Information Technology Services

Nathan T. Weeks

Contact

LAST_NAME@iastate.edu (replace LAST_NAME with my surname)

Current Affiliations

• Systems Analyst II, High Performance Computing Group (ITS), Iowa State University
• IT Specialist, USDA Agricultural Research Service Corn Insects and Crop Genetics Research Unit
• Member, Upsilon Pi Epsilon
• Member, Golden Key International Honour Society

Education

M.S. Computer Science, Iowa State University 2012

B.S. Mathematics, South Dakota State University 2003
B.S. Computer Science, South Dakota State University 2002

Research Interests

Bioinformatics, Parallelism and Concurrency

Software

ipcmd - A command-line interface to SysV semaphores and message queues

Publications

In Press

• Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J, Couger M, Eccles D, Li B, Lieber M, MacManes M, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey C, Henschel R, LeDuc R, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nature Protocols. [In Press]

2013

• Weeks NT, Kraeva M, Luecke G. ipcmd: a command-line interface to System V semaphores and message queues. Concurrency Computat.: Pract. Exper. [Published online ahead of print 2013 Jan 29]. doi: 10.1002/cpe.3001

2012

• Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra B, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma T, May GD, Singh NK, Varshney RK. A comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms. Molecular Plant. 2012 Sep.

2011

• Woody JL, Severin AJ, Bolon YT, Joseph B, Diers BW, Farmer AD, Weeks N, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 2011 Jan;54(1):10-8.

2010

• Bolon YT, Joseph B, Cannon SB, Graham MA, Diers BW, Farmer AD, May GD, Muehlbauer GJ, Specht JE, Tu ZJ, Weeks N, Xu WW, Shoemaker RC, Vance CP. Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biol. 2010 Mar 3;10(1):41.
• Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics. 2010 Jan 15;11(1):38.

Technical Reports

Daniel Steinwand, Brian Davis, Nathan Weeks, "GeoWall: Investigations into Low-cost Stereo Display Systems", 2002 USGS Open File Report.", 2002 USGS Open File Report

Teaching Experience

Spring 2003, Math 102 - College Algebra (at South Dakota State University)

News Articles

"Lab harvests kernels of information." Iowa Farmer Today 4 Feb. 2009.

"Iowa State now home to crop genomics lab." Feedstuffs 17 Nov. 2008.

Other Work

2012

• Acknowledged in: Miller N, Jing S, Sappington TW. High-Throughput Transcriptome Sequencing for SNP and Gene Discovery in a Moth. Environmental Entomology. 2012 Aug.
• Acknowledged in: Henschel R, Nista PM, Lieber M, Haas BJ, Wu L. Trinity RNA-Seq assembler performance optimization. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond. XSEDE '12. doi: 10.1145/2335755.2335842.

2011

• Acknowledged in: Severin AJ, Cannon SB, Graham MM, Grant D, Shoemaker RC. Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy. Plant Cell. 2011 Sep;23(9):3129-36. Epub 2011 Sep 13.
• Acknowledged in: Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J. 2011 May 25. doi: 10.1111/j.1467-7652.2011.00625.x. [Epub ahead of print]
• Acknowledged in: Bolon YT, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol. 2011 May;156(1):240-53. Epub 2011 Feb 14.

2010

• Acknowledged in: Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biol. 2010 Aug 5;10(1):160.
• Acknowledged in: Severin AJ, Peiffer GA, Xu WW, Hyten DL, Bucciarelli B, O'Rourke JA, Bolon YT, Grant D, Farmer AD, May GD, Vance CP, Shoemaker RC, Stupar RM. An integrative approach to genomic introgression mapping. Plant Physiol. 2010 Sep;154(1):3-12. Epub 2010 Jul 23.
• Acknowledged in: Cannon SB, Ilut D, Farmer AD, Maki SL, May GD, Singer SR, Doyle JJ. Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes. PLoS One. 2010 Jul 16;5(7):e11630.
• Acknowledged in: Peto M, Grant DM, Shoemaker RC, Cannon SB. Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences. Adv Bioinformatics. 2010. pii: 976792.
• Acknowledged in: Du J et al. SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics. 2010 Feb 17;11(1):113.
• Acknowledged in: Schmutz J et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010 Jan 14;463(7278):178-83.
• Acknowledged in: Grant D et al. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010 Jan;38 (Database issue):D843-6.

2009

• Bio::DB::SeqFeature::Store::DBI::SQLite - Perl module for the storage and retrieval of sequence annotation data using an SQLite database. I created this from the existing MySQL version, then contributed it to the bioperl project.
• mpipipe - MPI-based parallelized Unix pipe for serial filter programs (final project for Com S 525 "Numerical Analysis of High Performance Computing") [presentation, manual page].
• EST_GENOME_GPU - GPU program (based on EST_GENOME) for spliced alignment of transcript sequences to genomic DNA. A "finished" CUDA version and preliminary OpenCL port were done. Final project for Com S 590 "Research and Development in GPU Computing with CUDA". [presentation].