Naomi Altman

VITA

 

Naomi S. Altman                                                 

Dept. of Statistics                                                 

Penn State University                                                     

University Park, PA 16802                                              

814-865-3791 (office)

814-863-7114 (fax)                                               

nsa1@psu.edu

 

Current Position

 

Professor of Statistics and Bioinformatics, Penn State University

 

 

Education

 

Ph.D.           1988  In Statistics from Stanford University

                   Advisor:  Iain Johnstone

Topic:         Smoothing Data with Correlated Errors

 

M.S.            1979  In Statistics from the University of Toronto

B.Sc.           1974  In Mathematics from the University of Toronto

 

 

Awards

 

1991           "Best Manuscript" from North Atlanta Area Office of the Director, USDA, for Gray et al

2004           The Canadian Journal of Statistics (best paper) with J. Villarreal     

2009            Fellow of the American Statistical Association

 

 

Student Paper Awards (advisor for)

 

1996 Johnson, K.W.  Title: Canonical Correspondence Analysis as an Approximation to Gaussian Ordination.  Student Paper/Travel Award: American Statistical Association Section on Statistics and the Environment.  MS Advisor: Naomi Altman

 

2008 Zeifman, Lubov     Title: Independent Component Analysis of fMRI data Phi Beta Kappa Honors Thesis Award.  Undergraduate Honors Advisor: Naomi Altman

 

 

Positions Held

 

2019-          Professor Emeritus

2013-          Contributing Editor, Nature Methods

2012-2013  Visiting Professor – Statistical and Mathematical Sciences Institute, NC

2011-2019  Professor, Dept. of Statistics, PSU

2001-11      Associate Professor, Dept. of Statistics, PSU

2002-05      Associate Director – Bioinformatics Consulting Center, PSU

1997-01      Co-director of the Environmental Statistics Program,

                   Dept. of Biometrics, Cornell University

1997-00      Chair, Department of Biometrics, Cornell University

1995-01      Associate Professor, Department of Biometrics, Cornell University.

1996-97      Visiting Associate Professor, Bioacoustics Laboratory, Cornell University 

1987-95     Assistant Professor, Biometrics Unit, Cornell University

1991           Visiting Researcher, Departement d'Informatique et Recherche Operationelle,

University of Montreal

1984-86      Statistical consultant, Department of Statistics and Stanford Linear Accelerator

                   Center, Stanford University

1981-83      Research Associate, University of British Columbia, Department of Medical Genetics

1979-81     Statistical Consultant, Computing Centre, Simon Fraser University

1979           Statistical Consultant, Computing Centre, University of Toronto

1978           APL Consultant, Computing Centre, University of Toronto

1975-77      Teacher, Government Teacher's Training College, Lafia, Nigeria.

 

 

Published  Peer Reviewed Papers

 

1.     (1988) Altman, N.S. Bit-wise Behavior of Random Number Generators.  SIAM Journal of Scientific and Statistical Computing, 941-949.

 

2.     (1990) Altman, N.S, Kernel Smoothing of Data with Correlated Errors.   Journal of the American Statistical Association, 85, 749-758

 

3.     (1990) Wimpfheimer, L., Altman, N.S. and Hotchkiss, J.H., Growth of L. monocytogenes Scott A, serotype 4 and competitive spoilage organisms in raw chicken packaged under modified atmospheres and in air.  International Journal of Food Microbiology, 11, 205-214. PMID: 2126442

 

4.     (1991) Altman, N.S., Banks, D., Chen, P., Duffy, D., Hardwick, J., Leger, C., Owen, A.and Stukel, T.  Meeting the needs of New Statistical Researchers.  Statistical Science, 6, 163-174.

 

5.     (1991) Altman, N.S., Discussion of  “Some Tools for Functional Data Analysis”.  Journal of the Royal Statistical Society, Ser.  B. 53, 566.

 

6.     (1991) Gray, S.M., Power, A.G., Smith, D.M., Seaman, A.J., Altman, N.S.  Aphid Transmission of Barley Yellow Dwarf Virus:  Acquisition Access Periods and Virus Concentration Requirements.  Vector Relations, 81,  539-545.

 

7.     (1992) Altman, N.S.,  An Iterated Cochrane-Orcutt Procedure for Nonparametric Regression.  Journal of Statistical Computation and Simulation, 40, 93-108.

 

8.     (1992) Altman, N.S.,  An Introduction to Kernel and Nearest Neighbors Nonparametric Regression.  The American Statistician, 46, 175-185.

 

9.     (1993) Altman, N.S., Estimating Error Correlation in Nonparametric Regression Models.  Statistics and Probability Letters, 18, 213-218.

 

10.  (1993) Altman, N.S. and Paulson, C., Some Remarks about the Gasser-Sroka-Jennen-Steinmetz Variance Estimator.  Communications in Statistics, 22, 1045-1052.

 

11.   (1993) Léger, C. and Altman, N.S.,  Assessing Influence in Variable Selection  Problems.  Journal of the American Statistical Association, 88, 547-556.

 

12.  (1993) Gray, S.M., Smith, D. and Altman, N.S.,  Barley Yellow Dwarf Virus Isolate-Specific Resistance in Spring Oats Reduced Virus Accumulation and Aphid Transmission. Phytopathology, 83, 716-720.

 

13.  (1993) Todhunter, R.J., Altman, N.S., Kallfelz, F.A., Nersesian, D.P., Lust, G. Use of Scintimetry to Assess Effects of Exercise and Polysulfated Glycosaminoglycan on Equine Carpal Joints With Osteochondral Defects.  American Journal of Veterinary Research, 54, 997-1006.

 

14.  (1993) Langston, S.W., Altman, N.S., and Hotchkiss, J.H.   Within and between sample comparisons of Gompertz parameters for Salmonella enteritidis and aerobic plate counts in chicken stored air and modified atmosphere. International Journal of Food Biology, 18, 43-52.

 

15.  (1994) Kuesten, C.L., McLellan, M.R. and Altman, N.S.,  Computerized Panel Training: Effects of Using Graphic Feedback on Scale Usage.  Journal of Sensory Studies,  9, 413-444.

 

16.  (1994) Kuesten, C.L., McLellan, M.R. and Altman, N.S.,  Influence of Computerized Panel Training on Contextual Effects.  Journal of Sensory Studies, 9, 401-412.

 

17.  (1994) Ramsay, J.O., Altman, N.S. and Bock, R.D.  Variation in Height Acceleration in the Fels Growth Data.  Canadian Journal of Statistics, 22, 89-102.

 

18.  (1994) Todhunter, R.J., Wootton, J.W., Altman, N.S., Lust, G., and Minor, R.R. Cross-validation of cyanogen bromide-peptide ratios to measure the proportion of type II collagen in pepsin digests of equine articular cartilage, meniscus, and cartilage repair tissue. Analytical Biochemistry, 216, 195-204. PMID: 8135352

 

19.  (1995) Altman, N.S. and Casella, G.  Nonparametric Empirical Bayes Growth Curve Analysis.  Journal of the American Statistical Association, 90, 508-515

 

20.  (1995) Altman, N.S. and Léger, C.  A Note on Bandwidth Selection in Kernel Distribution Function Estimation.  Journal of Statistical Planning and Inference, 46, 195-214.

 

21.   (1997) Federer, Walter T., Newton, Elizabeth A. and Altman, Naomi S.,  Combining Standard Block  Analyses With Spatial Analyses Under a Random Effects Model.  In Modeling Longitudinal and Spatially Correlated Data: Methods, Applications, and Future Directions. Gregoire, Brillinger, Diggle, Russek-Cohen, Warren, Wolfinger eds. Springer-Verlag (Berlin; New York): 373--386.

 

22.   (1997) Hobert, J.P.,  Altman, N.S. and Schofield, C.L.  Spatial Analysis of  the Fish Species Richness of Adirondack Lakes:  Applications of Geostatistics and Nonparametric Regression.  Journal of the American Statistical Association, 92, 846-854.

 

23.   (1997) Altman, N.S. and Léger, C.  On the Optimality of Prediction Based Selection Criteria and the Convergence Rates of Estimators.  Journal Royal Statistical Society, Series B, 59, 205-216.

 

24.  (1998) Altman, N.S. and MacGibbon, B.  Consistent Bandwidth Selection for Kernel Binary Regression, Journal of Statistical Planning and Inference, 70, 121-137.

 

25.  (1999) Johnson, K.W. and Altman, N.S.,  Canonical Correspondence Analysis as an Approximation to Gaussian Ordination. Environmetrics, 10, 39-52.

