on Manifold-valued Data. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition Workshops (pp. 20-29).

Spencer S Ericksen, Haozhen Wu, Huikun Zhang, Lauren A Michael, Michael A Newton, F Michael Hoffmann, Scott A Wildman (2017). Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening Journal of Chemical Information and Modeling 57 (7), 1579-1590.

Rhonda Bacher, Li-Fang Chu, Ning Leng, Audrey P Gasch, James A Thomson, Ron M Stewart, Michael Newton & Christina Kendziorski (2017). SCnorm: robust normalization of single-cell RNA-seq data. Nature Methods 14, 584-586. pdf

Jamie L. Barger, James M. Vann, Nicole L. Cray, Thomas D. Pugh, Angela Mastaloudis, Shelly N. Hester, Steven M. Wood, Michael A. Newton, Richard Weindruch, Tomas A Prolla (2017). Identification of Tissue-specific Transcriptional Markers of Caloric Restriction in the Mouse and Their Use to Evaluate Caloric Restriction Mimetics. Aging Cell DOI: 10.1111/acel.12608. Early view ; pdf ; Statistical Supplement

Tyler M. Foley, Susan N. Payne, Cheri A. Pasch, Alex E. Yueh, Dana R. Van De Hey, Demetra P. Korkos, Linda Clipson, Molly E. Maher, Kristina A. Matkowskyj, Michael A. Newton and Dustin A. Deming (2017). Dual PI3K/mTOR Inhibition in Colorectal Cancers with APC and PIK3CA Mutations . Molecular Cancer Research 15 (3), 317-327. DOI 10.1158/1541-7786.MCR-16-0256

KD Korthauer, LF Chu, MA Newton, Y Li, J Thomson, R Stewart, C Kendziorski (2016). scDD: A statistical approach for identifying differential distributions in single-cell RNA-seq experiments, Genome Biology 17(1): 222. pubmed , Springer-Nature open-access version

C Bodelon, S Vinokurova, JN Sampson, JA den Boon, JL Walker, MA Horswill, K Korthauer, M Schiffman, ME Sherman, RE Zuna, J Mitchell, X Zhang, JF Boland, AK Chaturvedi, ST Dunn, MA Newton, P Ahlquist, SS Wang, N Wentzensen (2016). Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer Carcinogenesis , 37(2), 188-196. pdf

JN Hadac, DD Miller, IC Grimes, L Clipson, MA Newton, WR Schelman, RB Halberg (2016). Heterochromatin Protein 1 Binding Protein 3 Expression as a Candidate Marker of Intrinsic 5-Fluorouracil Resistance. Anticancer research 36(3), 845-852. pdf

CK Sievers, LS Zou, PJ Pickhardt, KA Matkowskyj, DM Albrecht, LClipson, JW Bacher, BD Pooler, FJ Moawad, BD Cash, M Reichelderfer, TN Vo, MA Newton, BR Larget, RB Halberg (2016). Subclonal diversity arises early even in small colorectal tumours and contributes to differential growth fates. Gut 0, 1-9. doi:10.1136/gutjnl-2016-312232 pdf

Gasch, A. P., Hose, J., Newton, M. A., Sardi, M., Yong, M., and Wang, Z. (2016). Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. eLife, 5, e14409.

CD Zahm, JM Szulczewski, AA Leystra, TJP Olson, L Clipson, DM Albrecht, M Middlebrooks, AT Thliveris, KA Matkowskyj, MK Washington, MA Newton, KW Eliceiri, RB Halberg (2016). Advanced Intestinal Cancers often Maintain a Multi-Ancestral Architecture , PLOS One . 10.1371/journal.pone.0150170

Henderson, NC and Newton, MA, 2016. Making the cut: improved ranking and selection for large-scale inference. J. Roy. Statist. Soc. B , 78 (4), 781-804. pdf . CRAN software package rvalues. Supplementary Material. Technical report versions. PMC

Gupta, Aditya, Michael Place, Steven Goldstein, Deepayan Sarkar, Shiguo Zhou, Konstantinos Potamousis, Jaehyup Kim et al. Single-molecule analysis reveals widespread structural variation in multiple myeloma. Proceedings of the National Academy of Sciences 112, no. 25 (2015): 7689-7694.

den Boon, J. A., Pyeon, D., Wang, S. S., Horswill, M., Schiffman, M., Sherman, M., Zuna, R. E., Wang, Z., Hewitt, S. M., Pearson, R., Schott, M., Chung, L., He, Q., Lambert, P., Walker, J., Newton, M. A., Wentzensen, N., and Ahlquist, P. Molecular Transitions from Papillomavirus Infection to Cervical Precancer and Cancer: Role of Stromal Estrogen Receptor Signaling.. Proceedings of the National Academy of Sciences 112(25), E3255-E3264. Access the recommendation on F1000Prime.

