PiNGO: a Cytoscape plugin to find candidate genes

http://www.ncbi.nlm.nih.gov/m/pubmed/21278188/?i=5&from=/23547033/related

The stem cell code in oral epithelial tissue

http://www.ncbi.nlm.nih.gov/m/pubmed/20599480/

FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data

http://bioinformatics.oxfordjournals.org/content/early/2013/04/24/bioinformatics.btt151.short?rss=1&buffer_share=c5ca4&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer%253A%252BSAGRudd%252Bon%252Btwitter

Genome Biology | Abstract | TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

http://genomebiology.com/2013/14/4/R36/abstract

The Long and Short of MicroRNA

http://www.cell.com/abstract/S0092-8674(13)00402-9?buffer_share=d1953&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer%253A%252BSAGRudd%252Bon%252Btwitter

Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit8.17. doi: 10.1002/0471250953.bi0817s41.

Using MEMo to Discover Mutual Exclusivity Modules in Cancer.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N.

Source

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.

Abstract

Although individual tumors show surprisingly diverse genomic alterations, these events tend to occur in a limited number of pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. While pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in Cancer (MEMo). The method searches and identifies modules characterized by three properties: (1) member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the modules are mutually exclusive. MEMo integrates multiple data types and maps genomic alterations to biological pathways. MEMo's mutual exclusivity uses a statistical model that preserves the number of alterations per gene and per sample. The MEMo software, source code and sample data sets are available for download at: http://cbio.mskcc.org/memo. Curr. Protoc. Bioinform. 41:8.17.1-8.17.12. © 2013 by John Wiley & Sons, Inc.

http://www.ncbi.nlm.nih.gov/pubmed/23504936

Gene-pair expression signatures reveal lineage control : Nature Methods : Nature Publishing Group

http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2445.html

Deanna Church on the Reference Genome Past, Present and Future - Bio-IT World

http://www.bio-itworld.com/2013/4/22/church-on-reference-genomes-past-present-future.html

GRC38

( METAGENOMICS) FunFrame: functional gene ecological analysis pipeline

http://bioinformatics.oxfordjournals.org/content/29/9/1212.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+bioinformatics_today+%2528Bioinformatics%2529

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

http://bioinformatics.oxfordjournals.org/content/29/9/1210.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+bioinformatics_today+%2528Bioinformatics%2529