 

26.  (2000) Altman, N.S.  Krige, Smooth, Both or Neither? (with discussion) Australian and New Zealand Journal of Statistics, 42, 441-461

 

27.  (2001) Ahrens, C. Altman, N.S., Casella, G.C., Malaika, E., Hwang, J.T., Staudenmayer, J., Stefanescu, C.  Leukemia Clusters and TCE Waste Sites in Upstate New York:  How Adding Covariates Changes the Story.  Environmetrics, 12, 659-672.

 

28.  (2001) Altman, N.S., Bernstein, E, Cottrell, K, Dhondt, A.A., Hochachka, W., Slothower, R. Measuring Bird Migration Using Spatial and Temporal Counts.  Chance, 14, 7-14.

 

29.   (2001) Altman, N.S. Discussion of " Estimation of Fetal Growth and Gestation in Bowhead Whales" by C. Shane Reese, James A. Calvin, John. C. George, and Raymond J. Tarpley.  (JASA Invited Discussion Paper) JASA, 96, 923-925

 

30.  (2001) Altman, N.S. and Sullivan, P. Discussion of "What shall we teach in environmental statistics?" by Walter Piegorsch and Don Edwards. (Environmental and Ecological Statistics Invited Discussion), 9, 139-140.

 

31.  (2001) Flecker, A.S., Taylor, B.W., Bernhardt, E.S., Hood, J., Cornwell, W.K., Cassatt, S.R., Vanni, M.J., Altman, N.S.  Interactions Between Herbivorous Fishes and Limiting Nutrients in a Tropical Stream Ecosystem. Ecology, 83, 1831-1844.

 

32.   (2002) Bargo, F., Muller, L.  and Altman, N.S.  Milk Response to Bovine Somatotropin of High-Producing Dairy Cows with Three Different Feeding Systems Combining Pasture and Total Mixed Rations, The Professional Animal Scientist, 19, 10-18.

 

33.   (2004) Altman N.S. and Villarreal, J. Self-Modelling Regression with Random Effects using Penalized Splines, Canadian Journal of Statistics, 32, 251-268.

 

34.  (2004) Wang G., Kong H., Sun Y., Zhang X., Zhang W., Altman N.S., dePamphilis, C.W., Ma, H. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins, Plant Physiology, 135, 1084-1099. PMID: 15208425.

 

35.  (2005) Altman, N.S. Replication, Variation and Normalization in Microarray Experiments Applied Bioinformatics, 4, 33-44. PMID: 1600001.

 

36.   (2005) Zhang, X., Zhang, D., Feng, B., Altman, N.S., Ma, H. Genome-wide Expression Profiling and Identification of Gene Activities during Early Flower Development in Arabidopsis,  Plant Molecular Biology, 58, 401-419. PMID: 16021403.

 

37.  (2005) Walters, E., Altman, N.S., Elnitski, L. Clustering of Gene Locations, J. Computational Statistics and Data Analysis, 50, 2920-2932.

 

38.  (2006) Duarte, J., Cui, L., Wall, K., Zhang, Q., Zhang, X., Leebens-Mack, J., Ma, H., Altman, N.S., and dePamphilis, C.  Expression pattern shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis. Molecular Biology and Evolution 2006, 23(2):469-478.  PMID: 16280546. oxfordjournals

 

39.  (2006) Naomi Altman, Jim Leebens-Mack, Laura Zahn, André Chanderbali,
Donglan Tian, Lillian Werner, Hong Ma, and Claude dePamphilis.  Behind the Scenes: Planning a Multispecies Microarray Experiment, Chance, Vol 19, No. 3, p. 27-38.

 

40.  (2006) Clark, C.W.; Altman, N.S.; Acoustic detections of blue whale (Balaenoptera musculus) and fin whale (B. physalus) sounds during a SURTASS LFA exercise, IEEE Journal of Oceanic Engineering,Vol 31, No. 1, p. 120 – 128.

 

41.  (2006) Altman, N.S., Hua, J. Extending the loop design for 2-channel microarray experiments Genetical Research, Vol 88, No. 3, p. 153-163. PMID: 17371610.

 

42.  (2007) William R. Evans, Yukio Akashi, Naomi Altman, and Albert Manville.  Response of night migrating birds in cloud to colored and flashing light North American Bird, Vol 60, No 4, p. 476-488.

 

43.  (2007) Vineet Sangar, Daniel J. Blankenberg, Naomi Altman and Arthur M. Lesk. Quantitative Sequence Function Relationships in Proteins Based on the Gene Ontology. BMC Bioinformatics, Vol 8, p.  294.  PMID: 17686158.

 

44.  (2007) P. Kerr Wall, Jim Leebens-Mack, Kai Müller, Dawn Field, Naomi S. Altman, Claude W. dePamphilis. PlantTribes:  A gene and gene family resource for comparative genomics in plants.  Nucleic Acids Research, 36, 970-976. PMID: 18073194.

 

45.  (2007) Soltis D.E., Ma H., Frohlich M.W., Soltis P.S., Albert V.A., Oppenheimer D.G., Altman N.S., dePamphilis C.W. and Leebens-Mack J.H.. (2007) The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science 12(8):358-367. PMID: 17658290.

 

46.  (2008) Madsen, L., Ruppert, D. and Altman, N.S.,  Regression with Spatially Misaligned Data Environmetrics, 19: 453–467 www.environmetrics.org.

 

47.  (2008) Soltis, D.E., Albert V.A., Leebens-Mack J., Palmer J., Wing R., dePamphilis C.W., Ma H., Carlson J.E.,  Altman N.S., Kim S., Wall P. K., Zuccolo A., Soltis P.   The Amborella genome: an evolutionary reference for plant biology. BMC

 

48.  (2008) Han, B., Altman, N.S., Mong, J.A., Klein, L.C., Pfaff, D.W. and Vandenbergh, D. Comparing Quantitative Trait Loci and Gene Expression Data Associated with a Complex Trait, Advances in Bioinformatics  Article ID 719818, 6 pages

 

49.  (2009) André S. Chanderbali, Victor A. Albert, Jim Leebens-Mack, Naomi S. Altman, Douglas E. Soltis, and Pamela S. Soltis .Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae).  PNAS,  106, 8929-8934; doi:10.1073/pnas.0811476106

 

50.  (2009) Wall, P.K., Leebens-Mack J., Chanderbali A., Barakat, A., Wolcott, E., Liang, H., Landherr, L., Tomsho, L.P., Hu, Y., Carlson J.E., Ma H., Schuster S.C., Soltis D.E., Soltis P.S., Altman N.S., and dePamphilis C.W.. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics, 10:347.

(the most viewed article in BMC Genomics 2009-2010)

 

51.  (2009) Philip J. Jensen,×Izabela Makalowska, Naomi Altman, Gennaro Fazio, Craig Praul, Siela N. Maximova, Robert M. Crassweller, James W. Travis, Timothy W. McNellis Rootstock-regulated gene expression in apple tree scions. Tree Genetics and Genomes, 6, 1614-2942, doi: 10.1007/s11295-009-0228-7.

 

52.  (2009) Han, X., Wu X., Chung W.-Y., Li T., Nekrutenko A., Altman N.S., Chen G., and Ma H., Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. Proceedings of the National Academy of Sciences, vol. 106, no. 31, pp. 12741-6.

 

53.  (2010) Li, B., Kim, M.K., Altman, N.S. On dimension folding of matrix or array valued statistical objects. Annals of Statistics,. 38, 1094-1121; doi:10.1214/09-AOS737

 

54.  (2010) Altman, N.S., Wang, Q., Karwa, V. and Slavkovic, A. Resolving Isoform Expression using Digital Gene Expression Data.  Journal of the Indian Society of Agricultural Statistics, special issue on Statistical Genomics, 4, 19-31.

 

55.  (2010) André S. Chanderbali, Mi-Jeong Yoo, Laura M. Zahn, Samuel Brockington, P.Kerr Wall, Victor A. Albert, Jim Leebens-Mack, Naomi S. Altman, Matthew A. Gitzendanner, Hong Ma, Claude dePamphilis, Douglas E. Soltis, and Pamela S. Soltis.  Conservation and Canalization of Gene Expression During Angiosperm Diversification Accompany the Origin and Evolution of the Flower,  PNAS, 107,   22570-22575. Doi: 10.1073/pnas.1013395108

 

56.  (2010) Zahn, LM, Ma,X, Altman, NS, Zhang, Q, Wall, PK, Tian, D., Gibas, CJ, Gharaibeh, R, Leebens-Mack, JH, dePamphilis, CW and Ma, H.  Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biology, 11:R101. http://genomebiology.com/2010/11/10/R101

 

57.  (2010) Mi-Jeong Yoo, André S. Chanderbali, Naomi S. Altman, Pamela S. Soltis, and Douglas E. Soltis.  Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae) feature article: The Plant Journal, Volume 64, Issue 4, 687–698.

