Probe selection algorithms with applications in the analysis of microbial communities. - James Borneman; Marek Chrobak; Gianluca Della Vedova; Andres Figueroa; Tao Jiang 001 (ISMB (Supplement of Bioinformatics), 2001)

Clustering Binary Fingerprint Vectors with Missing Values for DNA Array Data Analysis. - Andres Figueroa; James Borneman; Tao Jiang 001 (J. Comput. Biol., 2004)

A Fast Algorithm for Approximate String Matching on Gene Sequences. - Zheng Liu; Xin Chen 037; James Borneman; Tao Jiang 001 (CPM, 2005)

Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses. - Katechan Jampachaisri; Lea Valinsky; James Borneman; S. James Press (Bioinform., 2005)

A software system for gene sequence database construction based on fast approximate string matching. - Zheng Liu; James Borneman; Tao Jiang 001 (Int. J. Bioinform. Res. Appl., 2005)

Algorithmic Approaches to Selecting Control Clones in DNA Array Hybridization Experiments. - Qi Fu; Elizabeth Bent; James Borneman; Marek Chrobak; Neal E. Young (J. Bioinform. Comput. Biol., 2007)

Polony Identification Using the EM Algorithm Based on a Gaussian Mixture Model. - Wei Li 035; Paul M. Ruegger; James Borneman; Tao Jiang 001 (BIBE, 2010)

Clustering Scatter Plots Using Data Depth Measures. - Zhanpan Zhang; Xinping Cui; Daniel R. Jeske; Xiaoxiao Li; Jonathan Braun; James Borneman (DMIN, 2010)

Separating Metagenomic Short Reads into Genomes via Clustering - (Extended Abstract). - Olga Tanaseichuk; James Borneman; Tao Jiang 001 (WABI, 2011)

Improving Probe Set Selection for Microbial Community Analysis by Leveraging Taxonomic Information of Training Sequences. - Paul M. Ruegger; Gianluca Della Vedova; Tao Jiang 001; James Borneman (BMC Bioinform., 2011)

A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads. - Olga Tanaseichuk; James Borneman; Tao Jiang 001 (WABI, 2012)

Separating metagenomic short reads into genomes via clustering. - Olga Tanaseichuk; James Borneman; Tao Jiang 001 (Algorithms Mol. Biol., 2012)

Biclustering scatter plots using data depth measures. - Zhanpan Zhang; Xinping Cui; Daniel R. Jeske; James Borneman (Stat. Anal. Data Min., 2013)

Phylogeny-based classification of microbial communities. - Olga Tanaseichuk; James Borneman; Tao Jiang 001 (Bioinform., 2014)

PRISE2: Software for designing sequence-selective PCR primers and probes. - Yu-Ting Huang; Jiue-in Yang; Marek Chrobak; James Borneman (BMC Bioinform., 2014)