Hose, J, Mun Yong, C, Sardi, M, Wang, Z, Newton, MA, and Gasch, AP (2015). Dosage compensation can buffer copy-number variation in wild yeast. eLife ; 10.7554/eLife.05462.

Newton, MA and Wang Z (2015). Multiset statistics for gene set analysis. Annual Review of Statistics and Its Application, Vol. 2: 95-111 e-print PMC

Wang, Z, He, Q, Larget, B, and Newton, MA (2015). A multi-functional analyzer uses parameter constraints to improve the efficiency of model-based gene-set analysis. Annals of Applied Statistics , 9, 225-246. Earlier versions: Technical report 1174, Department of Statistics, University of Wisconsin, Madison. arXiv ; Supplementary material ; Code .

Barger, JL, Anderson, RM, Newton, MA, da Silva, C, Vann, JA, Pugh, TD, Someya, S, Prolla, TA, and Weindruch, R (2015). A conserved transcriptional signature of delayed aging and reduced vulnerability is partially mediated by SIRT3. PLoS ONE 10(4): e0120738.

L.C. de Sa Rodrigues, K.E. Holmes, V. Thompson, C.M. Piskun, S.E. Lana, M.A. Newton, and T.J. Stein (2015). Osteosarcoma tissues and cell lines from patients with differing serum alkaline phosphatase concentrations display minimal differences in gene expression patterns. Veterinary and Comparative Oncology. doi: 10.1111/vco.12132. pdf

L.C. de Sa Rodrigues, K.E. Holmes, V. Thompson, M.A. Newton, and T.J. Stein (2015). Tumourigenic canine osteosarcoma cell lines associated with frizzled-6 up-regulation and enhanced side population cell frequency. Veterinary and Comparative Oncology. doi: 10.1111/vco.12138. pdf

Newton, MA (2014). Buried treasures. In, Past, Present, and Future of Statistical Science, Lin, Genest, Banks, Molenberghs, Scott, and Wang Eds. CRC Press and COPSS, Chapter 36, pp. 405 - 412. pdf

Dove, WF, Shedlovsky, A, Clipson, C, Amos-Landgraf, JM, Halberg, RB, Krentz, KJ, Boehm, FJ, Newton, MA, Adams, DJ, and Keane, TM (2014). A strategy to identify dominant point mutant modifiers of a quantitative trait. G3: Genes|Genomes|Genetics . DOI 10.1534/g3.114.010595 pdf , supplement files (stat methods) , ENUpack.tar.gz; R package, with lifespan data .

Hao, L, Lindenback, B, Wang, X, Dye, B, Kushner, D, He, Q, Newton, MA, Ahlquist, P (2014). Genome-Wide Analysis of Host Factors in Nodavirus RNA Replication PLoS One, 9(4) e95799. pdf

Olson, TJP, Hadac, JN, Sievers, CK, Leystra, AA, Deming, DA, Zahm, CD, Albrecht, DM, Nomura, A, Nettekoven, LA, Plesh, LK, Clipson, L, Sullivan, R, Newton, MA, Schelman, WR, and Halberg, RB (2014). Dynamic tumor growth patterns in a novel murine model of colorectal cancer . Cancer Prevention Research , 7, 105-113.

Pei, Q, Zuleger, CL, Macklin, MD, Albertini, MR, and Newton, MA (2014). A conditional predictive p-value to compare a multinomial with an overdispersed multinomial in the analysis of T-cell populations . Biostatistics , 15, 129-139. Advance access publication on October 4, 2013. doi: 10.1093/biostatistics/kxt039. pdf . R package dod_2.0.tar.gz .

Costello, James C., et al. A community effort to assess and improve drug sensitivity prediction algorithms. Nature biotechnology 32.12 (2014): 1202-1212.

Bansal, Mukesh, et al. A community computational challenge to predict the activity of pairs of compounds. Nature biotechnology, 32.12 (2014): 1213-1222.

Hao, L, He, Q, Wang, Z, Craven, M, Newton, MA, and Ahlquist, P (2013). Limited agreement of independent RNAi screens for virus-required host genes owes more to false-negative than false-positive factors. PLoS Comput Biol 9(9): e1003235. doi:10.1371/journal.pcbi.1003235. R package metaflu_1.0.tar.gz .

Ray, M, Goldstein, S, Zhou, S, KPotamousis, K, Sarkar, D, Newton, MA, Esterberg, E, Kendziorski, C, Bolgler, O, and Schwartz, DC (2013). Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis . BMC Genomics 14, 505. pdf

Thliveris, AT, Schwefel, B, Clipson, L, Plesh, L, Zahm, CD, Leystra, AA, Washington, MK, Sullivan, R, Deming, DA, Newton, MA, and Halberg, RB (2013). Transformation of epithelial cells through recruitment leads to polyclonal intestinal tumors. Proc. Natl. Acad. Sci. , 110 (28): 11523-11528. Abstract . pdf .