 

58.  (2011) Walter C. Kolczynski, Jr., David R. Stauffer, Sue Ellen Haupt, Naomi S. Altman, Aijun Deng Investigation of Linear Variance Calibration For Spread-Error Relationship Using a Stochastic Model Monthly Weather Review Vol. 139, No. 12 3954-3963.

 

59.  (2012) Philip J Jensen, Noemi Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig Praul, Siela N Maximova, Henry K Ngugi, Robert M Crassweller, James W Travis, Timothy W McNellis. Rootstock-regulated gene expression patterns associated with fire blight resistance in apple. BMC Genomics, 13:9 doi:10.1186/1471-2164-13-9

 

60.  (2012) Polato, Nicholas R., Altman, Naomi S. and Baums, Iliana B. Variation in the transcriptional response of threatened coral larvae to elevated temperatures Molecular Ecology DOI: 10.1111/mec.12163

 

61.  (2013) Luo, W. and Altman, N. S.  A Characterization of Conjugate Priors in Linear Exponential Families with application to Dimension Reduction.  Statistics and Probability Letters, 83, 650-654.

 

62.  (2013) I. B. Baums, M. K. Devlin-Durante, N. R. Polato, D. Xu, S. Giri, N. S. Altman, D. Ruiz, J. E. Parkinson, J. N. Boulay. Genotypic variation influences reproductive success and thermal stress tolerance in the reef building coral, Acropora palmate. Coral Reefs 

DOI 10.1007/s00338-013-1012-6

 

63.  (2013) Honaas, L. A., Wafula, E. K., Yang, Z., Der, J. P., Wickett, N. J., Altman, N. S., Taylor, C. G., Yoder, I. Y., Timko, M. P., Westwood, J. H. & Depamphilis, C. W. (2013). Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC plant biology, 13(1), 9.

 

64.   (2013) Altman, N. S., G. Balco, C. Crainiceanu, W. R. Gehrels, J. Qiu, J. Staudenmayer, and P. Sullivan. "Statistical modeling of changes in relative sea level in Maine during the Holocene Era." Environmetrics.

 

65.  (2013) Smyth, G.K. and Altman, N.S.  Separate-Channel Analysis of Two-Channel Microarrays: recovering inter-spot information.  BMC Bioinformatics 14:165  doi:10.1186/1471-2105-14-165

 

66.  (2013) Amborella Genome Project "The Amborella Genome and the Evolution of Flowering Plants”  Science.    20: 1241089 [DOI:10.1126/science.1241089]

 

67.  (2014) Philip J Jensen, Gennaro Fazio, Naomi Altman, Craig Praul and Timothy McNellis. Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.  BMC Genomics 15:261 http://www.biomedcentral.com/1471-2164/15/261

 

68.  (2014) Stefanie R. Austin, Isaac Dialsingh, Naomi Altman. Multiple Hypothesis Testing: A review.  J. Indian Soc. Of Agricultural Stat. 68: 303-314.

 

69.  (2014) Zhenzhen Yang,Eric K. Wafula, Loren A. Honaas, Huiting Zhang, Malay Das, Monica Fernandez-Aparicio, Kan Huang, Pradeepa C.G. Bandaranayake, Biao Wu, Joshua P. Der, Christopher R. Clarke, Paula E. Ralph, Lena Landherr, Naomi S. Altman, Michael P. Timko, John I. Yoder, James H. Westwood, and Claude W. dePamphilis.  Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. Molecular Biology and Evolution.  DOI: 10.1093/molbev/msu343

 

70.  (2015) Dialsingh, I., Austin, S. and Altman, N.S. Estimating the Percentage of True Null Hypotheses when the Statistics are Discrete. 31(14) 2302-2309 Bioinformatics doi:10.1093/bioinformatics/btv104

71.  (2015) Parkinson, J. E., Banaszak, A. T., Altman, N. S., LaJeunesse, T. C., & Baums, I. B. Intraspecific diversity among partners drives functional variation in coral symbioses.Scientific reports,5.

 

72.  (2016) Honaas, Wafula, E.K., Wickett, N.J, Der, J.P.,  Zhang, Y., Egder, P.P., Altman, N.S., Pires, J.C., Leebens-Mack, J.H., dePamphilis, C.W. Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome  PLoS ONE 11(1): e0146062. doi: 10.1371/journal.pone.0146062

 

73.   (2016) Sharma, A., Da Motta, V. E., Choi, J. G., & Altman, N. S. Economic production in hospitality and tourism industry: how do we compare to other services?. International Journal of Contemporary Hospitality Management, 28(5).

 

74.  (2016) Altman, N. S. Comment on The ASA's Statement on p-Values: Context, Process, and Purpose.(R. Wasserstein and N. Lazar) The American Statistician, 70(2)   doi:/10.1080/00031305.2016.1154108

75.  (2016) Zhenzhen Yang*, Yeting Zhang*, Eric Wafula, Loren A. Honaas, Paula E. Ralph, Sam Jones, Huiting Zhang, Naomi S. Altman, Michael P. Timko, John I. Yoder, James H. Westwood, Claude W. dePamphilis. Horizontal gene transfer is more frequent with increased heterotrophy and may contribute to parasite adaptation. Proc. Natl. Acad. Sci. U.S.A., 113 (45). doi: 10.1073/pnas.1608765113

76.  (2016) Mario Padilla, M., Amsalem, E., Altman, N., Hefetz, A., & Grozinger, C. M. . Chemical communication is not sufficient to explain reproductive inhibition in the bumblebee Bombus impatiens. Royal Society open science3(10), 160576.

77.   (2017) Qingyu Wang, Cooduvalli S. Shashikant, Naomi S. Altman, Santhosh Girirajan.. Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity. Scientific Reports, 7(1), 885.

78.  (2017) Etya Ansalem, Padilla, M, Schreiber, P.M., Altman, N.S. , Hefetz, A., Grozinger, C.M. Do bumble bee (Bombus impatiens) queens signal their reproductive and mating status to their workers?  J. Chemical Ecology) 43: 563. https://doi.org/10.1007/s10886-017-0858-4

79.  (2017) Gary A Clawson, Ph.D., M.D.; Gail L. Matters; Ping Xin; Christopher McGovern; Eric Wafula Wafula; Claude dePamphilis; Morgan Meckley; Joyce Wong; Luke Stewart; Christopher D'Jamoos; Naomi Altman; Yuka Imamura Kawasawa; Zhen Du; Loren Honaas; Thomas Abraham; "Stealth Dissemination" of Macrophage-Tumor Cell Fusions Cultured from Blood of Patients with Pancreatic Ductal Adenocarcinoma. PLOS ONE 12(9) e0184451. https://doi.org/10.1371/journal.pone.0184451

80.  (2019) Zhenzhen Yang, Eric K. Wafula, Gunjune Kim, Saima Shahid, Joel R. McNeal, Paula E. Ralph, Prakash R. Timilsena, Wen-bin Yu, Elizabeth A. Kelly, Huiting Zhang,Thomas Nate Person, Naomi S. Altman, Michael J. Axtell, James H. Westwood, and Claude W. dePamphilis. Convergent horizontal gene transfer and crosstalk of mobile nucleic acids in parasitic plants. Nature Plants,

81.  (2019) Loren A. Honaas, Sam Jones, Nina Farell, William Kamerow, Huiting Zhang, Kathryn Vescio, Naomi S. Altman, John I. Yoder and Claude W. dePamphilis. (2019) Risk versus reward: host dependent parasite mortality rates and phenotypes in the facultative generalist Triphysaria versicolor. BMC Plant Biology.

 

Invited Columns (47)

 

1. Krzywinski, M., & Altman, N. (2013). Points of significance: Importance of being uncertain. Nature methods, 10(9), 809-810. doi:10.1038/nmeth.2613 

 

2. Krzywinski, M., & Altman, N. (2013). Points of Significance: Error bars. Nature methods, 10(10), 921-922.

 

3. Krzywinski, M., & Altman, N. (2013). Points of significance: Significance, P values and t-tests. Nature methods, 10(11), 1041-104

 

4. Krzywinski, M., & Altman, N. (2013). Points of significance: Power and sample size. Nature Methods, 10(12), 1139-1140.

