2016 UC Berkeley / UC Davis Joint Statistics Colloquium: Bin Yu

2016 UC Berkeley / UC Davis Joint Statistics Colloquium

Please join us for the 2016 UC Berkeley / UC Davis Joint Statistics Colloquium.

This year the event will take place at the University of California, Davis, from 4:10pm in MSB 1147, and will be followed by a STUDENT SYMPOSIUM at 5:30pm in MSB 1143.


Thursday April 14th 4:10pm, MSB 1147 (Colloquium Room)

Refreshments at 3:30pm

Speaker:              Bin Yu (UC Berkeley)

Title:                      “Unveiling the mysteries in spatial gene expression”

Abstract:              Genome-wide data reveal an intricate landscape where gene activities are highly differentiated across diverse spatial areas. These gene actions and interactions play a critical role in the development and function of both normal and abnormal tissues. As a result, understanding spatial heterogeneity of gene networks is key to developing treatments for human diseases. Despite the abundance of recent spatial gene expression data, extracting meaningful information remains a challenge for local gene interaction discoveries. In response, we have developed staNMF, a method that combines a powerful unsupervised learning algorithm, nonnegative matrix factorization (NMF), with a new stability criterion that selects the size of the dictionary. Using staNMF, we generate biologically meaningful Principle Patterns (PP), which provide a novel and concise representation of Drosophila embryonic spatial expression patterns that correspond to pre-organ areas of the developing embryo. Furthermore, we show how this new representation can be used to automatically predict manual annotations, categorize gene expression patterns, and reconstruct the local gap gene network with high accuracy. Finally, we discuss on-going crispr/cas9 knock-out experiments on Drosophila to verify predicted local gene-gene interactions involving gap-genes, and an open-source software that is being built based on SPARK and Fiji.

(This talk is based on collaborative work of a multi-disciplinary team (co-lead Erwin Frise) from the Yu group at UC Berkeley, the Celniker group at the Lawrence Berkeley National Lab (LBNL), and the Xu group at Tsinghua Univ.)


5:30pm following the Colloquium, MSB 1143 (Seminar Room)

Graduate students from UC Berkeley and UC Davis will make short presentations about their statistical research.

Pizza will be served. All grad students welcome.

This seminar also counts as part of STA 290 Spring Seminar Series.