Newton, MA, 2012. Model-based statistical analysis with examples from cancer and stem-cell biology. In, Statistics: Discovering Your Future Power . Q Meng Ed. pdf .

Thliveris, AT, Clipson, L, Sommer, LL, Schoenike, BA, Hasenstein, JR, Schlamp, CL, Alexander, CM, Newton, MA, Dove, WF, and Amos-Landgraf, JM (2012). Regulated expression of chromobox homolog 5 revealed in tumors of Apc(Min/+) ROSA11 gene trap mice. G3 , 2, 569-78. PubMed .

Amos-Landgraf, JM, Clipson, L, Newton, MA, Dove, WF (2012). The many ways to open the gate to colon cancer. Cell Cycle. link

Amos-Landgraf, JM, Irving, AA, Hartman, C, Hunter, A, Laube, B, Chen, X, Clipson, L, Newton, MA, and Dove, WF (2012). Monoallelic silencing and haploinsufficiency in early murine neoplasms. Proc. Natl. Acad. Sci. 109, 2060-2065. link ; pdf (including supplement)

Sarkar, D, Goldstein, S, Schwartz, DC, and Newton, MA. Statistical significance of optical map alignments (2012). Journal of Computational Biology , 19(5): 1-15. pdf . PubMed .

Newton, MA, He, Q, and Kendziorski, C (2012). A model-based analysis to infer the functional content of a gene list. Statistical applications in genetics and molecular biology: Vol. 11: Iss. 2, Article 9. pdf , link PMC

Schiro, MM, Stauber, SE, Peterson, TL, Krueger, C, Darnell, SJ, Satyshur, KA, Drinkwater, NR, Newton, MA, and Hoffmann, FM, 2011. Mutations in Protein-Binding Hot-Spots on the Hub Protein Smad3 Differentially Affect Its Protein Interactions and Smad3-Regulated Gene Expression. PLoS One , 6(9) e25021. link

Gancarz BL, Hao L, He Q, Newton MA, Ahlquist P, 2011. Systematic Identification of Novel, Essential Host Genes Affecting Bromovirus RNA Replication. PLoS ONE 6(8): e23988. doi:10.1371/journal.pone.0023988. link

Taapken, SM, Nisler, BS, Newton, MA, Sampsell-Barron, TL, Leonhard, KA, McIntire, EM, and Montgomery, KD (2011). Karyotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nature Biotechnology , 29, 313-314. link

Thliveris, AT, Clipson, L, White, A, Waggoner, J, Plesh, L, Skinner, BL, Zahm, CD, Sullivan, R, Dove, WF, Newton, MA, and Halberg, RB (2011). Clonal structure of carcinogen-induced intestinal tumors in mice. Cancer Prevention Research, 4(6): 916-23. pdf , link

Zuleger, CL, Macklin, MD, Bostwick, BL, Pei, Q, Newton, MA, and Albertini, MR (in press). In vivo 6-thioguanine-resistant T cells from melanoma patients have public TCR and share TCR beta amino acid sequences with melanoma-reactive T cells. Journal of Immunological Methods 182, 40.15.

Teague, B., Waterman, MS, Goldstein, S, Potamousis, K, Zhou, S, Reslewic, S, Sarkar, D, Valouev, A, Churas, C, Kidd, JM, Kohn, S, Runnheim, R, Lamers, C, Forrest, D, Newton, MA, Eichler, EE, Kent-First, M, Surti, U, Livny, M, and Schwartz, DC (2010). High resolution human genome structure by single-molecule analysis. Proceedings of the National Academy of Sciences June 15, 2010, 107, 10848-10853. link

Newton, MA and Chung, LM (2010). Gamma-based clustering via ordered means with application to gene expression analysis. Annals of Statistics, 38, 3217-3244. project euclid ; PMCID: PMC2990889

Huttlin, EL, Chen, X, Barrett-Wilt, GA, Hegeman, AD, Halberg, RB, Harms, AC, Newton, MA, Dove, WF, and Sussman, MR (2009). Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution. Proceedings of the National Academy of Sciences , 106, 17235-40. doi:10.1073/pnas.09092821. link

Newton, MA (2009). Introducing the discussion paper by Szekely and Rizzo. Annals of Applied Statistics, 3, 1233-1235. arXiv

Stanhope, SA, Sengupta, S, den Boon, J, Ahlquist, P, and Newton, MA. (2009). Statistical use of Argonaute expression and RISC assembly in microRNA target identification. PLoS Computational Biology , 5(9): e1000516. doi:10.1371/journal.pcbi.100516. link