 

5. Krzywinski, M., & Altman, N. (2013). Points of significance: Visualizing samples with box plots. Nature Methods, 11(2), 119–120, doi:10.1038/nmeth.2813

 

6. Krzywinski, M., & Altman, N. (2014). Points of significance: Comparing Samples - Part 1. Nature Methods, 11(3),  215–216, doi:10.1038/nmeth.2858

 

7. Krzywinski, M., & Altman, N. (2014). Points of significance: Comparing Samples - Part II. Nature Methods, 11(4),  355–356, doi:10.1038/nmeth.2900

 

8. Krzywinski, M., & Altman, N. (2014). Points of significance: Nonparametric Tests. Nature Methods, 11(5), 467-468, doi:10.1038/nmeth.2937

 

9. Krzywinski, M., & Altman, N. (2014). Points of significance: Designing comparative experiments. Nature Methods, 11(6),  597-598, doi:10.1038/nmeth.2974

 

10. Krzywinski, M., & Altman, N. (2014). Points of significance: Analysis of Variance and Blocking. Nature Methods, 11(7), 699-700  doi:10.1038/nmeth.3005

 

11. Blainey, P. & Krzywinski, M., & Altman, N. (2014). Points of significance: Replication. Nature Methods, 11(8), 879-880  doi:10.1038/nmeth.3091

 

12. Krzywinski, M., Altman, N. & Blainey, P. (2014).  Points of Significance: Nested designs. Nature Methods, 11(10), 977-978  doi:10.1038/nmeth.3137

 

13. Krzywinski, M., &  Altman, N.  (2014) Points of Significance: Two-factor designs. Nature Methods, 11(12), 1187-1188  doi:10.1038/nmeth.3180

 

14. Krzywinski, M., &  Altman, N.  (2015) Points of Significance: Sources of variation. Nature Methods, 12(1), 5-6  doi:10.1038/nmeth.3224

 

15. Krzywinski, M., &  Altman, N.  (2015) Points of Significance: Split plot design. Nature Methods, 12(3), 165-166  doi:10.1038/nmeth.3293

 

16.Puga, J. L., Krzywinski, M., & Altman, N. (2015). Points of significance: Bayes’ Theorem. Nature Methods, 12(4), 277-278 doi:10.1038/nmeth.3335

 

17. Puga, J. L., Krzywinski, M., & Altman, N. (2015). Points of significance: Bayesian Statistics. Nature Methods, 12(5), 377-378 doi:10.1038/nmeth.3368

 

18. Kulesa, A.,Krzywinski, M., Blainey, P. & Altman, N. (2015). Points of significance: Sampling distributions and the bootstrap. Nature Methods, 12(6), doi:10.1038/nmeth.33

 

19. Puga, J. L., Krzywinski, M., & Altman, N. (2015). Points of significance: Bayesian networks. Nature Methods, 12(8), 799–800 doi:10.1038/nmeth.3550

 

20. Altman, N. & Krzywinski, M. (2015). Points of Significance: Association, correlation and causation. Nature Methods, 12(10), 899-900. doi:10.1038/nmeth.3587

 

21. Altman, N. & Krzywinski, M. (2015). Points of Significance: Simple Linear Regression. Nature Methods, 12(11), 999-1000. doi:10.1038/nmeth.3627

 

22. Krzywinski, M., & Altman, N. (2015). Points of Significance: Multiple linear regression.Nature Methods,12(12), 1103-1104. doi:10.1038/nmeth.3665

 

23. Altman, N. & Krzywinski, M. (2016). Points of Significance: Analyzing outliers: influential or nuisance. Nature Methods, 13(4), 281-282. doi:10.1038/nmeth.3812

 

24. Altman, N. & Krzywinski, M. (2016). Points of Significance: Regression diagnostics. Nature Methods, 13(5), 385-386. doi:10.1038/nmeth.3854

 

25. Lever, J., Krzywinski, M. & ., Altman, N. (2016). Points of Significance: Logistic regression. Nature Methods, 13(7), 541-542. doi:10.1038/nmeth.3904

 

26. Lever, J., Krzywinski, M. & ., Altman, N. (2016). Points of Significance: Classification Evaluation. Nature Methods, 13(8), 603-604. doi:10.1038/nmeth.3945

 

27. Lever, J., Krzywinski, M. & ., Altman, N. (2016). Points of Significance: Model Selection and Overfitting. Nature Methods, 13(9), 703-704. doi:10.1038/nmeth.3968

 

28. Lever, J., Krzywinski, M., & Altman, N. (2016). Points of significance: Regularization. Nature Methods13(10), 803-804. doi:10.1038/nmeth.4014

 

29. Altman, N. and Krzywinski, M. (2017) Points of significance: P values and the search for significance." Nature Methods 14(1), 3-4. doi:10.1038/nmeth.4100

 

30. Altman, N., & Krzywinski, M. (2017). Points of Significance: Interpreting P values. Nature Methods14(3), 213-214. doi:10.1038/nmeth.4210

 

31. Altman, N., & Krzywinski, M. (2017). Points of Significance: Tabular data. Nature Methods14(4), 329-330. doi:10.1038/nmeth.4239

 

32. Altman, N., & Krzywinski, M. (2017). Points of Significance: Clustering. Nature Methods14(6), 545-546. doi:10.1038/nmeth.4299

 

33. Lever, J., Krzywinski, M., & Altman, N. (2017). Points of Significance: Principal component analysis. Nature Methods14(7), 641-642. doi:10.1038/nmeth.4346

 

34. Krzywinski, M. & Altman, N. (2017) Points of Significance: Classification and regression trees. Nature Methods14(8), pp.757-758. doi:10.1038/nmeth.4370

 

35. Altman, N. & Krzywinski, M. (2017) Points of Significance: Ensemble Methods - Bagging and Random Forest.  Nature Methods, 14 (10) pp. 933-934. doi:10.1038/nmeth.4438

 

36. Bzdok, D., Krzywinski, M. & Altman, N. (2017) Points of Significance: Machine Learning: a primer.  Nature Methods, 14 (11) pp.1119-1120. doi:10.1038/nmeth.4526

 

37. Bzdok, D., Krzywinski, M. & Altman, N. (2018) Points of Significance: Machine Learning: supervised methods.  Nature Methods, 15 (1) pp.5-6. doi:10.1038/nmeth.4551

 

38. Bzdok, D., Krzywinski, M. & Altman, N. (2018) Points of Significance: Statistics vs Machine Learning.  Nature Methods, 15 (4) pp.233-234. doi:10.1038/nmeth.4659

 

39. Altman, N. & Krzywinski, M. (2018) Points of Significance: The curse(s) of dimensionality. Nature Methods, 15 (6) pp. 399-400. Doi: 10.1038/s41592-018-0019-x

 

40. Smucker, B., Krzywinski, M. & and Altman, N. (2019) Points of Significance: Optimal experimental design. 15(8) pp. 559-560. Doi: 10.1038/s41592-018-0083-2

 

41. Altman, N. & Krzywinski, M. (2018) Points of Significance:  Predicting with confidence and tolerance 15(11), pp. 841–845. Doi: 10.1038/s241592-018-0196-7

 

42. Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of Significance: Two-level factorial experiments. 16(2) pp. 209-212 Doi: 10.1038/ s41592-019-0335-9.

 

43. Greco, L., Luta, G. Krzywinski, M. & Altman, N. (2019) Points of Significance: Analyzing outliers: robust methods to the rescue 16(3) pp. 275–276 doi:10.1038/s41592-019-0369-z

 

44. Das, K., Krzywinski, M. & Altman, N. (2019) Points of Significance: Quantile regression. 16(6), pp. 451-452.

 

45. Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of Significance: Markov Models -- Markov Chains. 16(8) pp. 663–664  doi:10.1038/s41592-019-0476-x

 

46. Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of Significance: Markov Models -- Hidden Markov Models. 16(9) pp. 795–796 (2019) doi:10.1038/s41592-019-0532-6

 

47. Grewal, J., Krzywinski, M. & Altman, N. (2020) Points of Significance: Markov Models -- Training and Evaluation of Hidden Markov Models. 17 (2) pp.  

 

 

Book Chapters

 

1. (2009) Altman, N.S. Batches and Blocks, Sample Pools and Subsamples in the Design and Analysis of Gene Expression Studies. in Batch Effects and Noise in Microarray Experiments: Sources and Solutions. A. Scherer (editor).  John Wiley & Sons, Chichester.

