BTRY 6940 Graduate Special Topics in Biometry and Statistics

Instructor: Jim Booth
Time: 2:15 PM on Fridays
Place: 1181 Comstock Hall
1 credit

The goal of this class is to review the current state of the literature on statistical and computational methods for network and pathway discovery in biological systems.

The class will meet one hour per week. Students signed up for credit will be expected to do a presentation (say 30 minutes) on a relevant paper or set of related papers.

Ordered List by Date: Presenter :: Topic ::: Background Readings

  1. September 12 2014 : Kelson Zawack :: The graphical lasso and the nonparanormal skeptic model with applications to some mass spectrometry data (PDF slides 2068KB) ::: Methodology papers for graphical lasso and nonparanormal skeptic.
  2. September 19 2014 : Irina Gaynanova :: Introduction to Lasso and Graphical Lasso (PDF slides 244KB) ::: See lasso for a simple explanation and the original paper.
  3. September 26 2014 : David Sinclair :: Introduction to Networks in Brain Imaging (PDF slides 508KB) ::: See Network diffusion accurately models the relationship between structural and functional brain connectivity networks and Network modelling methods for FMRI.
  4. October 03 2014 : James Booth :: Introduction to Factor Analysis and eQTL (PDF slides 1768KB) ::: See eQTL/factor analysis paper by Gao et al..
  5. October 08 2014 : Adam Rothman :: Properties of optimizations used in penalized Gaussian likelihood inverse covariance matrix estimation (PDF slides 432KB).
  6. October 10 2014 : Christian Mueller (Center for Genomics and Systems Biology, NYU) :: Inference of microbial ecological interaction networks with SParse InversE Covariance selection for Ecologial ASsociation Inference [SPIEC-EASI] (PDF slides 19MB) ::: See
  7. October 17 2014 : Daqian Sun :: Large Metabolic Networks (PDF slides 296KB) ::: See Metabolic Network paper by Barabasi Lab and the Chapter on Preferential Attachment in
  8. October 31 2014 : Yrjo Tapio Grohn (Cornell College of Veterinary Medicine) :: Progression to multi-scale models and the application to food system intevention strategies (in press in Preventitive Veterinary Medicine)
  9. November 5 2014 : Rachael Hageman Blair (University at Buffalo) :: Belief Propagation in Genotype-Phenotype Networks (PDF slides 4.9MB) : See Graduate Lectures in Graphical Models and Causal Inference at Steffen L. Lauritzen's page and his Wald lectures (2012 Istanbul) for theoretical background on Rachel's talk.
  10. November 14 2014 : Raazesh Sainudiin (University of Canterbury, Christchurch, New Zealand; on Sabbatical at Dept.~of Mathematics, Cornell) :: Some Experiments in Phylodynamic Epidemiology (PDF scan of white-board lecture notes 3.0MB) ::: See Phylogenetic tree shapes resolve disease transmission patterns, Caroline Colijn and Jennifer Gardy, Evolution Medicine and Public Health Advances, OUP, June 9, 2014 for applied statistical/public-heath motivation of the lecture-discussion and see Unifying the Epidemiological and Evolutionary Dynamics of Pathogens for one of the "founding paper(s)". For a current-affairs perspective on how the host-contact network structure is based on family bonds derived from pedigrees see For a Liberian Family, Ebola Turns Loving Care Into Deadly Risk, By Norimitsu Onishinov on November 13, 2014, NY Times. For a recent work on notions of ancestries in a population's pedigree within which cytoplasmic parasites such as Wolbachia are transmitted see Ancestries of a Recombining Diploid Population, Raazesh Sainudiin, Bhalchandra Thatte, and Amandine Véber, UCDMS Research Report 2014/3, 42 pages, 2014.

Some Stats Seminars of Possible Interest

Background reading on Gaussian Graphical Models (from Lingzhou Xue via Kelson Zawack)

Unordered List of Potential relevant Topics

We will decide at the first meeting about other presenters and topics. Here are several papers that might be interesting to examine in detail. If you have suggestions for other topics send a link with a brief description in plan ASCII text to my email address.

Coordinated by Raazesh Sainudiin
with partial support from:
2014 Sabbatical grant from College of Engineering, University of Canterbury, Christchurch, New Zealand and
a Visiting Scholarship to Department of Mathematics, Cornell University, Ithaca, New York