Durkee, BY, Shinki, K, Newton, MA, Iverson, CE, Weichert, JP, Dove, WF, and Halberg, RB. (2009). Longitudinal assessment of colonic tumor fate in mice by computed tomography and optical colonoscopy. Academic Radiology , 16, 1475-1482. link

Albertini MR, Macklin MD, Zuleger CL, Newton MA, Judice SA, Albertini RJ (2008). Clonal expansions of 6-thioguanine resistant T lymphocytes in the blood and tumor of melanoma patients. Environ Mol Mutagen. Aug 19. [Epub ahead of print] PMID: 18712786. PubMed ; full text

Wu, C.Y., Bird, A.J., Chung, L.M., Newton, M.A., Winge, D.R., and Eide, D.J. (2008). Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae. BMC Genomics , 9:370. goto

Hao, L., Sakurai, A., Watanabe, T., Sorensen, E., Nidom, C.A., Newton, M.A., Ahlquist, P., and Kawaoka, Y. (2008). Drospophila RNAi screen identifies host genes important for influenza virus replication. Nature , 454, 890-893. goto

Sengupta, S., den Boon, J., Chen, I.H., Newton, M.A., Stanhope, S.A., Cheng, Y.J., Chen, C.J., Hildesheim, A., Sugden, B., and Ahlquist, P. (2008). MicroRNA 29c is down-regulated in nasopharyngeal carcinomas, up-regulating mRNAs encoding extracellular matrix proteins. Proceedings of the National Academy of Sciences , 105, 5874-5878. pdf

Logan, J., Hoff, P., and Newton, M.A. (2008). Two-sided estimation of mate preferences for similarities in age, education, and religion. J. Amer. Statist. Assoc. , 103, 559-569.

Newton, M.A.. Introduction to, ``Large scale simultaneous hypothesis testing: the choice of a null hypothesis,'' By B. Efron. In, {\em The Science of Bradley Efron}, C.N. Morris, R. Tibshirani eds., pages 480-81. Springer, 2008.

Pyeon, D, Newton, MA, Lambert, PF, den Boon, JA, Sengupta, S, Marsit, CJ, Woodworth, CD, Connor, JP, Haugen, TH, Smith, EM, Kelsey, KT, Turek, LP, and Ahlquist, P. (2007). Fundamental differences in cell cycle deregulation in human papillomavirus-positive and human paillomavirus-negative head/neck and cervical cancers. Cancer Research 67, 4605-4619. pdf . link .

Newton, M.A., Quintana, F.A., den Boon, J.A., Sengupta, S. and Ahlquist, P. (2007). Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. Annals of Applied Statistics , 1, 85-106. pdf ,

Dahl, D.B. and Newton, M.A. (2007). Multiple hypothesis testing by clustering treatment effects. J. Amer. Statist. Assoc. , 102, 517-526. pdf . link.

Raftery, A.E., Newton, M.A., Satagopan, J., and Krivitsky, P. (2007). Estimating the integrated likelihood via posterior simulation using the harmonic mean identiy (with discussion). In Bayesian Statistics 8, pp 1-45, J.M. Bernardo, et al. (Eds.) Oxford University Press. pdf

Newton, M.A. (2007). A formula for the correlation between random-set enrichment scores. University of Wisconsin Statistics Department Technical Report \#1134. pdf .

Dodd, L, Sengupta, S, Chen, I-H, den Boon, JA, Cheng, Y-J, Westra, W, Newton, MA, Mittl, BF, McShane, L, Chen, C-J, Ahlquist, P, and Hildesheim, A (2006). Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are disregulated in nasopharyngeal carcinoma (NPC). Cancer Epidemiology, Biomarkers, and Prevention , 15: 2216-2225. link . pdf .

Newton, M.A., Wang, P. and Kendziorski C. (2006). Hierarchical mixture models for expression profiles. In, Bayesian inference for gene expression and proteomics, K. Ahn Do, P.M. Mueller, and M. Vannucci, eds. Cambridge University Press. pdf

S. Sengupta, J.A. den Boon, I-H. Chen, M.A. Newton, D.B. Dahl, M. Chen, Y-J. Cheng, W.H. Westra, C-J. Chen, A. Hildesheim, B. Sugden, and P. Ahlquist (2006). Genome-wide expression profiling reveals Epstein Barr virus-associated inhibition of MHC class I expression in nasopharyngeal carcinoma. Cancer Research, , 66(16) 7999-8006. pdf; (CR paper) supplementary methods (describes random-set enrichment calculations); supplementary tables

M. A. Newton (2006). On estimating the polyclonal fraction in lineage marker studies of tumor origin. Biostatistics , 7(4), 503-514. Abstract . pdf . (Revision of Technical Report 1099 .)

