In 1947 a Bedouin shepherd found a bunch of ancient scrolls in a cave near the Dead Sea. These scrolls, now known as the Dead Sea scrolls, included some of the oldest known Biblical texts as well as other Jewish religious writing. Over the next few decades, these scrolls - of …
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(with Camille Scott, Michael Crusoe, and Leigh Sheneman; Josh Rosenthal contributed to eel-pond; and Adina Howe contributed to kalamazoo)
This summer, I spent a lot of time writing up computational protocols for both mRNAseq and metagenome assembly in the Amazon cloud.
I'm happy to announce that they are now available …
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Question: What do Nick Loman, Jared Simpson, Lex Nederbragt, and I all have in common?
Answer: We all spend way too much time thinking about assembly.
Question: What does Jonathan Eisen's lab do?
Answer: Sequence lots of really weird things that they'd like to assemble.
Motivated by …
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The paper Howison et al., 2013, just appeared in early form in Bioinformatics. Here is my first round review, which they handily addressed in their revisions; since I was quite positive I felt I might as well post the whole thing, though.
Note that a relevant paper from Mihai Pop …
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Two papers on the Haemonchus contortus genome just came out (Schwarz et al. and Laing et al.), and I'm an author on one of them (Schwarz et al.). H. contortus, or Haemonch (as I affectionately called it) is a nasty parasitic nematode that feasts on the mucosal blood of ruminants …
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So, I got this grant. And, um, it looks like khmer has a future, which means... so does my lab.
What is khmer?
khmer is my lab's software for doing various things to sequencing data, and is largely focused on providing good demo implementations of low-memory data structures …
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(with Adina Howe, James Tiedje, Titus Brown)
I have been working on the assembly of big shotgun metagenomic data from ARMO (Amazon Rain Forest Microbial Observatory) project. The biggest challenge is the huge data size, 2TB in fastq and more than 6 billions reads after read trimming. One lucky thing …
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