## Recent & Upcoming Events

Jun 30, 2016

CPCP Second Annual Retreat

A day-long retreat highlighting recent research in the Center; featuring talks, posters, and lunch.

Apr 21, 2016

CPCP Seminar: Mining Structures from Massive Bio-Text Data: A Data-Driven Approach by Dr. Jiawei Han

Jiawei Han from the BD2K KnowEng Center-UIUC discussed mining structures from massive bio-text data.

Nov 10, 2015

CPCP Seminar: Transforming Your Research with High-Throughput Computing by Lauren Michael

Lauren Michael from the CHTC discussed high-throughput computing approaches to Big Data.

## Training Resources

CPCP Seminar: Transforming Your Research Through High Throughput Computing * Seminar Video*

Presented by Lauren Michael

Big Privacy Symposium: Introductory and Welcoming Remarks * Symposium Video*

Presented by David Page, PhD

Big Privacy Symposium: Big Data, Big Headaches: Cultivating Public Trust in an Age of Unconsented Access to Identifiable Data * Symposium Video*

Presented by Barbara J. Evans PhD, JD, LLM

Big Privacy Symposium: Does Publishing a Predictive Model for Precision Medicine Put Patient Privacy at Risk? * Symposium Video*

Presented by Matt Fredrikson, PhD

## Recent Publications

A hierarchical framework for state space matrix inference and clustering. Zuo C, Chen K, Hewitt K, Bresnick EH, Keles S. *Annals of Applied Statistics, 2016*

Anytime exploration for multi-armed bandits using confidence information. Jun K-S, Nowak R. *Proceedings of the 33rd International Conference on Machine Learning, 2016*

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. Siahpirani A, Ay F, Roy S. *Genome Biology 17:114, 2016*

A MAD-Bayes algorithm for state-space inference and clustering with application to querying large collections of ChIP-seq data sets. Zuo C, Chen K, Keles S. *Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2016*

## Recent Resources

GADGET *software*

GADGET is a web tool that for finding and ranking genes and metabolites that are associated with a given query in the biomedical literature. It's like a version of PubMed that returns genes and metabolites instead of articles.

rvalues *software*

rvalues is an R package for computing "r-values" from various kinds of user input such as a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.

atSNP *software*

atSNP (Affinity Test for regulatory SNP detection) is an R package for computing and testing large-scale motif-SNP interactions. It provides three main functions: (1) Computing the binding affinity scores for both the reference and the SNP alleles based on position weight matrices; (2) Computing the p-values of the affinity scores for each allele; (3) Computing the p-values of the affinity score changes between the reference and the SNP alleles.

MBASIC *software*

MBASIC (Matrix Based Analysis for State-space Inference and Clustering) is a statistical framework for integrative analysis of many related experiments where observations are collected over a set of units. The MBASIC framework allows for simultaneous projection of the observations onto a discrete state space and clustering the units based on their state-space profiles. MBASIC is applicable to many high throughput sequencing datasets. For example, it enables analysis of large collections of ChIP-seq datasets by simultaneously identifying genomic loci with peaks and similar peak patterns across multiple conditions.