M.A. Newton, L. Clipson, A.T. Thliveris, R. Halberg (2006). A statistical test of the hypothesis that polyclonal intestinal tumors arise by random collision of initiated clones. Biometrics, 62(3),721-727. pdf .

M.A. Newton and D.I. Hastie (2006). Assessing Poisson variation of intestinal tumor multiplicity in Min mice carrying a Robertsonian translocation. Applied Statistics, 55 , pp. 123-138. pdf .

S.J. Leedham, S. Schier, A.T. Thliveris, R.B. Halberg, M.A. Newton, and N.A. Wright (2005). From gene mutations to tumours -- stem cells in gastrointestinal carcinogenesis. Cell Proliferation , 38 , 387-405. pdf .

Thliveris, AT, Halberg, RB, Clipson, L, Dove, WF, Sullivan, R, Washington, MK, Stanhope, S, and Newton, MA (2005). Polyclonality of familial murine adenomas: Analyses of mouse chimeras with low tumor multiplicity suggest short-range interactions. Proc. Natl. Acad. Sci. USA, 102, 6960-6965. (From the Cover.) pdf .

J.G. Perrigoue, J.A. den Boon, A. Friedl, M. A. Newton, P. Ahlquist, and B. Sugden (2005). Lack of Association between EBV and Breast Carcinoma. Cancer Epidemiology, Biomarkers, and Prevention, 14(4):809-814. pdf .

K.A. Gould, M. Tochacek, B.S. Schaffer, T.M. Reindl, C.R. Murrin, C.M. Lachel, E.A. VanderWoude, K.L. Pennington, L.A. Flood, K.K. Bynote, J.L. Meza, M.A. Newton, and J.D. Shull (2004). Genetic Determination of Susceptibility to Estrogen-Induced Mammary Cancer in the ACI Rat: Mapping of Emca1 and Emca2 to Chromosomes 5 and 18. Genetics, 168, 2113-2125.

M.A. Newton, A. Noueiry, D. Sarkar, and P. Ahlquist (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5, 155-176. pdf

M.A. Newton, STATISTICAL METHODS IN LABORATORY AND BASIC SCIENCE RESEARCH, in Modern Biometry, [Eds Susan R. Wilson and Conrad J. Burden], in Encyclopedia of Life Support Systems (EOLSS) , Developed under the Auspices of the UNESCO, Eolss Publishers, Oxford,UK, 2004. pdf

Kendziorski, C.M., M.A. Newton, H. Lan, and M.N. Gould (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistics in Medicine, 22, 3899-914. Abstract: Pub Med. This paper is the basis of the EBarrays R package. See bioconductor development packages.

M.A. Newton , H. Yang, P. Gorman, I. Tomlinson, and R. Roylance (2003). A statistical approach to modeling genomic aberrations in cancer cells (with discussion). In Bayesian Statistics 7 , J.M. Bernardo, M.J. Bayarri, J.O. Berger, A.P. Dawid, D. Hecherman, A.F.M. Smith and M. West (Eds.) Oxford University Press. pdf

Newton, M.A. and C.M. Kendziorski. Parametric Empirical Bayes Methods for Microarrays in The analysis of gene expression data: methods and software. Eds. G. Parmigiani, E.S. Garrett, R. Irizarry and S.L. Zeger, New York: Springer Verlag, 2003.

M.A. Newton (2002). Discovering combinations of genomic alterations associated with cancer. Journal of the American Statististical Association 97 931-942. Abstract . pdf .

M.A. Newton (2002). On a nonparametric recursive estimator of the mixing distribution.  Sankhya . Series A, 64, 1-17. More info from author, Abstract and Full Text: Sankhya website.

Hoff, P.D., Halberg, R.B., Shedlovsky, A., Dove, W.F., and M.A. Newton (2002). Identifying Carriers of a Genetic Modifier Using Nonparametric Bayes Methods, Case Studies in Bayesian Statistics , 5, 329-343.

M.R. Albertini, D.M. King, M.A. Newton , P.M. Vacek (2001). In vivo mutant frequency of thioguanine-resistant T-cells in the peripheral blood and lymph nodes of melanoma patients. Mutation Research, 476 , 83-97. Abstract: Pub Med.

M.A. Newton, C.M. Kendziorski, C.S. Richmond, F.R. Blattner, K.W. Tsui (2001). On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. Journal of Computational Biology, 8, 37-52. See also Biostatistics Technical Report #139, more info from author. Abstract: Pub Med.