 

2. (2016) Honaas L.A., Altman N.S., Krzywinski M. (2016) Study Design for Sequencing Studies. In: Mathé E., Davis S. (eds) Statistical Genomics. Methods in Molecular Biology, vol 1418. Humana Press, New York, NY

 

Published Proceedings

 

1.   (1988) Altman, N.S.  Smoothing Data with Correlated Errors.  Computer Science and Statistics: Proceedings of the 20th Symposium on the Interface, 246-253.

 

2.  (1994) Altman, N.S. and Léger, C.  Cross-validation, the Bootstrap, and Related Methods for Tuning Parameter Selection. Proceedings of the Statistical Computing Section of the American Statistical Association, 41-50.

 

3.   (1994) Léger, C.  and Altman, N.S.  On the Optimality of Prediction Based Selection Criteria and  the Convergence Rates of Estimators   Proceedings of the Statistical Computing Section of the American Statistical Association, 112-117.

 

4.  (1996) Altman, N.S.,  Semi-Parametric Methods for Longitudinal Data Analysis. Proceedings of the Biometrics  Section of the American Statistical Association, 49-57.

 

5.  (1997) Altman, N.S., Krige, Smooth, Both or Neither. Proceedings of the Biometrics Section of the American Statistical Association,  60-65.

 

6.  (1997) Aragaki, A. and Altman, N.S.  Local Polynomial Regression for Binary Response.  Computer Science and Statistics: Proceedings of the 29th Symposium on the Interface,  467-472.

 

7.  (2001) Villarreal, J. and Altman N.S. Inference for Self-Modeling Regression with Random Effects. Computer Science and Statistics: Proceedings of the 33rd Symposium on the Interface of Computing Science and Statistics.

 

8.  (2004) Altman, N.S. Extending the Loop Design for Microarray Experiments Computer Science and Statistics: Proceedings of the 33rd Symposium on the Interface of Computing Science and Statistics.

 

9.  (2004) Walters, E., Altman, N.S., Elnitski, L., Are Gene Locations Clustered on Chromosomes? (Proceedings of the Joint Statistical Meetings).

 

 

Technical Reports

 

1.     (1984) Altman, N.S.,  Expert Systems and Statistical Expertise, Part 1: Statistical Expert Systems.  Department of Statistics, Stanford, Technical Report LCS 17.

 

2.     (1987) Altman, N.S.,  Smoothing Data with Correlated Errors.  Ph.D. Thesis, and Department of Statistics, Stanford, Technical Report No. 280.

 

3.     (1990) Altman, N.S. et al, Report of the New Researchers' Committee of the IMS.  Biometrics Unit Technical Report BU-1066-M, Cornell University.

 

4.     (1990) Ward, R.H., Altman, N.S., and Prior, I.A.M., Patterns of Blood Pressure Response in Migrant and Nonmigrant Tokelauans I:  Defining response.  Biometrics Unit Technical Report BU-994-M, Cornell University.

 

5.     (1990) Altman, N.S., Ward, R.H., and Prior, I.A.M., Patterns of Blood Pressure Response in Migrant and Nonmigrant Tokelauans II: Physiological and Socio-Cultural Correlates of Blood Pressure Response.  Biometrics Unit Technical Report BU-995-M, Cornell University.

 

6.     (1990) Altman, N.S., Ward, R.H., and Prior, I.A.M., Patterns of Blood Pressure Response in Migrant and Nonmigrant Tokelauans III:  Response in Tokelauan Children. Biometrics Unit Technical Report BU-996-M, Cornell University.

 

7.     (1992) Altman, N.S. and Ramsay, J.O.  Reducing Bias in Nonparametric Regression Problems Involving Families of Curves.  Biometrics Unit Technical Report BU-1175-M, Cornell University.

 

8.     (1994) Altman, N.S. and Léger, C.  Cross-Validation, the Bootstrap and Related Techniques for Tuning Parameter Selection.  Biometrics Unit Technical Report BU-1216-M, Cornell University.

 

9.     (1997) Aragaki, A. and Altman, N.S.,  Local Polynomial Regression for Binary Response. Biometrics Unit Technical Report BU-1379-M, Cornell University

 

10.  (2009) Han, B., Arnold, S.F., Altman, N.S.   A Bayesian Approach to Large Scale Simultaneous Inference Based on False Discovery Rate.  Statistics Dept. Technical Report TR 09-01, Penn State.

 

 

Invited Conference Talks

 

1986    Expert Systems and Statistical Expertise, at the Statistical Society Society of Canada, Winnipeg, CAN  (Altman)

 

1988  Smoothing Data with Correlated Errors, at the 20th Symposium on the Interface: Computing

          Science and Statistics, Reston, VA. (Altman)

 

1990  Issues in Kernel Regression Estimation for Data with Correlated Errors,

          Mathematical Sciences Institute, Ithaca, NY (Altman)

 

1994  On the Use of Cross-Validation and Adjusted Residual Sum of Squares for Parameter

          Selection, at the Meeting of the Statistics Society of Canada, Banff, CAN. (Altman (presenter),

          Leger)

 

1996  Semi-parametric Methods for Longitudinal Data Analysis, at the Joint

          Statistical Meetings, Chicago, IL (Altman)

 

1997    Discussant for : “The Use of Nonparametric Regression in the Analysis

            of Biomedical Data” at the meetings of the International Biometrics Society, ENAR, Memphis, TN.  (Altman)

 

2000    Self-Modeling Regression for Longitudinal Data. Los Alamos National Laboratory, Los Alamos, NM. (Altman)

 

2001    Self-modeling Regression With Random Effects Using Penalized Regression Splines. National Institute of Standards and Technology, Gaithersberg, MD. (Altman (presenter), Villarreal)

 

2001  Discussant for “Estimation of Fetal Growth and Gestation in Bowhead Whales" by C. Shane   Reese, James A. Calvin, John. C. George, and Raymond J. Tartly at the Joint Statistical       Meetings Atlanta, GA (Altman)

 

2003    P-splines as a tool for Semiparametric Longitudinal Modeling at ENAR, Tampa, FL. (Altman (presenter), Villarreal)

 

2005    Self-Modeling Regression for Longitudinal Data with Time-Invariant Covariates, Statistical Society of Canada, Saskatoon, SK (Journal of the Canadian Statistical Society Award)(Altman (presenter), Villarreal)

 

2005    Global Classification of (Plant) Proteins across Multiple Species at ENAR, Austin, TX (Altman (presenter), Wall, Leebens-Mack, Albert, Field, Ma, dePamphilis)

 

2010  The Biology, Technology, and Statistical Modeling of High-throughput Genomics Data.  Meeting

          of the Canadian Statistical Society, Quebec City, PQ (Altman)

 

2010     Isoform detection from RNA-seq with restriction enzyme fragmentation, Data Analysis and

            Statistical Foundations III: A Conference in Honour of D.A.S. Fraser, Toronto, CAN. (Altman (presenter), Wang, Karwa, Slavkovic)

 

2012    Adaptive FDR Estimation for High Dimensional Discrete Data. 16th ADNAT Conference on Animal Genetics and Geomics, C.R. Rao Institute, Hyderabad, India. (Altman (presenter), Dialsingh)

 

2013    The Many Roles of Principal Component Analysis. Joint Statistical Meetings Montreal. (Altman (presenter), Raskutti, Wei Luo)

 

2013    Data Obesity: Inflated Estimation and Irreproducible Results with High Throughput Data. Indian Institute of Science, Bangalore, India. (Altman)

 

2013    Statistics: Taskmistress or Temptress? International Conference on the Role of Statistics in the Advancement of Science and Technology.  U. of Pune, Pune, India. (Altman)

 

2014    Differential Expression Analysis. Association of Biomolecular Resource Facilities, Albuquerque, NM. (Altman)

 

2014    Generalizing Principal Components Analysis. The 1st International Conference on Big Data & Applied Statistics Renmin University, Beijing, China (Altman)

 

2015    Generalizing Principal Components Analysis. Fields Institute -Program on Statistical Inference, Learning, and Models for Big Data, Toronto, Canada (Altman)

 

2015  (invited workshop presentations on various topics) Dagstuhl Seminar 15351 Computational Mass

          Spectrometry, Dagstuhl, Germany (Altman)

 

2016  Communication, Consultation and Collaboration in Cross-Discipinary Studies, Women in Statistics

          and Data Science Conference, Charlotte, NC (Altman)

