Faculty

Daniel Q. Naiman

Professor, Director of Graduate Studies and Director of Financial Mathematics M.S.E. Program

Research Interests

  • Statistics
  • Computational Probability
  • Bioinformatics
Education
  • Ph.D. 1982, University of Illinois/Urbana
  • M.S. 1979, University of Illinois/Urbana
  • A.B. 1977, Cornell University
Experience
  • July 1, 2008 - Present:  Director, JHU WSE Financial Mathematics Masters Program
  • 1992 - Present:  Professor, JHU Department of Applied Mathematics and Statistics
  • July 1, 2004 - June 30, 2014:  Department Chair, JHU Dept. of Applied Mathematics and Statistics
  • 2004:  Department Chair, JHU Dept. of Applied Mathematics and Statistics
  • 2003 - 2004:  Visiting Investigator, Inherited Disease Branch of National Human Genome Research Institute, NIH
  • 1988 - 1992:  Associate Professor, JHU Department of Mathematical Sciences
  • 1982 - 1988:  Assistant Professor, JHU Department of Mathematical Sciences
Research Areas
  • Genomics
  • Geometry
  • Probability
  • Statistical genetics
  • Statistics
  • System reliability
Awards
  • 2005:  Erskine Fellow - University of Canterbury
  • 1997:  Elected Fellow of the Institute of Mathematical Statistics
  • 1977:  University Fellow - University of Illinois/Urbana
Journal Articles
  • Niknafs, N., Beleva-Guthrie, V., Naiman, D., Karchin, R. (2015).  SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.  PLoS Comput Biol.  11(10).  e1004416.
  • LaKind, J. S., Naiman, D. (2015).  Temporal trends in bisphenol A exposure in the United States from 2003–2012 and factors associated with BPA exposure: Spot samples and urine dilution complicate data interpretation.  Environmental Research.  142.  84-95.
  • Cope, L., Naiman, D., Parmigiani, G. (2014).  Integrative correlation: Properties and relation to canonical correlations.  Journal of Multivariate Analysis.  123.  270-280.
  • Tosto, M. G., Petrill, S. A., Halberda, J., Trzaskowski, M., Tikhomirova, T. N., Bogdanova, O. Y., Ly, R., Wilmer, J. B., Naiman, D., Germine, L., Plomin, R., Kovas, Y. (2014).  Why do we differ in number sense? Evidence from a genetically sensitive investigation.  Intelligence.  43(0).  35-46.
  • Marchitti, S. A., LaKind, J. S., Naiman, D., Berlin, C. M., Kenneke, J. F. (2013).  Improving Infant Exposure and Health Risk Estimates: Using Serum Data to Predict Polybrominated Diphenyl Ether Concentrations in Breast Milk.  Environmental Science & Technology.  47(9).  4787-4795.
  • LaKind, J. S., Levesque, J., Dumas, P., Bryan, S., Clarke, J., Naiman, D. (2012).  Comparing United States and Canadian population exposures from National Biomonitoring Surveys: Bisphenol A intake as a case study.  Journal of Exposure Science and Environmental Epidemiology.  22(3).  219-226.
  • Lecover, R., Williams, N., Markovic, N., Reich, D., Naiman, D., Katz, H. (2012).  Next-Generation Polymer Solar Cell Materials: Designed Control of Interfacial Variables.  Acs Nano.  6(4).  2865-2870.
  • Halberda, J., Ly, R., Wilmer, J. B., Naiman, D., Germine, L. (2012).  Number sense across the lifespan as revealed by a massive Internet-based sample.  Proceedings of the National Academy of Sciences of the United States of America.  109(28).  11116-11120.
  • LaKind, J. S., Goodman, M., Naiman, D. (2012).  Use of NHANES Data to Link Chemical Exposures to Chronic Diseases: A Cautionary Tale.  Plos One.  7(12).
  • Lakind, J. S., Naiman, D. (2011).  Daily intake of bisphenol A and potential sources of exposure: 2005-2006 National Health and Nutrition Examination Survey.  Journal of Exposure Science and Environmental Epidemiology.  21(3).  272-279.