Lan, H., C.M. Kendziorski, L.A. Shepel, J.D. Haag, M.A. Newton and M.N. Gould (2001). Genetic loci controlling breast cancer susceptibility in the Wistar-Kyoto rat. Genetics, 157, 331-339. Abstract and Full Text: Genetics website.

M.M. Fisher, J.L. Klug, G. Lauster, M.A. Newton and E.W. Triplett (2000). Effects of resources and trophic interactions on freshwater bacterioplankton. Microbial Ecology, 40, 125-138. Abstract: Pub Med.

F. A. Quintana and M. A. Newton (2000). Computational aspects of nonparametric Bayesian analysis with applications to the modeling of multiple binary sequences. Journal of Computational and Graphical Statistics, 9, 711-737.

J.G. Teeguarden, M.A. Newton , Y.P. Dragan, H.C. Pitot (2000). Genome-wide loss of heterozygosity analysis of chemically induced rat hepatocellular carcinomas reveals elevated frequency of allelic imbalances on chromosomes 1, 6, 8, 11, 15, 17, and 20. Molecular Carcinogenesis, 28, 51-61. Abstract: Pub Med.

M.A. Newton , and Y. Lee (2000). Inferring the location and effect of tumor suppressor genes by instability-selection modeling of allelic-loss data. Biometrics, 56, 1088-1097. More info from author, Abstract: Pub Med.

F. A. Quintana and M. A. Newton (1999). Parametric Partially Exchangeable Models for Multiple Binary Sequences . Brazilian Journal of Probability and Statistics, 13, 55-76. More info from author.

D.F. Jarrard, S. Sarkar, Y. Shi, T.R. Yeager, G. Magrane, H. Kinoshita, N. Nassif, L. Meisner, M.A. Newton , F.M. Waldman, and C.A. Reznikoff (1999). p16/pRb Pathway Alterations Are Required for Bypassing Senescence in Human Prostate Epithelial Cells. Cancer Research, 59, 2957-64. Abstract: Pub Med, Full Text: Cancer Research website.

J. Lee, M. Lascoux, M.A. Newton , E. Nordheim (1999). A study of deleterious gene structure in plants using Markov chain Monte Carlo. Biometrics, 55, 376-386. Abstract: Pub Med.

J.D. Haag G. M. Brasic, L.A. Shepel, M. A. Newton C.J. Grubbs, R.A. Lubet, J.G. Kelloff, and M.N. Gould (1999). A comparative analysis of allelic-imbalance events in chemically induced rat mammary colon and bladder tumors. Molecular Carcinogenesis, 24, 47-56. Abstract: Pub Med.

H. Tao, M. Palta, B.S. Yandell, and M. A. Newton (1999). An estimation method for the semiparametric mixed effects model. Biometrics, 55, 199-202. More info from author, Abstract: Pub Med.

Bob Mau, M.A. Newton , and Bret Larget (1999). Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics, 55, 234-249. pdf

M.A. Newton , and Y. Zhang (1999). A recursive algorithm for nonparametric analysis with missing data. Biometrika, 86, 15-26. More info from author.

M. A. Newton , T. Yeager, and C.A. Reznikoff (1999). A statistical analysis of cancer genome variation. IMA Volumes in Mathematics and its Applications. M. Elizabeth Halloran, Seymour Geisser (eds), 112, 223-236, Springer-Verlag.

M. A. Newton , Bob Mau, and Bret Larget (1999). Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences. In F. Seillier-Moseiwitch (Ed.), Statistics in Molecular Biology and Genetics. IMS Lecture Notes-Monograph Series, 33, 143-162. More info from author.

A.R. Shoemaker, A.R. Moser, C.A. Midgley, L. Clipson, M.A. Newton , W.F. Dove (1998). A resistant genetic background leading to incomplete penetrance of intestinal neoplasia and reduced loss of heterozygosity in Apc(Min)/+ mice. Proc. Natl. Acad. Sci. USA, 95, 10826-10831. Abstract: Pub Med, Full Text: PNAS Online.

R.R. Love, R. Jacoby, M. A. Newton , K.D. Tutsch, K. Simon, M. Pomplun, A.K. Verma (1998). A randomized, placebo-controlled trial of low dose $\alpha-$difluoromethylornithine in individuals at risk for colorectal cancer. Cancer Epidemiology, Biomarkers, and Prevention ,7, 11, 989-992. Abtract: Pub Med.

L.A. Shepel, H. Lan, J.D. Haag, G.M. Brasic, M.E. Gheen, J.S. Simon, P. Hoff, M. A. Newton , and M.N. Gould (1998). Genetic identification of multiple loci that control breast cancer susceptibility in the rat. Genetics, 149 , 289-299. Abstract: Pub Med, Full Text: Genetics website.

