CS 260 (Seminar in Bioinformatics) Homepage


Venue : WCH 141

Time : TuTh 12:40-2pm

Instructor :

Tao Jiang (jiang@cs.ucr.edu)
Office hours: TuTh 2-3pm. Office: WCH 336.

The theme for this year's seminar is the Analysis and Applications of High-Throughput Sequencing Data. Every student will be expected to present one or two papers from the following lists:

RNA-Seq Based Splicing and Expression Analysis
Functional Analysis of mRNA Isoforms
Metagenomic Data Analysis
Structure-Seq, CLIP-Seq, Hi-C Data Analysis

The following is the tentative schedule of student presentations:

4/5 Tao Jiang: Differential gene expression analysis using coexpression and RNA-Seq data

4/12 Jillian Foster: Translating RNA sequencing into clinical diagnostics: opportunities and challenges

4/26 Noel Llanura: SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

5/3 Dipan Shaw: Gene expression inference with deep learning

5/5 Ashraful Arefeen: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

5/10 Hoang Anh Dau: Deep learning

5/12 Yi Wu: Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

5/17 Weihua Pan: Bayesian transcriptome assembly

5/19 Sandesh Basrur: Simultaneous isoform discovery and quantification from RNA-seq

5/24 Kiran Gangadevi: Estimating optimal window size for analysis of low-coverage next-generation sequence data

5/26 Hui Yang: GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads

6/2 Fatemeh Tavakkoli: RNA secondary structure prediction based on SHAPE data in helix regions