  • Martin, D. C., Kim, H., Mackin, N. A., Maldonado-Baez, L., Evangelista, C. C., Beaudry, V. G., Dudgeon, D. D., Naiman, D., Erdman, S. E., Cunningham, K. (2011).  New Regulators of a High Affinity Ca2+ Influx System Revealed through a Genome-wide Screen in Yeast.  Journal of Biological Chemistry.  286(12).  10744-10754.
  • Lakind, J. S., Naiman, D., Hays, S. M., Aylward, L. L., Blount, B. C. (2010).  Public health interpretation of trihalomethane blood levels in the United States: NHANES 1999-2004.  Journal of Exposure Science and Environmental Epidemiology.  20(3).  255-262.
  • Feng, J., Naiman, D., Cooper, B. (2009).  Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing.  Molecular Biosystems.  5(12).  1679-1687.
  • Feng, J., Garrett, W. M., Naiman, D., Cooper, B. (2009).  Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification.  Journal of Proteome Research.  8(11).  5396-5405.
  • LaKind, J. S., Berlin, C. M., Sjodin, A., Turner, W., Wang, R., Needham, L. L., Paul, I. M., Stokes, J. L., Naiman, D., Patterson, D. G. (2009).  Do Human Milk Concentrations of Persistent Organic Chemicals Really Decline During Lactation? Chemical Concentrations During Lactation and Milk/Serum Partitioning.  Environmental Health Perspectives.  117(10).  1625-1631.
  • Lakind, J. S., Hays, S. M., Aylward, L. L., Naiman, D. (2009).  Perspective on serum dioxin levels in the United States: an evaluation of the NHANES data.  Journal of Exposure Science and Environmental Epidemiology.  19(4).  435-441.
  • Lee, J., Feng, J., Campbell, K. B., Scheffler, B. E., Garrett, W. M., Thibivilliers, S., Stacey, G., Naiman, D., Tucker, M. L., Pastor-Corrales, M. A., Cooper, B. (2009).  Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus.  Molecular & Cellular Proteomics.  8(1).  19-31.
  • Lin, X., Afsari, B., Marchionni, L., Cope, L., Parmigiani, G., Naiman, D., Geman, D. (2009).  The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.  BMC bioinformatics.  10(1).  256.
  • Lakind, J. S., Naiman, D. (2008).  Bisphenol A (BPA) daily intakes in the United States: Estimates from the 2003-2004 NHANES urinary BPA data.  Journal of Exposure Science and Environmental Epidemiology.  18(6).  608-615.
  • Feng, J., Naiman, D., Cooper, B. (2008).  Combined dynamic arrays for storing and searching semi-ordered tandem mass spectrometry data.  Journal of Computational Biology.  15(4).  457-468.
  • Geman, D., Afsari, B., Tan, A. C., Naiman, D. (2008).  Microarray classification from several two-gene expression comparisons.  Seventh International Conference on Machine Learning and Applications, Proceedings.  583-585.
  • Uhl, G. R., Drgon, T., Johnson, C., Li, C., Contoreggi, C., Hess, J., Naiman, D., Liu, Q. R. (2008).  Molecular Genetics of Addiction and Related Heritable Phenotypes Genome-Wide Association Approaches Identify "Connectivity Constellation" and Drug Target Genes with Pleiotropic Effects.  Addiction Reviews 2008.  1141.  318-381.
  • Song, W., Juhn, F. S., Naiman, D., Konstantinidis, K. T., Gardner, T. S., Ward, M. J. (2008).  Predicting sigma(28) promoters in eleven Shewanella genomes.  Fems Microbiology Letters.  283(2).  223-230.
  • Needham, L. L., Naiman, D., Patterson, D. G., LaKind, J. S. (2007).  Assigning concentration values for dioxin and furan congeners in human serum when measurements are below limits of detection: An observational approach.  Chemosphere.  67(3).  439-447.