W.F. Dove, R.T. Cormier, K.A. Gould, R.B. Halberg, A.J. Merritt, M. A. Newton , and A.R. Shoemaker (1998). The intestinal epithelium and its neoplasms: genetic, cellular and tissue interactions. Phil. Trans. R. Soc. Lond. B, 353, 915-923. Abstract: Pub Med.

M.A. Newton , M.N. Gould, C. A. Reznikoff, and J.D. Haag (1998). On the statistical analysis of allelic-loss data. Statistics in Medicine, 17, 1425-1445. More info from author, Abstract: Pub Med.

M.A. Newton , F.A. Quintana, and Y. Zhang (1998). Nonparametric Bayes methods using predictive updating. In Practical nonparametric and semiparametric Bayesian statistics (eds D. Dey, P. Muller, and D. Sinha), pp 45-61. New York: Springer. Full Text: pdf preprint. [ Tack example Splus code ] [ Censoring example Splus code ]

T.R. Yeager, S. DeVries, D.F. Jarrard, C. Kao, S.Y. Nakada, T.D. Moon, R. Bruskewitz, W.M. Stadler, L.F. Meisner, K.W. Gilchrist, M.A. Newton , F.M. Waldman, and C.A. Reznikoff (1998). Overcoming cellular senescence in human cancer pathogenesis. Genes and Development, 12, 163--174. Abstract: Pub Med, Full Text: Genes and Development website.

F. A. Quintana and M.A. Newton (1998). Assessing the Order of Dependence for Partially Exchangeable Binary Data. Journal of the American Statistical Association , 93, 194--202. More info from author, JASA website.

B.A. Craig and M.A. Newton (1997). Modeling the history of diabetic retinophathy. In Case Studies in Bayesian Statistics III . C. Gatsonis et al. (eds.). New York: Springer-Verlag, 305--323. More info from author.

B. A. Craig, M.A. Newton , R. A. Garrott, J. E. Reynolds III, and J. R. Wilcox (1997). Analysis of aerial survey data on Florida Manatee using Markov chain Monte Carlo. Biometrics, 53, 129--146. (Student paper prize, ENAR, 1996.). More info from author, Abstract: Pub Med.

Bob Mau and M.A. Newton (1997). Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. Journal of Computational and Graphical Statistics, 6 , 122-131. (Student paper prize, Statistical Computing Section of ASA, 1996). More info from author.

E. Savelieva, C.D. Belair, M.A. Newton , S. DeVries, J.W. Gray, F. Waldman, and C. A. Reznikoff (1997). 20q gain associates with immortalization: 20q13.2 correlates with genome instability in human papillomavirus 16 E7 transformed human uroepithelial cells. Oncogene , 14 , 551-560. Abstract: Pub Med, Full Text: Oncogene website.

W.F. Dove, L. Clipson, K.A. Gould, C. Luongo, D.J. Marshall, A.R. Moser, M.A. Newton , and R.F. Jacoby (1997). Intestinal neoplasia in the Apc-Min Mouse: Independence from the microbial and natural killer (beige Locus) status. Cancer Research, 57 , 812-814. More info from author, Abstract: Pub Med.

J.D. Haag, L.-C. Hsu, M.A. Newton , M.N. Gould (1996). Allelic Imbalance in Mammary Carcinomas Induced by Either 7,12-Dimethylbenz[a]anthracene or Ionizing Radiation in Rats Carrying Genes Conferring Differential Susceptibilities to Mammary Carcinogenesis. Molecular Carcinogenesis , 17, 134--143. Abstract: Pub Med.

J. M. Satagopan, B. S. Yandell, M.A. Newton , and T. C. Osborn (1996). A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo . Genetics, 144 , 805--816. More info from author, Abstract: Pub Med, Full Text: Genetics website.

S.-Q. Wu, G. R. Hajez, W. Xing, M.A. Newton , X.-R. Chen, and E. Messing (1996). Chromosome 14q Loss in Non-papillary Renal Cell Carcinoma Correlation with Histopathologic Grade, Clinical Stage, and Outcome. Cancer, 77, 1154-1160. Abstract: Pub Med.

R.F. Jacoby, D.J. Marshall, M.A. Newton , K. Novakovic, K. Tutsch, C.E. Cole, R.A. Lubet, G.J. Kelloff, A. Verma, A. R. Moser, and W.F. Dove (1996). Chemoprevention of Spontaneous Intestinal Adenomas in the Apc Min Mouse Model by the Non-Steroidal Anti-Inflammatory Drug Piroxicam. Cancer Research, 56, 710-714. Abstract: Pub Med.

M.A. Newton , (1996). Bootstrapping phylogenies: Large deviations and dispersion effects. Biometrika, 83, 315--328. (G.W. Snedecor Award, 1997). pdf

M.A. Newton , C. Czado, and R. Chappell (1996). Bayesian inference for semiparametric binary regression. Journal of the American Statistical Association, 91, 142-153. More info from author, JASA website.

