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Statistics Department

We have been awarded an NIH Transformative Research Award (High Risk High Rewards) to develop multitable methods to predict Resilience in the Human Microbiome with David Relman. See announcement .

Research News:
PLOS ONE Phyloseq paper is highly accessed!:
April 2013 : Journal Article Published Link:PLOS ONE
PSB paper (2012) PHYLOSEQ: A Bioconductor package for handling and analysis of highthroughput phylogenetic sequence data
Comparison between DPCOA and Unifrac paper accepted to PSB 2012: Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies
Science News: Ants Take a Cue From Facebook on Noa Pinter-Wollman's ant study

Papers and Chapters:
Just appeared: PC Kashyap, A Marcobal, LK Ursell, S Smits, E Sonnenburg, E Costello, S Higginbottom, SE Domino, S Holmes, DA Relman, R Knight, JI Gordon, and JL Sonnenburg Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota PNAS 2013 published ahead of print September 23, 2013, doi:10.1073/pnas.1306070110 [PNAS paper]>
Our chapter on Statistical Data Analysis Challenges from the Microbiome appeared in the National Academies volume, see here:
Nelson Ray presents Kaggle in Class for Stats202, 2010
CAUSEweb: The Role of a Wine Pricing Competition in Teaching Data Mining at Stanford with Susan Holmes & Nelson Ray, Stanford - April 26th, 2011
November 2010, ACM Data Mining Camp: How to get started in Data Mining

Links to some slides from (old) Talks:
Studying the Immune System and Cancer with Multivariate Statistics Massive Data Sets 2010: Challenges of Heterogeneous Data
Image Analysis and Data collection in Biology: the data, all the data Confidence regions for phylogenetic trees
Singapore workshop on Trees and Graphs in Biology: Treespace Omar dela Cruz : NIPS workshop Talk on tensors and kernels
Summer Institute: Metagenomics
Statistics without Probability?
October 18th, 2011: What R can and can't do Conference on Extra Large Databases
IMA: Multivariate Statistics for Smart People
(who don't know any statistics),
October 3rd, 2013: Quick overview of PCA, MDS, using metrics (and a bit of bootstrap)

  © 2011 Susan Holmes