Fall 2010 - Spring 2011

Multiomics Journal Club Schedule
Speaker Date Paper
Robert B Norgren 10/20/10 The sequence and de novo assembly of the giant panda genome
Robert J Boissy


Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
James D Eudy


Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations
Adrian A Epstein 11/10/10 Activation of a Metabolic Gene Regulatory Network Downstream of mTOR Complex 1
Adam Cornish 11/17/10 A map of human genome variation from population-scale sequencing
Alok Dhar 12/08/10 Molecular Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the Whole Exome
Babu Guda 12/15/10 Dynamic modularity in protein interaction networks predicts breast cancer outcome
Yeong C Kim 1/13/2011 Limitations of next-generation genome sequence assembly.
Jeff Kittrell 1/20/2011 High-quality draft assemblies of mammalian genomes from massively parallel sequence datat
Akram Mohammed 1/27/2011 A computational tool for identifying minimotifs in protein–protein interactions and improving the accuracy of minimotif predictions
Sanjit Pandey 2/3/2011 ABySS: A parallel assembler for short read sequence data
Suleyman Vural 2/10/2011 Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
San Ming Wang 2/17/2011

"BIG or BGI"

Satish Mahadevan Srinivasan 2/24/2011 Data structures and compression algorithms for high-throughput sequencing technologies
Robert J Boissy 3/3/2011 Statistical Design and Analysis of RNA Sequencing Data
Adam Cornish 3/10/2011 An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
Alok Dhar 3/17/2011 Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
Adrian A Epstein 3/24/2011

Relationships between gene expression and brain wiring in the adult rodent brain.

Additional Papers:
James D Eudy 3/31/2011 Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease
Yeong C Kim 4/7/2011 Mapping copy number variation by population-scale genome sequencing
Babu Guda 4/14/2011 Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation

Additional Paper:
Jeff Kittrell 4/21/2011 A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies
Satish Mahadevan Srinivasan 4/28/2011 N-gram analysis of 970 microbial organisms reveals presence of biological language models
Robert B Norgren 5/5/2011

23 & Me

Sanjit Pandey 5/12/2011 Connectedness of PPI network neighborhoods identifies regulatory hub proteins
Suleyman Vural 5/18/2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome
San Ming Wang 5/25/2011 An overview of Dr. Wang's lab research.