Research Projects
BIOINFORMATICS SOFTWARE
Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LDF, Petruska JC, Rouchka EC:categoryCompare, an analytical tool based on feature annotations.Frontiers in Genetics 2014, 5:98. doi: 10.3389/fgene.2014.00098
Available as R bioconductor package
Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC: AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities.BMC Bioinformatics 2012, 13:229. doi:10.1186/1471-2105-13-229.
Available as web interface and virtual machine
Rouchka EC, Khalyfa A, Cooper NGF. (2005) MPrime: efficient large scale multiple primer and oligonucleotide design for cutomized gene arrays. BMC Bioinformatics, 6:175. (doi:10.1186/1471-2105-6-175).
Available as a web interface
Rouchka, EC. (2010) Database of exact tandem repeats in the Zebrafish genome.BMC Genomics11:347. doi:10.1186/1471-2164-11-347
Available as a web interface and genome browser tracks
Rouchka EC, Hardin CT (2007). rMotifGen: random motif generator for DNA and protein sequences.BMC Bioinformatics, 8:292. (doi:10.1186/1471-2105-8-292).
Available as a web interface and source code
Mahdi RN, Rouchka EC. (2009) RBF-TSS: Identification of transcription start site in human using radial basis functions network and oligonucleotide positional freqeuncies.PLoS One, 4(3):e4878. (10.1371/journal.pone.0004878)
Available as source code
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J,"DiffSplice: the genome-wide detection of differential splicing events with RNA-seq", Nucleic Acids Res. 2013 Jan;41(2):e39. (doi:10.1093/nar/gks1026)
Available as source code
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J: MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research 2010; (doi: 10.1093/nar/gkq622)
Available as source code
Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu Z: A probabilistic framework for aligning paired-end RNA-seq data. Bioinformatics 2010, 26(16):1950-1957. (doi"101093/bioinformatics/btq336).
Available as source code
Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF: FDM: A graph-based statistical method to detect differential transcription using RNA-seq data.Bioinformatics 2011, 27(19)2633-2640. (doi: 10.1093/bioinformatics/btr458).
Available as source code
Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J: A robust method for transcript quantification with RNA-seq data. J Comput Biol 2013, 20(3):167-187. (doi: 10.1089/cmb.2012.0230)
Available as source code
Huang Y, Hu Y, Liu J: Piecing the Puzzle Together: a Revisit to Transcript Reconstruction Problem in RNA-seq. RECOMB-seq: fourth annual RECOMB satellite workshop on massively parallel sequencing 2012.
Available as source code
Carreer WJ, Flight RM, Moseley HNB: A Computational Framework for High-Throughput Isotopic Natural Abundance Correction of Omics-Level Ultra-High Resolution FT-MS Datasets. Metabolites 2013, 3(4):853-866. (doi: 10.3390/metabo3040853).
Available as source code
Barton MD, Barton HA: Genomer: A swiss army knife for genome scaffolding. PLoS One 2013, 8(6):e66922. (doi: 10.1371/journal.pone.0066922).
Available as source code
Kim S, Li L: A novel global search algorithm for nonlinear mixed-effects models using particle swarm optimization. J Pharmacokinet Pharmacodyn 2011, 38(4): 471-495. (doi: 10.1007/s10928-011-9204-6).
Available as source code upon request