  • Feng, J., Naiman, D., Cooper, B. (2007).  Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry data.  Analytical Chemistry.  79(10).  3901-3911.
  • Feng, J., Naiman, D., Cooper, B. (2007).  Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies.  Bioinformatics.  23(17).  2210-2217.
  • Song, W. J., Maiste, P. J., Naiman, D., Ward, M. J. (2007).  Sigma 28 promoter prediction in members of the Gammaproteobacteria.  Fems Microbiology Letters.  271(2).  222-229.
  • Tosun, D., Rettmann, M. E., Naiman, D., Resnick, S. M., Kraut, M. A., Prince, J. (2006).  Cortical reconstruction using implicit surface evolution: accuracyand precision analysis.  NeuroImage.  29(3).  838–852.
  • Baier-Anderson, C., Blount, B. C., LaKind, J. S., Naiman, D., Wilbur, S. B., Tan, S. (2006).  Estimates of exposures to perchlorate from consumption of human milk, dairy milk, and water, and comparison to current reference dose.  Journal of Toxicology and Environmental Health-Part a-Current Issues.  69(4).  319-330.
  • Naiman, D. (2006).  Random data set generation to support microarray analysis.  DNA Microarrays, Part B: Databases and Statistics.  411.  312-325.
  • Wu, X. L., Naiman, D. (2005).  p-Value simulation for affected sib pair multiple testing.  Human Heredity.  59(4).  190-200.
  • Xu, L., Tan, A. C., Naiman, D., Geman, D., Winslow, R. L. (2005).  Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data.  Bioinformatics.  21(20).  3905–3911.
  • Tan, A. C., Naiman, D., Xu, L., Winslow, R. L., Geman, D. (2005).  Simple decision rules for classifying human cancers from gene expression profiles.  Bioinformatics.  21(20).  3896–3904.
  • Dominici, F., Cope, L., Naiman, D., Zeger, S. (2005).  Smooth quantile ratio estimation.  Biometrika.  92(3).  543-557.
  • Naiman, D., Wynn, H. P. (2005).  The algebra of Bonferroni bounds: discrete tubes and extensions.  Metrika.  62(2-3).  139-147.
  • Anthony, L. G., Anthony, B. J., Glanville, D. N., Naiman, D., Waanders, C., Shaffer, S. (2005).  The relationships between parenting stress, parenting behaviour and preschoolers’ social competence and behaviour problems in the classroom.  Infant and Child Development.  14(2).  133-154.
  • Parisi, M., Nuttall, R., Edwards, P., Minor, J., Naiman, D., Lu, J. N., Doctolero, M., Vainer, M., Chan, C., Malley, J., Eastman, S., Oliver, B. (2004).  A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults.  Genome Biology.  5(6).
  • Geman, D., d’Avignon, C., Naiman, D., Winslow, R. L. (2004).  Classifying gene expression profiles from pairwise mRNA comparisons.  Statistical applications in genetics and molecular biology.  3(1).
  • Geman, D., d’Avignon, C., Naiman, D., Winslow, R., Zeboulon, A. (2004).  Gene expression comparisons for class prediction in cancer studies.  Proceedings 36’th Symposium on the Interface: Computing Science and Statistics.
  • Naiman, D. (2004).  Statistical anomaly detection via httpd data analysis.  Computational Statistics & Data Analysis.  45(1).  51-67.
  • Klein, A. P., Kovac, I., Sorant, A. J., Baffoe-Bonnie, A., Doan, B. Q., Ibay, G., Lockwood, E., Mandal, D., Santhosh, L., Weissbecker, K., Woo, J., Zambelli-Weiner, A., Zhang, J., Naiman, D., Malley, J., Bailey-Wilson, J. E. (2003).  Importance sampling method of correction for multiple testing in affected sib-pair linkage analysis.  Bmc Genetics.  4.
  • Parisi, M. J., Nuttall, R., Lu, J. N., Chan, C., Vainer, M., Minor, J., Lash, A., Eastman, S., Malley, J., Naiman, D., Oliver, B. (2003).  Microarray analysis of sexual dimorphism in Drosophila..  Developmental Biology.  259(2).  528-528.