 

2017  P-values: Variability, Reproducibility and Lessons from Multiple Testing, Joint Statistical Meetings

          Baltimore (Altman)

 

2017  Discussion of  "Enabling Reproducibility in Statistical Translations of Genomics Data for

          Biomedical Research" Joint Statistical Meetings, Baltimore (Altman)

 

2018  Discussion of " Building a computing age #StatisticsCurriculum for biomedical scientists" Joint      Statistical Meetings, Vancouver, CA (Altman)

 

2019  Understanding Principal Components Analysis. Conference on Applied Probability and Statistics,   Hanoi, Viet Nam (Altman)

 

2019  The Review and Revise Cycle: Ushering your paper through peer review, Joint Statistical    Meetings, Denver, CO (Altman)

 

 

Invited Talks at Other Venues since 2001

 

2001    Self-modeling Regression for Longitudinal Data  (Lawrence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State U.) (Altman)

 

2001    Self-modeling Regression for Longitudinal Data (Dept. of Biostatistics, U. Michigan) (Altman)

 

2002    A Semi-parametric Model for Longitudinal Data with Mixed Effects. (Dept. of Statistics, U. Pittsburgh) (Altman)

 

2002    Analysis of Controlled Experiments in Which the Response is a Curve (with inference) (Dept. of Biostatistics, U. Rochester) (Altman)

 

2004    Hybridization Design for 2-Channel Microarray Experiments (NSF-RCN Retreat on Microarrays, New Paltz, NY) (Altman)

 

2005    Interface Global Classification of (Plant) Proteins across Multiple Species (Dept. of Statistics, Temple U.) (Altman (presenter),  Wall, Leebens-Mack, Albert, Field, Ma, dePamphilis)

 

2010    Resolving Isoform Expression using Digital Gene Expression Data (Dept. of Statistics, Iowa State U.) (Altman (presenter), Wang, Karwa, Slavkovic)

 

2014    Generalizing Principal Components Analysis (Dept. of Statistics, Tsinghua University, Beijing, China) (Altman)

 

2015  Matrix Decompositions: The Polar Vortex, Human Population Structure and the Netflix (Dept. of

          Mathematics, Juniata College, Huntingdon, PA) (Altman)

 

2015    Reproducible Research and Multiple Testing (Dept. of Biology, Juniata College, Huntingdon, PA) (Altman)

 

2016    P-values: Preaching to the Choir or Prancing with the Devil?  (Memorial Sloan Kettering Cancer Centre, NYC), NY (Altman)

 

2018    Minding your P's and Q's.  (Dept. of Statistics, Miami U of Ohio, Miami OH) (Altman)

 

2018    Rethinking Principal Components Analysis (Dept. of Statistics, Oregon State U., Corvallis, OR)

 

2019    Experimental Design for High Throughput Biology Studies. (Shanghai Tech University, School of Life Science and Technology, Shanghai, China) (Altman)

 

 

Contributed Conference Talks and Posters (since January, 2001)

 

2001    Inference for Self-Modeling Regression With Random Effects, (Interface Symposium, Costa Mesa, CA) (Altman)

 

2002    Analysis of Controlled Experiments in Which the Response is a Curve, (Joint Statistical Meetings, New York City, NY) (Altman)

 

2002    Bayesian Penalized Splines in Semi-Parametric Modeling (interface Symposium, Montreal, CAN). (Altman)

 

2003    A Semi-parametric Model for Longitudinal Data with Mixed Effects.  (IMS Meeting on Functional Data Analysis, U. Florida) (Altman)

 

2003    Confidence Sets for Clusterings of Microarray Data, (NSF-RCN Retreat on Microarrays, New Paltz, NY) (Altman)

 

2003    Design and Analysis of cDNA Microarray Studies When Most Genes Express Differentially (Joint Statistical Meetings, San Francisco, CA) (Altman)

 

2004    Extending the Loop Design for Microarray Experiments (Interface Symposium, Baltimore, MD) (Altman)

 

2004    Strong evidence for extensive regulatory Subfunctionalization driving maintenance of duplicated genes in regulatory gene families of Arabidopsis thaliana.(Genomes and Evolution 2004, University Park, PA) (Ricker (presenter), Cui, Wall, Zhang, Zhang, Leebens-Mack, Ma, Altman, dePamphilis)

 

2005    Global Classification of (Plant) Proteins across Multiple Species (Interface Symposium, St. Louis, Mo) (Altman (presenter), Wall, Leebens-Mack, Albert, Field, Ma, dePamphilis)

 

2005    Maintenance Of Duplicated Regulatory Genes In Arabidopsis (Plant and Animal Genome Conference, San Diego, Ca).  (Ricker (presenter), Zhang, Wall, Cui,  Zhang, Leebens-Mack, Altman, Ma, dePamphilis)

 

2005    PlantTribes: A Global Classification For Arabidopsis And Rice Proteins (Plant and Animal Genome Conference, San Diego, Ca.)  (Wall (presenter), Altman, Leebens-Mack, Ma, Albert, Field, and DePamphilis.)

 

2006    Some Technical Issues in Microarray Experiments (The Australian Statistical Conference/ New Zealand Statistical Association Conference, Auckland, NZ. ( Werner (presenter), Altman)

 

2006    The Floral Genome Project (Plant and Animal Genome Conference, San Diego, Ca.) (dePamphilis (presenter), Ma, Soltis, Soltis, Leebens-Mack, Oppenheimer, Carlson, Farmerie, Frohlich, Zahn, Kim, Buzgo, Altman, Zheng, Chanderbali, Wall, Cui, Solow, Mueller, Albert, Doyle, Barakat, Landherr)

 

2006    Populus Genome Aids Identification Of Gene Families Across The Angiosperms (Plant and Animal Genome Conference, San Diego, Ca.) (Wall (presenter), Leebens-Mack, Carlson, Albert, Field, Altman, Ma, dePamphilis)

 

2006    Apple Tree Functional Genomics: Getting To The Rootstock Of It (Plant and Animal Genome Conference, San Diego, Ca.)(Jensen (presenter), Altman, Crassweller, Makalowska, Maximova, Praul, Travis, McNellis)

 

2007    The ancestral angiosperm: steps toward a genetic and genomic understanding of the origin of flowering plants. (Botany & Plant Biology 2007 Joint Congress, Chicago) (DePamphilis (presenter), Altman, Carlson, Clifton, J.L. Goicoechea, Kudrna, Landherr, Leebens-Mack, Ma, Soltis, Soltis, Wall and Wing.)

 

2007    Development Of Gene Expression Phenotypic Markers For Apple (Plant and Animal Genome Conference, San Diego, Ca.  (McNellis (presenter), Jensen, Crassweller, Maximova, Travis, Altman, Makalowska, Praul, Fazio)

 

2007    Microarray Expression Profiling Of Persea americana Flowers: In Search Of Organ-Specific Regulatory Networks (Plant and Animal Genome Conference, San Diego, Ca.  (Chanderbali (presenter). Altman, Soltis, Soltis).

 

2008    Rootstock-Regulated Gene Expression Profiling In Apple Trees Reveals Genes Whose Expression Levels Are Associated With Growth Vigor (Plant and Animal Genome Conference, San Diego, Ca.) (Jensen (presenter), Makalowska, Altman, Praul, Maximova, Crassweller, Travis, Fazio, McNellis).

 

2008    The Ancestral Angiosperm Genome Project (AAGP): Toward A Genetic And Genomic Understanding Of The Origin Of Flowering Plants (Plant and Animal Genome Conference, San Diego, Ca.) (dePamphilis (presenter), Altman, Bliss, Carlson, Chanderbali, Clifton, Collura, Duarte, Goicoechea, Hu, Kudrna, Landherr, Liang, Leebens-Mack, Ma, Ralph, Schlarblum, Soltis, Soltis, Wall, Yu, Zuccolo, Wing)

 

2008    Gene Expression Patterns In Floral And Vegetative Parts Of Nuphar advena  (Plant and Animal Genome Conference, San Diego, Ca.) (Yoo (presenter), Chanderbali, Altman, Soltis, Soltis)

 

2009    Using Ambiguous Tags in Digital Tag Analysis, (Joint Statistical Meetings, Washington, DC) (Altman)

 

2009    The Ancestral Angiosperm genetic toolkit. (Botany and Mycology 2009, Snowbird, UT) (DePamphilis (presenter) Ayyampalayam, Bliss, Brockington, Chanderbali, Duarte, Hu, Jiao, Liang, Landherr, Ralph, Altman, Carlson, Clifton, Ma, Leebens-Mack, Schlarbaum, Soltis, Soltis, Stevenson) .