A Jara's R Package CSDPBinary

J. F. Pendergast, S. J. Gange, M. J. Lindstrom, M.A. Newton , M. Palta, and M. R. Fisher (1996). A survey of methods for analyzing clustered binary response data. International Statistical Review, 64, 1-30.

E. M. Messing, T. B. Young, V. B. Hunt, K. W. Gilchrist, M.A. Newton , L. L. Bram, W. J. Hisgen, E. B. Greenberg, M. E. Kuglitsch and J. D. Wegenke (1995). Comparison of bladder cancer outcome in men undergoing hematuria home screening versus those with standard clinical presentations. Urology, 45, 387-397. Abstract: Pub Med, Full Text: Elsevier Science Direct.

M.A. Newton , P. Guttorp, S. Catlin, R. Assunção, and J. L. Abkowitz (1995). Stochastic modeling of early hematopoiesis. Journal of the American Statistical Association, 90, 1146-1155. More info from author.

J.K. Lee, M.A. Newton , E. Nordheim, and H. Kang (1994). Inference on lethal gene studies via Bayesian Markov chain simulation. Computer Science and Statistics, 26, 410--414. Interface Foundation of North America.

M.A. Newton (1994). A diffuse prior limit in semiparametric binary regression. American Statistical Association Proceedings of the Section on Bayesian Statistical Science , 181--186. Also UW Madison Department of Statistics Technical Report 936, More info from author.

C. Reznikoff, C. Belair, E. Savelieva, Y. Zhai, K. Pfeifer, T. Yeager, K. J. Thompson, Sandy DeVries, C. Bindley, M.A. Newton , G. Sekhon, and F. Waldman (1994). Long term genome stability and minimal genotypic and phenotypic alterations in HPV16 E7, but not E6 immortalized human uroepithelial cells. Genes and Development, 8, 2227-2240. Abstract: Pub Med.

M.A. Newton and C. J. Geyer (1994). Bootstrap Recycling: A Monte Carlo alternative to the nested bootstrap. Journal of the American Statistical Association, 89, 905-912. More info from author.

M.A. Newton , S. Q. Wu, and C. A. Reznikoff (1994). Assessing the significance of chromosome-loss data: Where are the suppressor genes for bladder cancer? Statistics in Medicine, 13, 839-858. Abstract: Pub Med.

M.A. Newton and A. E. Raftery (1994). Approximate Bayesian inference with the weighted likelihood bootstrap (with discussion). Journal of the Royal Statistical Society, Series b, 56, 3-48. PDF

J. L. Abkowitz, M. L. Linenberger, M.A. Newton , M. Persik, and P. Guttorp (1993). Behavior of Feline Hematopoietic Stem Cells Years After Busulfan Exposure. Blood, 82, 2096-2103. Abstract: Pub Med.

C. A. Reznikoff, C. Kao, E. M. Messing, M.A. Newton and S. Swaminathan (1993). Molecular genetic model of human bladder carcinogenesis. Seminars in Cancer Biology, 4, 143-152. Abstract: Pub Med.

M.A. Newton , P. Guttorp, and J. A. Abkowitz (1992). Bayesian inference by simulation in a stochastic model from hematology. Computer Science and Statistics, 24, 449--455. H. J. Newton, Editor. Interface Foundation of North America. Full Text: Postscript.

J. D. Haag, M.A. Newton , and M. N. Gould (1992). Mammary carcinoma suppressor and susceptibility genes in the Wistar-Kyoto rat. Carcinogenesis, 13, 1933-1935. Abstract: Pub Med.

D.M. Mason and M.A. Newton (1992). A rank statistics approach to the consistency of a general bootstrap. Annals of Statistics, 20, 1611-1624.

E. Haeusler, D.M. Mason, and M.A. Newton (1991). Weighted Bootstrapping of Means, Centrum voor Wiskunde en Informatica Quarterly, 4, 213-228.

P. Guttorp, M.A. Newton and J. L. Abkowitz (1990). A Stochastic Model for Hematopoiesis in Cats, IMA Journal of Mathematics Applied in Medicine and Biology, 7, 125-143. Abstract: Pub Med.

J.L. Abkowitz, M.L. Linenberger, M.A. Newton , G.H. Shelton, R.L. Ott, and P. Guttorp (1990). Evidence for the maintenance of hematopoiesis in a large animal by the sequential activation of stem-cell clones, Proc. Natl. Acad. of Sci. USA, 87, 9062-9066. Abstract: Pub Med, Full Text: PNAS Online.

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Thanks to Jim Cumming for web assistance.