Provost Office Published Articles
https://hdl.handle.net/1808/57
2024-03-29T06:31:16ZFunding and the Future of U.S. Public Research Universities
https://hdl.handle.net/1808/14952
Funding and the Future of U.S. Public Research Universities
McPherson, Peter; Gobstein, Howard J.; Shulenburger, David E.
Innovation through research is a critical element to a nation's success in the highly competitive global marketplace. University research provides the base from which an important part of the most competitive innovations arise. The modern research university, with synergy flowing from a mix of research, graduate study and undergraduate instruction, is vital to simultaneously generating needed knowledge while also educating future generations of researchers and able graduates primed to take advantage of research findings. In the U.S. the very high proportion of research and graduate education done by public universities makes their futures key the future competitive success of the country.
This is the author's accepted manuscript. The original publication can be found at http://www.mitpressjournals.org/loi/itgg.
2010-03-01T00:00:00ZCISC controls and the union/non-union wage ratio
https://hdl.handle.net/1808/14935
CISC controls and the union/non-union wage ratio
Shulenburger, David E.; McLean, Robert; Rasch, Sara B.
This article was published in the Journal of Behavioral Economics, Vol 13: David Shulenburger, Robert A. McLean, Sara B. Rasch, CISC controls and the union/non-union wage ratio, Pages 57-66. Copyright Elsevier (1984).
1984-06-01T00:00:00ZOptimal External Memory Interval Management
https://hdl.handle.net/1808/13800
Optimal External Memory Interval Management
Arge, Lars; Vitter, Jeffrey Scott
In this paper we present the external interval tree, an optimal external memory data
structure for answering stabbing queries on a set of dynamically maintained intervals. The external
interval tree can be usedin an optimal solution to the dynamic interval management problem, which
is a central problem for object-orientedandtemp oral databases andfor constraint logic programming.
Part of the structure uses a weight-balancing technique for efficient worst-case manipulation
of balanced trees, which is of independent interest. The external interval tree, as well as our new
balancing technique, have recently been used to develop several efficient external data structures.
This is the publisher's version, which is being shared on KU Scholarworks with permission. The original version may be found at the following link: http://dx.doi.org/10.1137/S009753970240481X
2003-01-01T00:00:00ZΨ-RA: a parallel sparse index for genomic read alignment
https://hdl.handle.net/1808/12849
Ψ-RA: a parallel sparse index for genomic read alignment
Külekci, M. Oğuzhan; Hon, Wing-Kai; Shah, Rahul; Vitter, Jeffrey Scott; Xu, Bojian
Background
Genomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same species share the majority of their genomes, short reads alignment provides an alternative and much more efficient way to sequence the genome of a particular individual than does direct sequencing. Among many strategies proposed for this alignment process, indexing the reference genome and short read searching over the index is a dominant technique. Our goal is to design a space-efficient indexing structure with fast searching capability to catch the massive short reads produced by the next generation high-throughput DNA sequencing technology.
Results
We concentrate on indexing DNA sequences via sparse suffix arrays (SSAs) and propose a new short read aligner named Ψ-RA (PSI-RA: parallel sparse index read aligner). The motivation in using SSAs is the ability to trade memory against time. It is possible to fine tune the space consumption of the index based on the available memory of the machine and the minimum length of the arriving pattern queries. Although SSAs have been studied before for exact matching of short reads, an elegant way of approximate matching capability was missing. We provide this by defining the rightmost mismatch criteria that prioritize the errors towards the end of the reads, where errors are more probable. Ψ-RA supports any number of mismatches in aligning reads. We give comparisons with some of the well-known short read aligners, and show that indexing a genome with SSA is a good alternative to the Burrows-Wheeler transform or seed-based solutions.
Conclusions
Ψ-RA is expected to serve as a valuable tool in the alignment of short reads generated by the next generation high-throughput sequencing technology. Ψ-RA is very fast in exact matching and also supports rightmost approximate matching. The SSA structure that Ψ-RA is built on naturally incorporates the modern multicore architecture and thus further speed-up can be gained. All the information, including the source code of Ψ-RA, can be downloaded at: http://www.busillis.com/o_kulekci/PSIRA.zip webcite.
2011-07-27T00:00:00Z