The authors here invited ACM KDD Innovation Award and IEEE ICDM Research Contributions Award winners to each nominate up to 10 best-known algorithms in data mining, including the algorithm name, justification for nomination, and a representative publication reference. The list was voted on by other IEEE and ACM award winners to narrow this down to a top 10 list.

Suppose you have billions of reads from a hot new sequencing machine and you want to simultaneously align these reads and call SNPs very quickly on the cheap. Check out an open source tool called Crossbow and the recent paper in Genome Biology.

If you caught Soumya Raychaudhuri's seminar last week you heard a lot about the tool he developed at the broad called GRAIL - Gene Relationships Across Implicated Loci. You've got GWAS results and now you want to prioritize SNPs to follow up in replication or functional studies.

Bioinformatics is running a special issue on next generation sequencing, featuring lots of papers on alignment, assembly, Chip-Seq, RNA-Seq, and other related topics. This "virtual issue" will be continually updated as more developments are made. From the editors:Bioinformatics: Next generation sequencing issueGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

Has anyone ever used Galaxy? I saw their presentation at last year's ASHG. Seems like a great way to do collaborate on and keep a record of analyses in an easy web-GUI interface without having to download any software.

So you have found significant SNPs from a study, and you are investigating the region. Browsing through Ensembl or Entrez-Gene, you find a coding region nearby. Atop this coding region, you see a collection of letters that are commonly used to refer to this gene, lets say "MYLK". So you begin a PubMed search to find publications that describe the function of this gene, searching with "MYLK". Seems reasonable, right?Beware!

Just released last week by the makers of Mathematica, Wolfram Alpha is kind of like a search engine, calling itself a "computational knowledge engine," with the lofty goal as a "long-term project to make all systematic knowledge immediately computable by anyone."From their homepage you can link to a page showing examples of how to use it, but I was interested in seeing how much biology Wolfram Alpha knows, and I've got to say I'm impressed with

OpenHelix offers free access to a handful of their tutorials on genomics and bioinformatics resources, including the UCSC Genome Browser, Seattle SNPs, Genome Variation Server, and the VISTA Comparative Genomics tools.

I saw a demonstration of this tool at the workshop on network analysis I announced last week. Genes2Networks draws from a large background network consisting of several experimentally verified mammalian protein interaction databases. It will take a list of genes you provide as seed genes and identify all interacting genes that fall on paths through the background network between them.

Avi Ma'ayan, Ph.D., Assistant Professor in the Department of Pharmacology and Systems Therapeutics of Mount Sinai School of Medicine, will present "Network Analysis in Systems Biology", at 10:00 am on Wednesday, April 22 in Room 206 PRB.Following the lecture, Dr. Ma’ayan will hold a series of one-hour interactive workshops on "Computational Methods for Analyzing Lists of Genes/Proteins and Building Networks in Systems Biology," which will