omicsomics.blogspot.com
Omics! Omics!: September 2014
http://omicsomics.blogspot.com/2014_09_01_archive.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Tuesday, September 09, 2014. Reanalysis Lays Bare MinION Review's Spectacular Flaws. T and submit it to a journal. Links to this post. Friday, September 05, 2014. Oxford Takes Some Flak, Fires Back. Links to this post. Subscribe to: Posts (Atom). View my complete profile. Reanalysis Lays Bare MinION Reviews Spectacular F. Oxford Takes Some Flak, Fires Back. About a...
omicsomics.blogspot.com
Omics! Omics!: February 2014
http://omicsomics.blogspot.com/2014_02_01_archive.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Wednesday, February 26, 2014. NGS Saves A Young Life. Links to this post. Monday, February 24, 2014. A Sunset for Draft Genomes? Links to this post. Thursday, February 13, 2014. How will you deal with GRCh38? So, a significant advance, but a bit unpleasant one if you are in the space. You now have several ugly options before you with regard to your prior data m...
omicsomics.blogspot.com
Omics! Omics!: June 2015
http://omicsomics.blogspot.com/2015_06_01_archive.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Tuesday, June 30, 2015. June 2015: Busting Out All Over with Genomics Technology. 10X Genomics and a pair from Oxford Nanopore. Links to this post. Monday, June 08, 2015. BGI Unveils a Sequencing Factory to Go. When I was in George Churchs lab, he submitted a grant proposal (which, alas, was not funded) for a sequencing factory to generate one megabase. The Ion Tor...
omicsomics.blogspot.com
Omics! Omics!: Leaky clinical metagenomics pipelines are a very serious issue
http://omicsomics.blogspot.com/2015/07/leaky-clinical-metagenomics-pipelines.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Thursday, July 02, 2015. Leaky clinical metagenomics pipelines are a very serious issue. Update: Some significant issues with the tone of this post are discussed in a follow-up. The informatics methods used both in the case study and the paper in question were published as a separate paper in Genome Research. The other issue uncovered by Salzberg's group is also tr...
omicsomics.blogspot.com
Omics! Omics!: June 2015: Busting Out All Over with Genomics Technology
http://omicsomics.blogspot.com/2015/06/june-2015-busting-out-all-over-with.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Tuesday, June 30, 2015. June 2015: Busting Out All Over with Genomics Technology. 10X Genomics and a pair from Oxford Nanopore. Mountain for these technologies to summit are very large polyploid genomes. PacBio has a nice write-up on their blog. In case you don't (as I don't) have access to the paper in Nature Genetics. But nothing of real substance. Another hazy e...
omicsomics.blogspot.com
Omics! Omics!: The genomic history of a breast cancer revealed
http://omicsomics.blogspot.com/2009/10/genomic-history-of-breast-cancer.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Wednesday, October 07, 2009. The genomic history of a breast cancer revealed. A supplementary item that could easily be its own paper. One final thought: the next year will probably be filled with a lot of similar papers. Cancer genomics is gearing up in a huge way. With Wash U alone planning 150 genomes. 809-813 : 10.1038/nature08489. Incidentally, my Google alert...
omicsomics.blogspot.com
Omics! Omics!: Clinical Metagenomics Pipelines: Revisiting & Reflecting
http://omicsomics.blogspot.com/2015/07/clinical-metagenomics-pipelines.html
A computational biologists personal views on new technologies and publications on genomics and proteomics and their impact on drug discovery. Friday, July 10, 2015. Clinical Metagenomics Pipelines: Revisiting and Reflecting. Last week's piece concerned an F1000 paper by Steven Salzberg and colleagues which reanalyzed a clinical metagenomics dataset and alleged two serious problems. The first claim was that the software used in the paper failed to detect potential bacterial pathogens in the samples...
chburrus.wordpress.com
On Splitting Files… | Chad Burrus's Blog
https://chburrus.wordpress.com/2011/09/11/on-splitting-files
Chad Burrus's Blog. On Splitting Files…. Edit (2012/03/10): Updated the awk script to use “$0” instead of “$1” to prevent problems with spaces in FASTQ identifiers. Hat tip to Thasso via his comment below. Note: this is an older post I’ve had sitting around for a while–hope it helps someone. In bioinformatics, we often have to deal with huge FASTQ. The Illumina file into pieces, we could pull the reads we wanted out in parallel, and thus would get our results much faster than just waiting on the serial s...
chburrus.wordpress.com
Strange Loop 2010: Thursday | Chad Burrus's Blog
https://chburrus.wordpress.com/2010/10/17/strange-loop-2010-thursday
Chad Burrus's Blog. Strange Loop 2010: Thursday. Last week, I spent Thursday and Friday at the Strange Loop. Conference in St. Louis, Missouri. It turned out to be a pretty great conference, even if I missed out on a lot of interesting talks due to a school project I had to finish and a lot of time spent volunteering. The ones I did make it to were amazing, however. (You can access the slides for each of the talks at the Strange Loop presentations page. I started off with Hilary Mason. Better known as Ge...
chburrus.wordpress.com
Résumé | Chad Burrus's Blog
https://chburrus.wordpress.com/resume
Chad Burrus's Blog. This page represents my résumé on the web. You can download a PDF. Version if you like. Research Assistant, School of Informatics and Computing, Indiana University, Bloomington, Indiana. Jan. 2010 – present. Studying the principles of metagenomics. Developing methods to compare metagenomic samples. Writing Python and C code to analyze the differences in metagenomic samples. Developer Intern, Sentry Data Systems, Deerfield Beach, Florida. May 2010-Aug. 2010. Developer/Architect, LAT, I...
SOCIAL ENGAGEMENT