  • Parisi, M., Nuttall, R., Naiman, D., Bouffard, G., Malley, J., Andrews, J., Eastman, S., Oliver, B. (2003).  Paucity of genes on the Drosophila X chromosome showing male-biased expression.  Science.  299(5607).  697-700.
  • Malley, J. D., Naiman, D., Bailey-Wilson, J. E. (2002).  A comprehensive method for genome scans.  Human Heredity.  54(4).  174-185.
  • Giglio, B., Naiman, D., Wynn, H. P. (2002).  Grobner bases, abstract tubes, and inclusion-exclusion reliability bounds.  Ieee Transactions on Reliability.  51(3).  358-366.
  • Suzuki, T., Shen, H. F., Akagi, K., Morse, H. C., Malley, J. D., Naiman, D., Jenkins, N. A., Copeland, N. G. (2002).  New genes involved in cancer identified by retroviral tagging.  Nature Genetics.  32(1).  166-174.
  • Uhl, G. R., Liu, Q. R., Naiman, D. (2002).  Substance abuse vulnerability loci: converging genome scanning data.  Trends in Genetics.  18(8).  420-425.
  • Priebe, C., Naiman, D., Cope, L. M. (2001).  Importance sampling for spatial scan analysis: computing scan statistic p-values for marked point processes.  Computational Statistics and Data Analysis.  35(4).  475–485.
  • LaKind, J. S., Berlin, C. M., Naiman, D. (2001).  Infant exposure to chemicals in breast milk in the United States: What we need to learn from a breast milk monitoring program.  Environmental Health Perspectives.  109(1).  75-88.
  • Uhl, G. R., Liu, Q. R., Walther, D., Hess, J., Naiman, D. (2001).  Polysubstance abuse-vulnerability genes: Genome scans for association, using 1,004 subjects and 1,494 single-nucleotide polymorphisms.  American Journal of Human Genetics.  69(6).  1290-1300.
  • Naiman, D., Priebe, C. (2001).  Computing Scan Statistic p Values Using Importance Sampling, with Applications to Genetics and Medical Image Analysis.  Journal of Computational and Graphical Statistics.  10(2).  296–328.
  • LaKind, J. S., Berlin, C. M., Park, C. N., Naiman, D., Gudka, N. J. (2000).  Methodology for characterizing distributions of incremental body burdens of 2,3,7,8-TCDD and DDE from breast milk in North American nursing infants.  Journal of Toxicology and Environmental Health-Part A.  59(8).  605-639.
  • Schwartz, S. S., Naiman, D. (1999).  Bias and variance of planning level estimates of pollutant loads.  Water Resources Research.  35(11).  3475-3487.
  • LaKind, J. S., Ginevan, M. E., Naiman, D., James, A. C., Jenkins, R. A., Dourson, M. L., Felter, S. P., Graves, C. G., Tardiff, R. G. (1999).  Distribution of exposure concentrations and doses for constituents of environmental tobacco smoke.  Risk Analysis.  19(3).  375-390.
  • LaKind, J. S., Graves, C. G., Ginevan, M. E., Jenkins, R. A., Naiman, D., Tardiff, R. G. (1999).  Exposure to environmental tobacco smoke in the workplace and the impact of away-from-work exposure.  Risk Analysis.  19(3).  349-358.
  • Kleinman, N. L., Spall, J. C., Naiman, D. (1999).  Simulation-based optimization with stochastic approximation using common random numbers.  Management Science.  45(11).  1570-1578.
  • LaKind, J. S., Jenkins, R. A., Naiman, D., Ginevan, M. E., Graves, C. G., Tardiff, R. G. (1999).  Use of environmental tobacco smoke constituents as markers for exposure.  Risk Analysis.  19(3).  359-373.
  • Naiman, D., Stone, R. E. (1998).  A homological characterization of Q-matrices.  Mathematics of Operations Research.  23(2).  463-478.