 

2010    Isoform detection from RNA-seq with restriction enzyme fragmentation, (Statistical Society of Canada, Quebec City, CAN) (Altman (presenter), Wang, Karwa, Slavkovic)

 

2010    Resolving Isoform Expression using High-Throughput Sequence Data, (Joint Statistical Meetings, Vancouver, CAN) (Altman (presenter), Wang, Karwa, Slavkovic)

 

2011    FDR Control for Discrete Test Statistics (Joint Statistical Meetings, Miami Beach, FL) (Dialsingh (presenter), Altman)

 

2012    Estimating pi0 for High Dimensional Discrete Data, (Joint Statistical Meetings, San Diego, CA) (Altman (presenter), Dialsingh)

 

2014    Extending PCA to Non-elliptical Data, (Statistical Society of Canada, Toronto, CA) (Altman)

 

2014    Reproducible Research and Multiple Testing, (Joint Statistical Meetings, Boston, MA) (Altman)

 

 

Talks at Penn State and State College (Since January 2002)

 

2002    Analysis of Controlled Experiments in Which the Response is a Curve (and why an Animal Scientist Should Care) (Dept. of Animal Science)

 

2003    The MCL algorithm for clustering protein families. (Genomics Journal Club)

 

2003    How should we normalize Affymetrix microarray data?  (Genomics Journal Club)

 

2004 Confidence Sets for Clusterings (Dept. of Statistics, Alumni Workshop)

 

2004    Some Contributions of Statistics to the Genomics Revolution (PSU Statistics Club)

 

2006    Using Microarray Data with Comparative Sequence Analysis to Infer Evolutionary Relationships  (Health Evaluation Sciences, Hershey)

 

2006 Nonparametric regression in longitudinal studies (Social Science Statistics Partnership)

 

2008    Statistical Research (PSU Statistics Club)

 

2009    Statistics and Science (State College Area High School, AP Statistics Class)

 

2010  The Biology, Technology and Statistical Modeling of High-throughput Genomics Data

            (Dept. of Statistics and Huck Institute)

 

2010    Resolving Isoform Expression using RNA-seq Data (poster, Genetics Symposium)

 

2010    Resolving Isoform Expression using RNA-seq Data (talk, Bioinformatics and Genomics Retreat)

 

2014    Generalizing Principal Components Analysis (talk, Dept. of Statistics SMAC)

 

2015    Interpreting and Extending Principal Components Analysis (talk, Dept. of Meteorology)

 

2018    Principal Components Analysis: A general purpose tool for high dimensional data (talk, Big Data Social Science)

 

2018    The Biology and Technology of "Omics" Biological Data (talk, Statistics)

 

2018    Principal Components Analysis: Dimension reduction and pattern detection (talk, Data Science)

 

 

Conferences Organized

 

1996  Conference to honor Shayle R. Searle upon his retirement.

 

1997  Conference for the Inauguration of the New Department of Statistical Science at Cornell

 

 

Short Courses

 

1989  Nonparametric Regression - A Short Course.  Dept. of Mathematics, Statistics and Computer

          Science, Dalhousie University, Halifax, Canada.(sole lecturer)

 

2005  U. of Alabama at Birmingham First Plant Microarray Short Course, at U. Wisconsin, Madison,          WI  (2 sections – data analysis and design of microarray experiments)

 

2006    U. of Alabama at Birmingham Second Plant Microarray Short Course, at Boston MA..  (data analysis for microarray studies)

 

2010  Integrated Data Analysis 2010, Cold Spring Harbor Lab, NY (data analysis and experimental

design for gene expression studies)

 

2011  Statistical Analysis of Genomics Data, Cold Spring Harbor Lab, NY (data analysis and

experimental design for gene expression studies)

 

2012  Statistical Analysis of Genomics Data, Cold Spring Harbor Lab, NY (data analysis and

experimental design for gene expression studies)

 

2013  Statistical Analysis of Genomics Data, Cold Spring Harbor Lab, NY (data analysis and

experimental design for gene expression studies)

 

2013  Statistical Analysis of Gene Expression Data, U. of the West Indies, Port of Spain, Tobago.

 

2016  Bootcamp in data reproducibility and scientific transparency Penn State U. (data analysis)

 

2017  May Institute: Computation and statistics for mass spectrometry and proteomics Northeastern U.,

            Boston  (Multiple Testing)

 

 

Research Projects Funded

 

1987-92     USDA Hatch NYC 151410.  Semiparametric Techniques for Time and Spatially Related Data.  (PI: N. Altman,  $20,000)

 

1990-91     NSF DMS 8916245:  Computationally Intensive Problems in Statistics. (PI N. Altman co-PI G. Casella)

                  March 1, 1990 - Feb. 28, 1991 $20,000

 

1992-97     USDA Hatch NYC 151403.  Semiparametric Techniques for Time and Spatially Related Data.  (PI: N. Altman,  $5000 annually)

 

1996-99     NSF: Mathematical Sciences Computing Research Environments 9627207. (PI: N. Altman co-PIs: G. Casella, C. McCulloch, G.  Churchill and D. Ruppert)

                  August 15, 1996 - July 31, 1999   $58,756

 

1996-00     USDA Hatch NYC 151307.  Semi-Parametric Techniques for Longitudinal Data Analysis.  (PI: N. Altman,  $7000 annually)

 

1996-00     NSF DMS 9625350: Semi-Parametric Methods for Longitudinal Data Analysis.   (PI N. Altman)

                  July 1, 1996 - June 30, 2000   $50,000

 

2001-06     NSF PGRP 0115684:  Floral Genome Project  (PI:dePamphilis, co-PIs: Ma, Carlson, Miller, Tanksley, Doyle, Soltis, D., Soltis, P.,Oppenheimer, Leebens-Mack; N. Altman key collaborator, 2002-2003, co-PI 2003-2006)

                  October 1, 2001 - September 30, 2007  $7,471,263

 

2004-05     PSU Tobacco Settlement funds: Support of a Bioinformatics and Statistical Genomics Service Center for Penn State University (PI: J. Rosenberger, co-PIs : N. Altman, I. Makalowska, W. Liu, G. Chase

                  July 1, 2004 - June 30 2006   $162,260

 

2004-10     NSF PGRP 0420394:  Rootstock Dependent Gene Expression in Apple (PI: T. McNellis, co-PIs: R. Crassweller, S. Maximova, J. Travis; key collaborators: N. Altman, I. Makalowska)

                  September 1, 2004 - August 31, 2010  $2,269,241

 

2007-10     NSF PGRP 0638595: The Ancestral Angiosperm Genome Project  (PI: C. dePamphilis, Co-PIs: H. Ma J. Leebens-Mack, P. Soltis, D. Soltis;  Senior Personnel: S. Clifton, N. Altman (until 2009).)

                  January 1, 2007 - December 31, 2010  $2,967,113

 

2008-11     NSF OCE 0825979: Predicting the effects of ocean warming on larval dispersal by measuring adaptive potential of corals (PI: I. Baums; essential personnel: N. Altman)

                  September 1, 2008 - August 31, 2011 $474,000

 

2008-10     NSF IOS 0820729: Genetic and genomic approaches to understanding the role of auxin in shoot development (PI: P. McSteen, co-PIs: S. Malcomber, A. Gallavotti, Y. Zhao; Senior Personnel: N. Altman, R. Albert, R. Schmidt)

                  October 1, 2008 - June 30, 2010 $2,823,793

 

2010-13     NSF DMS 1007801: Statistical Methods for High Dimensional Discrete Data (PI: N. Altman)

                  June 1, 2010-May 31, 2013  (extension to May 31, 2015) $200,000

 

2010-16     GEPR: NSF IOS 0820729 (subcontract from U. Missouri): Genetic and genomic approaches to understanding the role of auxin in shoot development (PI: N. Altman)    July 1, 2010-June 30, 2016 $234,388

 

2011-16     NIH UL1RR033184: Institutional Clinical and Translational Science Awards (PI: LI Sinoway, multiple participants, biostatistician: N. Altman) $4,467,207

 

2012-13     Grant DMS-1127914 to the Statistical and Applied Mathematical Sciences Institute. (subcontract from U. North Carolina) (PI: N. Altman) Sept. 1, 2012 -May 31, 2013 $ 54,740

 

