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Undergraduate research project or internship
Acquire a statistical bioinformatics skill set by developing novel scientific software in the frontiers of genomics for high impact on medical science. Learn to analyze genomics data with newly created statistical methods. Make new biostatistics software accessible worldwide by improving the usability and functionality of the Statomics Lab’s data analysis code and by adding documentation. Providing scientists with these reliable biostatistical tools can advance medical research by improving the accuracy of conclusions drawn from genomics and clinical data.
Scientific breakthroughs from genome-sequencing projects brought the realization that reliable interpretation of the resulting information makes unprecedented demands for contemporaneous advances in computation and mathematical modeling. As the complexity of genomic data sets drives innovative statistics research, the Statomics Lab (http://davidbickel.com) aims to develop and apply novel methodology and algorithms to solve current problems in analyzing gene-expression, proteomics, metabolomics, SNP, ChIP-chip, and/or clinical data.
Intellectual curiosity and high mathematical aptitude are essential, as is the ability to quickly code and debug computer programs. Strong self motivation and good communication skills are also absolutely necessary. The following qualities are desirable but not required: coursework in bioinformatics, computer science, numerical methods, numerical analysis, software engineering, statistics, and/or biology; familiarly with BUGS, R, S-PLUS, C, Fortran, and/or LaTeX; experience with UNIX or Linux.
To be considered, send a PDF CV that has your GPA and contact information of two references to dbickel@uOttawa.ca with either “research project” or “internship” in the Subject line of the message and with a cover letter in the body of the message. Only those students selected for further consideration will receive a response.
Statistics & biostatistics graduate studentships
Reliable interpretation of genomic information makes unprecedented demands for innovations in statistical methodology and its application to biological systems. This unique opportunity drives research at the Statomics Lab of the Ottawa Institute of Systems Biology (http://davidbickel.com). The Statomics Lab seeks new graduate students who will conduct original research involving the creation and evaluation of novel statistical tools for application to the analysis of transcriptomics, proteomics, metabolomics, and/or genome-wide-association data.
Each student will work toward an MSc or PhD degree in the Mathematics and Statistics Program at the University of Ottawa. MSc students have the additional option of choosing a Bioinformatics or Biostatistics Specialization. Financial support is available.
Intellectual curiosity and high mathematical aptitude are essential, as is the ability to quickly code and debug computer programs. Strong self motivation and good communication skills are also absolutely necessary. The following qualities are desirable but not required: coursework in bioinformatics, computer science, numerical methods, numerical analysis, software engineering, statistics, and/or biology; familiarly with BUGS, R, S-PLUS, C, Fortran, and/or LaTeX; experience with UNIX or Linux.
Canadians (by citizenship or permanent residency) are especially encouraged to apply, as are all exceptional students. To be considered, send a PDF CV that has your GPA and contact information of two references to dbickel@uOttawa.ca with either “MSc” or “PhD” and any specialization in the Subject line of the message and with a cover letter in the body of the message. Only those selected for further consideration will receive a response.
Estimates of the local false discovery rate based on prior information: Application to GWAS
A. Karimnezhad and D. R. Bickel, “Incorporating prior knowledge about genetic variants into the analysis of genetic association data: An empirical Bayes approach,” Working Paper, University of Ottawa, deposited in uO Research at http://hdl.handle.net/10393/34889 (2016). 2016 preprint
Empirical Bayes single-comparison procedure
D. R. Bickel, “Small-scale inference: Empirical Bayes and confidence methods for as few as a single comparison,” International Statistical Review 82, 457-476 (2014). Published version | 2011 preprint | Simple explanation (link added 21 June 2017)
Parametric empirical Bayes methods of estimating the local false discovery rate by maximum likelihood apply not only to the large-scale settings for which they were developed, but, with a simple modification, also to small numbers of comparisons. In fact, data for a single comparison are sufficient under broad conditions, as seen from applications to measurements of the abundance levels of 20 proteins and from simulation studies with confidence-based inference as the competitor.
Adaptively selecting an empirical Bayes reference class
F. A. Aghababazadeh, M. Alvo, and D. R. Bickel, “Estimating the local false discovery rate via a bootstrap solution to the reference class problem,” Working Paper, University of Ottawa, deposited in uO Research at http://hdl.handle.net/10393/34295 (2016). 2016 preprint
Empirical Bayes software (R packages)
Empirical Bayes software packages:
Frequentist inference principles
On some principles of statistical inference.
Int. Stat. Rev. 83 (2015), no. 2, 293–308.
