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PATHOGEN DIAGNOSTICS

Pathogen Diagnostics

We aim to design probes for multiple bacterial and viral pathogens by identifying probes from the input target sequences that are unique with respect to all available non-target sequences. We customize these probes with respect to the diagnostic platform (currently supported for microarray and PCR data). The strain-typing algorithm uses single-nucleotide polymorphisms (SNPs) and small insertions or deletions to identify closely related strains from the same species.

Software

Publications

Vijaya Satya, R., N. Zavaljevski, and J. Reifman. A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Research. 2012 September 1; 40(16):e127. [PDF]

Yu, C., V. Desai, L. Cheng, and J. Reifman. QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. BMC Bioinformatics. 2012 June 22; 13:143. [PDF]

Vijaya Satya, R., N. Zavaljevski, and J. Reifman. SNIT: SNP identification for strain typing. Source Code Biology and Medicine. 2011 September 8; 6:14. [PDF]

Kumar, K., V. Desai, L. Cheng, M. Khitrov, D. Grover, R. Vijaya Satya, C. Yu, N. Zavaljevski, and J. Reifman. A web-based high-throughput tool for next-generation sequence annotation. Proceedings of the HPCMP Users Group Conference. Portland, OR. 2011 June 20-24; 320-326. [PDF]

Vijaya Satya, R., K. Kumar, N. Zavaljevski, and J. Reifman. A high-throughput pipeline for the design of real-time PCR signatures. BMC Bioinformatics. 2010 June 23; 11:340. [PDF]

Vijaya Satya, R., K. Kumar, N. Zavaljevski, and J. Reifman. Parallel implementation of a bioinformatics pipeline for the design of pathogen diagnostic assays. Proceedings of the HPCMP Users Group Conference. San Diego, CA. 2009 June 15-19; 213-218. [PDF]

Vijaya Satya, R., N. Zavaljevski, K. Kumar, E. Bode, S. Padilla, L. Wasieloski, J. Geyer, and J. Reifman. In silico microarray probe design for diagnosis of multiple pathogens. BMC Genomics. 2008 October 21; 9:496. [PDF]

Yu, C., V. Desai, N. Zavaljevski, and J. Reifman. PIPA: a high-throughput pipeline for protein function annotation. Proceedings of the HPCMP Users Group Conference. Seattle, WA. 2008 July 14-17; 241-246. [PDF]

Vijaya Satya, R., N. Zavaljevski, K. Kumar, and J. Reifman. A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinformatics. 2008 April 12; 9:185. [PDF]

Tembe, W., N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson, and J. Reifman. Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics. 2007 January 1; 23(1):5-13. [PDF]

Draghici, S., P. Khatri, Y. Liu, K. J. Chase, E. A. Bode, D. A. Kulesh, L. P. Wasieloski, D. A. Norwood, and J. Reifman. Identification of genomic signatures for the design of assays for the detection and monitoring of anthrax threats. Proceedings of the Pacific Symposium on Biocomputing. Maui, HI. 2005 January 4-8; 10:248-259. [PDF]

Draghici, S., D. Chen, and J. Reifman. Applications and challenges of DNA microarray technology in military medical research. Military Medicine. 2004 August; 169(8):654-659. [PDF]