  • Naiman, D., Wynn, H. P. (1997).  Abstract tubes, improved inclusion-exclusion identities and inequalities and importance sampling.  Annals of Statistics.  25(5).  1954-1983.
  • Naiman, D., Wynn, H. P. (1997).  On intersecting a point set with Euclidean balls.  Computational Geometry-Theory and Applications.  7(4).  237-244.
  • Lee, D., Naiman, D. (1996).  A hybrid estimator for the cumulative probability of detection of surveillance radars.  Ieee Transactions on Aerospace and Electronic Systems.  32(1).  476-480.
  • Naiman, D., Wynn, H. P. (1996).  Independence number and the complexity of families of sets.  Discrete Mathematics.  154(1-3).  203-216.
  • Chan, O., Naiman, D. (1995).  Some Simple U-Statistic Tests for Uniformity on Certain Homogeneous Spaces.  Journal of Multivariate Analysis.  54(2).  210-226.
  • Naiman, D., Wynn, H. P. (1993).  A Theorem on Independence.  Discrete Mathematics.  120(1-3).  287-289.
  • Aronov, B., Naiman, D., Pach, J., Sharir, M. (1993).  An Invariant Property of Balls in Arrangements of Hyperplanes.  Discrete & Computational Geometry.  10(4).  421-425.
  • Naiman, D., Wynn, H. P. (1993).  Independent Collections of Translates of Boxes and a Conjecture Due to Grunbaum.  Discrete & Computational Geometry.  9(1).  101-105.
  • Naiman, D., Wynn, H. P. (1992).  Inclusion-Exclusion-Bonferroni Identities and Inequalities for Discrete Tube-Like Problems Via Euler Characteristics.  Annals of Statistics.  20(1).  43-76.
  • Naiman, D. (1991).  On the Problem of Interactions in the Analysis of Variance - Comment.  Journal of the American Statistical Association.  86(414).  369-372.
  • Naiman, D. (1990).  Volumes of Tubular-Neighborhoods of Spherical Polyhedra and Statistical-Inference.  Annals of Statistics.  18(2).  685-716.
  • Casman, E. A., Naiman, D., Chamberlin, C. E. (1988).  Confronting the Ironies of Optimal-Design - Nonoptimal Sampling Designs with Desirable Properties.  Water Resources Research.  24(3).  409-415.
  • Naiman, D. (1987).  Characterization of Risk Sets for Simple Versus Simple Hypothesis-Testing.  American Statistician.  41(3).  218-220.
  • Naiman, D. (1987).  Minimax Regret Simultaneous Confidence Bands for Multiple-Regression Functions.  Journal of the American Statistical Association.  82(399).  894-901.
  • Naiman, D. (1987).  Simultaneous Confidence-Bounds in Multiple-Regression Using Predictor Variable Constraints.  Journal of the American Statistical Association.  82(397).  214-219.
  • Naiman, D. (1986).  Conservative Confidence Bands in Curvilinear Regression.  Annals of Statistics.  14(3).  896-906.
  • Naiman, D. (1984).  Average Width Optimality of Simultaneous Confidence-Bounds.  Annals of Statistics.  12(4).  1199-1214.
  • Naiman, D. (1984).  Optimal Simultaneous Confidence-Bounds.  Annals of Statistics.  12(2).  702-715.
  • Naiman, D. (1983).  Comparing Scheffe-Type to Constant-Width Confidence-Bounds in Regression.  Journal of the American Statistical Association.  78(384).  906-912.
Book Chapters
  • Tosun, D., Rettmann, M. E., Naiman, D., Resnick, S. M., Kraut, M. A., Prince, J. (2004).  Cortical reconstruction using implicit surface evolution: a landmarkvalidation study.  Medical Image Computing and Computer-Assisted Intervention–MICCAI2004.  Springer Berlin Heidelberg.  384–392.
Other Publications
  • Donohue, M., Naiman, D., Jin, G., Loehe, J. R. (1990).  Statistically designed study of the variables and parameters of carbon dioxide equations of state.  Johns Hopkins Univ., Baltimore, MD (USA).
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