Hui Hsien Chou
Affiliation: Iowa State University
- A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genesYoung Su Seo
Department of Plant Pathology, University of California, Davis, CA 95616, USA
BMC Microbiol 8:99. 2008..XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174...
- DNA sequence quality trimming and vector removalH H Chou
Department of Zoology and Genetics, Department of Computer Science, Iowa State University, Ames, IA 50011, USA
Bioinformatics 17:1093-104. 2001..This step is necessary before other genomic data processing stages can be carried out, such as fragment assembly or EST clustering. A specialized tool is therefore needed to solve this apparent dilemma...
- Shared probe design and existing microarray reanalysis using PICKYHui Hsien Chou
Department of Genetics, Development and Cell Biology, and Department of Computer Science, Iowa State University, Ames, IA, 50011 3223, USA
BMC Bioinformatics 11:196. 2010....
- Direct calibration of PICKY-designed microarraysHui Hsien Chou
Department of Genetics, Development and Cell Biology and Department of Computer Science, Iowa State University, Ames, IA 50011, USA
BMC Bioinformatics 10:347. 2009..Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples...
- VECT: an automatic visual Perl programming tool for nonprogrammersHui Hsien Chou
Department of Genetics, Development and Cell Biology and Computer Science, Iowa State University, Ames, IA 50011, USA
Biotechniques 38:615-21. 2005..VECT is released under the GNU General Public License and is freely available for all major computing platforms including Macintosh OS X, Linux, and Microsoft Windows at www.complex.iastate.edu...
- UBViz: a software tool for exploring metabolic pathways in 3-D spaceSong Li
Iowa State University, Ames, IA 50011, USA
Biotechniques 38:540, 542. 2005
- GRAMA: genetic mapping analysis of temperature gradient capillary electrophoresis dataPhilip M Maher
Department of Computer Science, Iowa State University, 503 Science II, Ames, IA 50011, USA
Theor Appl Genet 113:156-62. 2006..GRAMA is written in Java and is freely available at http://www.complex.iastate.edu ...
- Efficient combination of multiple word models for improved sequence comparisonXiaoqiu Huang
Department of Computer Science, Iowa State University, Ames, IA 50011 1040, USA
Bioinformatics 20:2529-33. 2004..Studies of efficient and sensitive sequence comparison methods are driven by a need to find homologous regions of weak similarity between large genomes...
- LUCY2: an interactive DNA sequence quality trimming and vector removal toolSong Li
Department of Computer Science, Iowa State University, Ames, IA 50011, USA
Bioinformatics 20:2865-6. 2004..Source code is also available for porting to the other platforms. AVAILABILITY: Lucy2 is distributed under the GNU General Public License and can be downloaded from www.complex.iastate.edu..
- Nearly identical paralogs: implications for maize (Zea mays L.) genome evolutionScott J Emrich
Interdepartmental Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa 50011, USA
Genetics 175:429-39. 2007..As such, NIPs may have played important roles during the evolution and domestication of maize and may contribute to the success of long-term selection experiments in this important crop species...
- Whole-genome thermodynamic analysis reduces siRNA off-target effectsXi Chen
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
PLoS ONE 8:e58326. 2013..Therefore, we recommend including Picky as an additional screening step in siRNA design...
- Picky: oligo microarray design for large genomesHui Hsien Chou
Bioinformatics 20:2893-902. 2004..Also, many existing tools operate in a batch mode that does not assure best designs...
- Visual Data Extraction and Conversion Programming ToolHui Hsien Chou; Fiscal Year: 2005..Therefore, this tool will provide great enabling power to biomedical scientists to help them make rapid advances in biomedical research and medicine. ..