2013-18     NIGMS GM102057 Computation, Bioinformatics and Statistics (CBIOS) Training Program (PI: Hardison, multiple participants, program co-director: N. Altman)  July 1, 2013 - June 30, 2018, $244,087

 

2013-18     NIMH GABAergic  Control of Depression-Related Brain States (PI: B. Luscher, biostatistician: N. Altman) 4/01/2013-3/31/2018, $2,740,394

 

2014-18     BSF United States-Israel Binational Science Foundation: Bumble bee sociogenomics (co-PIs: A. Hefetz, C. Grozinger, N. Altman) $49,408

 

2015 – 16 Penn State CTSI: RNASeq Analyses of individual circulating Macrophage-Tumor cell Fusions (MTFs) cultured from blood of patients with pancreatic ductal adenocarcinoma (PDAC) (PI:Gary A. Clawson, Co-Investigators: Thomas Abraham, Naomi Altman, Kirsten Eilertson, Yuka Imamura-Kawasawa, Gail Matters, Diane Thiboutot, Joyce Wong) $63687 

 

2016-21     NIGMS: (supplement to the CBIOS Training Program) Bootcamp in data reproducibility and scientific transparency $40,000 (PI: C. Shashikant, faculty: N. Altman)

 

2015-19     California Dried Plums: Randomized Control Trial of Dietary Supplementation with Dried Plums on Bone Density, Geometry and Estimated Bone Strength in Postmenopausal Women  12/01/2015 to 11/30/2019 $755,937 (PI: M. De Souza, co-investigator: N. Altman)

 

2016-21     NIH Penn State Biomedical Big Data to Knowledge (B2D2K) Training Program $1,604,971 03/01/2016-02/28/2021 (PI: M. Ritchie, core faculty and chair of Evaluation Committee: N. Altman)

 

 

Theses Supervised (5 Ph.D., 14 M.S.)

 

1992   Hobert, J. P.        M.S.  Spatial Analysis of the Fish Species Richness of Adirondack Lakes:

Applications of Geostatistics and Nonparametric Regression.

 

1992   Kudrak, K.E.        M.S. The Incorporation of Environmental Heterogeneity Into

the Analysis of Animal Movement Patterns and Space Use.

 

1995   Tatsuoka, C.M      Ph.D.          A Latent Class Problem on a Directed Lattice. (with M. Wells)

 

1995  Aragaki, A.K.         M.S.  A Simple Local Least Squares Approach for Estimating the Regression

Function of Binary Response Data and Related Data-Driven Bandwidth

Selection Procedures.

 

1995  Johnson, K.           M.S.  Canonical Correspondence Analysis as a Method for Determining

                                                 Environmental Gradients: A Simulation Experiment Testing

                                                 Performance

 

1998  Belue, R.     M.S.  Link Functions for Binary Response with Low Response Probability

 

1999  Madsen, L.  M.S.  Comparing Two Parametrizations of the Exponential Variogram in

                                                    REML Parameter Estimation and Spatial Prediction

 

2000  Jou, Ying-Ming     Ph.D. Estimation of Crossover Intensity and its Application to the Mouse

                                                   Genome (with G. Churchill)

 

2001  Villarreal, J.          M.S.  Self-Modeling Nonlinear Regression with Random Shifts and a

                                       Penalized Regression Spline Shape Function

 

2002  Denogean, L.        M.S.  Composite Likelihood Methods in the Coalescent

 

2003  Xu, Hong     M.S.  Nonparametric comparison of two regression curves using the

                                       penalized spline method.

 

2003  Walters, E.   M.S.  Detecting Gene Clustering on Chromosomes

 

2004  Madsen, L.  Ph.D. Regression with Spatially Misaligned Data (with D. Ruppert)

 

2004  Han, Bing    MS    Combining Functional Genomics Data with QTLs

 

2005  Hua, Tony   MS    Extending Loop Designs for Microarray Experiments

 

2007  Skinner, Jeff MS              Power and Sample Size for Balanced Incomplete Block Design (BIBD)

                                                Experiments with Dye-Balanced Two-channel Microarray Data

 

2007    Han, Bing        Ph.D.   A Bayesian Approach to False Discovery Rate for Large Scale

                                                Simultaneous Inference (with S. Arnold)

 

2011    Dialsingh, Isaac           PhD. False Discovery Rates when the Statistics are Discrete

 

2014    Austin, Stefanie           M.S.   False Discovery Rates for Discrete Data

 

2016  Wang, Qingyu       Ph.D. (Bioinformatics & Genomics, with Girirajan, Santhosh)

                                                Evaluation of Whole Exome Sequencing Technology in Cohort Dataset

                                                and Quantification of Phenotypic Alterations in a Model Organism

2019  Shen, Frank Ph.D.  (Statistics, with Li, Qunhua) Statistical analysis of chromosome conformation                                           data and other omic data

 

current graduate committees (2) 

                                                                                             

Recent graduates: (21)

 

graduate committees at PSU (already graduated) - 27

 

 

Undergraduate Theses Supervised

 

1998    Bernstein, Elliot           Quantifying Bird Migration Patterns

1999    Cottrell, Kevin              Statistical Analysis of Bird Migration

2005    Li, Xiao-Yi                   Clustering Microarray Data

2008    Zeifman, Lubov           Independent Component Analysis of fMRI data

2015    Megan Gearhart          Analysis of single-cell RNA-seq data

 

Professional Memberships

 

American Statistical Association

Canadian Statistical Society

Institute of Mathematical Statistics

 

 

Professional Responsibilities

 

2016 -                   Associate Editor, Canadian Journal of Statistics

2015           Committee on P-values, American Statistical Association

2013- 2017  Statistical Review Panel, Nature Publishing

2013-          Contributing Editor, Nature Methods

2012-15      Associate Editor, Journal of the Indian Society of Agricultural Statistics

2006-09      Associate Editor, Journal of the American Statistical Association

2002-05      Associate Director, Bioinformatics Consulting Center, PSU

1998-01      Member, Genomics Task Force, Cornell

1997-00      Chair, Department of Biometrics, Cornell

1998-00      Chair, Computational Genomics Curriculum Committee, Cornell

1996-99      Representative to the Council on Sections, Statistical Computing Section of the

American Statistical Association.

1992-97      Associate Editor, Journal of Computational and Graphical Statistics

1991-92      Member, Program Advisory Committee, Institute of Mathematical Statistics

1988-91      Chair, New Researchers Committee, Institute of Mathematical Statistics

1988-91      Member, Ad Hoc Committee for Outreach, Institute of Mathematical Statistics

 

Teaching (at Penn State)

 

Stat 414

Introduction to Probability Theory

F07, F08, S10,F11

Stat 440

Statistical Computing for Undergraduates

S09

Stat 503

Design of Experiments II

F09, F13 (WD)

Stat 511

Regression Analysis and Modeling

F01-06

Stat 512

Design and Analysis of Experiments

S02-08, S12

Stat 540

Statistical Computing for Graduate Students

F08-10

Stat 580

Statistical Consulting

F07, F14 (WD)

Stat 597C

Computing Environments

F05-07

Stat 598A/IBIOS 598E

Current Research in Statistical Genomics

F05-07

Stat/CSE 598D/Bio 597D

Bioinformatics II

S06, S11, S14

Stat 555

High Throughput Genomics Data

S15, F15 (WD), S16, F17, S17, F18

 

Departmental Duties at Penn State

 

2001 – 12   Faculty Advisory Board of Statistical Consulting Center (chair 2007-2011)

2001 -         Promotion and Tenure Committee

2002-06      representative, Eberly College of Science Climate Committee

2002-06      chair, departmental Climate Committee

2002-07      Undergraduate Program Committee Statistics

2002- 15     Graduate Admissions Committee Statistics (chair 2006 - 15)

2002-09      Undergraduate advisor

2006-07      Computing Committee

2006-09, 13-         Graduate Program Committee

2006- 14      Graduate Peer Advising Co-ordinator

2006 -                   Schreyer Honors advisor

2010 - 11    Faculty Search Committee

2013 -         CBIOS Program co-director

2015 -                   CBIOS Program Graduate Selection Committee

2015 -         Graduate Admissions Committee Bioinformatics and Statistics

2016           Chair, B2D2K Training Grant Evaluation Committee

2018           Graduate Admission Committee Statistics

2018           Graduate Program Chair

 

Other Activities

 

2001-05     organizer, Statistical Genomics Journal Club

2004-06     Martin Luther King Celebration Coordinator (ECoS)

                  prepared a week-long program for the college

2002-05     Associate Director of the Bioinformatics Consulting Center