Tag Archives:

Rethinking Data-Intensive Science Using Scalable Analytics Systems

Frank Austin Nothaft, Matt Massie, Timothy Danford, Zhao Zhang, Uri Laserson, Carl Yeksigian, Jey Kottalam, Michael Franklin, Anthony Joseph, David Patterson
ACM SIGMOD Conference, May. 2015.

Tags: genomics, spark

Changepoint Analysis for Efficient Variant Calling

Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael Jordan, David Patterson, Bin Yu, Yun S. Song
International Conference on Research in Computational Molecular Biology (RECOMB), Apr. 2014.

Tags: genomics

SMASH: A Benchmarking Toolkit for Human Genome Variant Calling

Ameet Talwalkar, Jesse Liptrap, Julie Newcomb, Chris Hartl, Jonathan Terhorst, Kristal Curtis, Ma'ayan Bresler, Yun S. Song, Michael Jordan, David Patterson
Bioinformatics, Jun. 2014.

Tags: genomics

Benefiting from Science is a Human Right!

Posted on March 10, 2014 by Patterson

Error: Unable to create directory uploads/2023/04. Is its parent directory writable by the server?

I was just at the Global Alliance for Genomics and Health (GA4GH) last week in London, and a person from … Continue reading →

ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing

Matt Massie, Frank Austin Nothaft, Chris Hartl, Christos Kozanitis, Andre Schumacher, Anthony Joseph, David Patterson
Dec. 2013.

Tags: genomics, spark

DNA Processing Pipeline

Another effort related to genomics underway at the AMP Lab involves developing a variant calling pipeline.  Variant calling is the … Continue reading →

DNA Sequence Alignment with SNAP

As the cost of DNA sequencing continues to drop faster than Moore’s Law, there is a growing need for tools … Continue reading →

Cancer Tumor Genomics: Fighting the Big C with the Big D

It may have been true once that expertise in computer science was needed only by computer scientists. But Big Data … Continue reading →