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+Visiting U. Arizona
+:author: C\. Titus Brown
+:tags: all_the_things,assembly,metagenomics,mrnaseq,neural_crest
+:date: 2012-08-12
+:slug: raising-arizona
+:category: science
+I'll be visiting the University of Arizona (the one in Tucson) in a week,
+Mon Aug 20th - Wed Aug 22nd. I offered to give one of three talks and
+they said "how about all three?" Uh, ok, I guess...
+If you are at U of A and want to meet up, let me know. I can see if
+there is room during meals esp; some of my breakfasts look
+suspiciously non-meetinged :).
+Without further ado:
+EEB Seminar
+Monday, 3:30-5pm, BioSciences West rm 208.
+**Visiting the Undiscovered Country: exploring non-model organisms and
+microbial communities with next-gen sequencing**
+(No abstract requested, but I blog about it a lot :)
+CSE Seminar
+Tuesday, 10:30am-12pm, room TBD.
+**Streaming lossy compression of biological sequence data using
+probabilistic data structures**
+ In recent years, next-generation DNA sequencing capacity has
+ completely outstripped our ability to computationally digest the
+ resulting volume of data. Driven by the need to actually analyze
+ the data, our lab has developed a suite of novel data structures and
+ algorithms for graph compression and data reduction; in addition to
+ being darned efficient on their own, our approaches make use of
+ probabilistic data structures that enable substantially lower memory
+ usage than the best possible exact approach. Using these approaches
+ we have been able to scale de novo data assembly approaches down to
+ cloud computing infrastructure, and we have also completed some of
+ the largest de novo assemblies of metagenomes ever done. Last but
+ not least, these approaches show the way to essentially infinite de
+ novo assembly of environmental microbial data.
+Biomedical Seminar
+Wednesday, 8:30am - 10am, Bio5 rm 103.
+**Sensitive detection of splice isoforms from mRNAseq data**
+ We can now deeply and quantitatively sample transcriptomes with
+ relative ease, but analyzing the data is more challenging: while
+ before researchers could largely ignore splice variants, mRNAseq has
+ shed quite a bit of light on the large diversity of splice isoforms
+ present in vertebrate tissue. Recovering these splice variants from
+ the data is difficult even with a good reference genome, but many
+ model organisms do not have sufficiently high quality genome
+ sequences for reference-based approaches to work. We have been
+ working on analyzing transcriptomes from chick development (neural
+ crest) and disease (Marek's Disease) as well as lamprey nerve chord
+ regeneration, and have developed a range of approaches for improving
+ the recovery of isoforms from mRNAseq data. I will also talk about
+ underacknowledged challenges in quantification, tissue-specific mRNA
+ isolation approaches, and detection of genome misassemblies using
+ mRNAseq.
+On the plus side, I will finally be able to show off the range of work
+my lab *actually* does. On the minus side, I am clearly schizophrenic
+- or would that be "possessed of multiple personalities"?
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