62A01 (62F05 62F15 62F25)
While agreeing with other frequentists on the necessity of guaranteeing good performance over repeated sampling, Reid and Cox also value neglected rules of inference such as the conditionality principle. Against the steady advance of nonparametric methods, Reid and Cox point to the interpretive power of parametric models.Frequentist decision theory is only mentioned. Glimpses of the authors’ perspectives on that appear in [D. R. Cox, Principles of statistical inference, Cambridge Univ. Press, Cambridge, 2006 (8.2); MR2278763 (2007g:62007)] and [N. M. Reid, Statist. Sci. 9 (1994), no. 3, 439–455; MR1325436 (95m:01020)].On the Bayes front, Reid and Cox highlight the success frequentist methods have enjoyed in scientific applications as a decisive victory over those Bayesian methods that are most consistent with their subjectivist foundations. Indeed, no one can deny what C. Howson and P. Urbach call the “social success” of frequentist methods [Scientific reasoning: the Bayesian approach, third edition, Open Court, Chicago, IL, 2005 (p. 9)]. Reid and Cox do not attribute their widespread use in scientific practice to political factors.
Rather, for scientific inference as opposed to individual decision making, they find frequentist methods more suitable in principle than fully Bayesian methods. For while the need for an agent to reach a decision recognizes no line between models of the phenomena under study and models of an agent’s thought, science requires clear reporting on the basis of the former without introducing biases from the latter. Although subjective considerations admittedly come into play in interpreting reports of statistical analyses, a dependence of the reports themselves on such considerations conflicts with scientific methodology. In short, the Bayesian theories supporting personal inference are irrelevant as far as science is concerned even if they are useful in personal decision making. This viewpoint stops short of that of Philip Stark, who went as far as to call the practicality of that private application of Bayesian inference into question [SIAM/ASA J. Uncertain. Quantif. 3 (2015), no. 1, 586–598; MR3372107].
On reference priors designed to minimize subjective input, Reid and Cox point out that those that perform well with low-dimensional parameters can fail in high dimensions. Eliminating the prior entirely leads to the pure likelihood approach, which, based on the strong likelihood principle, limits the scope even further, to problems with a scalar parameter of interest and no nuisance parameters [A. W. F. Edwards, Likelihood. An account of the statistical concept of likelihood and its application to scientific inference, Cambridge Univ. Press, London, 1972; MR0348869 (50 #1363)]. More recent developments of that approach were explained by R. M. Royall [Statistical evidence, Monogr. Statist. Appl. Probab., 71, Chapman & Hall, London, 1997; MR1629481 (99f:62012)] and C. A. Rohde [Introductory statistical inference with the likelihood function, Springer, Cham, 2014 (Chapter 18); MR3243684].
Reid and Cox see some utility in Bayesian methods that have good performance by frequentist standards, noting that such performance can require the prior to depend on which parameter happens to be of interest and, through model checking, on the data. Such dependence raises the question, “Is this, then, Bayesian? The prior distribution will then not represent prior knowledge of the parameter in [that] case, but an understanding of the model” [T. Schweder and N. L. Hjort, Scand. J. Statist. 29 (2002), no. 2, 309–332; MR1909788 (2003d:62085)].
Reviewed by David R. Bickel
This review first appeared at “On some principles of statistical inference” (Mathematical Reviews) and is used with permission from the American Mathematical Society.
Statistics & biostatistics graduate student stipends
Reliable interpretation of genomic information makes unprecedented demands for innovations in statistical methodology and its application to biological systems. This unique opportunity drives research at the Statomics Lab of the Ottawa Institute of Systems Biology (http://www.davidbickel.com/). The Statomics Lab seeks students who will conduct original research involving the application of novel statistical methods to the analysis transcriptomics, proteomics, metabolomics, and/or genome-wide-association data while earning a graduate degree in Mathematics and Statistics. The page https://davidbickel.com/career/ has information on careers in statistics and biostatistics.
Intellectual curiosity and high mathematical aptitude are essential, as is the ability to quickly code and debug computer programs. Strong self motivation, good communication skills, and a degree in bioinformatics, computer science, mathematics, physics, statistics, any field of engineering, or an equally quantitative field are also absolutely necessary. The following qualities are desirable but not required: coursework in computer science, numerical methods, numerical analysis, software engineering, statistics, and/or biology; familiarly with BUGS, R, S-PLUS, C, Fortran, and/or LaTeX; experience with UNIX or Linux.
To be considered, send a PDF CV that has your GPA and contact information of two references to dbickel@uOttawa.ca with the degree sought (MSc or PhD) in the Subject line of the message and with a cover letter in the body of the message. Only those students selected for further consideration will receive a response.
Coherent inference after checking a prior
D. R. Bickel, “Bayesian revision of a prior given prior-data conflict, expert opinion, or a similar insight: A large-deviation approach,” Working Paper, University of Ottawa, deposited in uO Research at http://hdl.handle.net/10393/34089/ (2015). 2015 preprint
David Bickel, statistician 
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