We’re excited to announce that we’ve just been awarded an Amazon Web Services (AWS) in Education Research Grant in support of our cancer biomarker project! This grant will allow us to run our proteogenomic software Peppy on the AWS Cloud, mining proteomic and genomic data for aberrations that may be at the root of breast cancer. Ultimately, this will help with the project’s larger goal of finding blood-based protein biomarkers for the disease. Rather than hunting through the protein data for a proverbial ‘needle in a haystack,’ we are focusing on the DNA mutations that give rise to cancer, then tracing a path outward to the proteins.

We’re in the discovery stage of a five-year project funded by the National Institutes of Health (NIH), as a member of the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our lab’s role in this project is in the computation: to mine the genomes of breast cancer patients for mutations that may be causing their disease. To do this, we use our unique proteogenomic mapping software, Peppy, capable of processing an entire human genome in a single run. By linking mass spectrometry data from proteins to an in silico translation and digestion of genomes, Peppy can pinpoint the genomic regions of breast cancer patients where aberrations may be causing cancer-related proteins to be over-expressed. Peppy requires a lot of computer memory and processing power to handle entire genomes, so running the program on the AWS Cloud is an obvious choice.

We’re thrilled about the possibilities now open to us by running Peppy on the Cloud, especially in accelerating the tempo of this research. Thank you, AWS!

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Check out a recent article in Genome Technology (scroll to pg. 21) to learn more about our cancer biomarker project!

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ENCODE project, Big Science, and the Web

September 14, 2012

This post will be reinstated shortly….

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Artificial intelligence isn’t intelligent

April 21, 2012

Will computers ever be smart?
I just wrote a new blog post on artificial intelligence, motivation, and creativity over at my other blog site.
The bottom line is that just making computers faster is not going to make them smarter, despite the common myth that Watson, the Jeopardy playing computer somehow proves that faster computers equal smarter [...]

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The “magic bullet” misses its target-how does this happen?

November 11, 2010

A failing promise-
They were called “magic bullets”- antibiotics, once held sacred as the panacea that would cure almost all kinds of infectious diseases. Their continued success is reflected by the decrease in the morbidity of bacterial infections during the past few decades. However, the increasing misuse of antibiotics for human and non-therapeutic animal treatment have [...]

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Dennis explains the blinking lights

July 13, 2010

Dennis Crenshaw talks about his work and helps us get our heads around the Ultra-Structure concept.

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Maarten’s Passions

July 8, 2010

Maarten Leerkes explains how his passions in the private sector have lead to his research interests as a post-doc.

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This is not groundbreaking!

July 5, 2010

Jainab tells us about her decision to enter bioinformatics and how our lab is working to find valuable information for gene therapy.

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How is bioinformatics like Sudoku?

June 29, 2010

Serguei Simonov mesmerizes us with a Russian poem and explains his path to bioinformatics.

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How to use a mini-espresso machine

June 24, 2010

Introducing Mark Holmes: Lab systems administrator; coffee aficionado.

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