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Sequencing and Annotation

Sequencing and Annotation

The annotation of genomes from high-throughput sequencing platforms needs to be rapid, high-throughput, automated, and fully integrated with any downstream analysis. We have deployed software systems for DoD high-performance computing assets for protein function annotation (PIPA), enzyme classification (CatFam), and strain identification (SNIT). Furthermore, we have developed a complete storage and annotation system for microbioal genome sequences (AGeS), with multiple functionalities.

Software

Publications

Woo, H. J., C. Yu, and J. Reifman. Collective genetic interaction effects and the role of antigen-presenting cells in autoimmune diseases. PLOS ONE. 2017 January 12; 12(1):e0169918. [PDF 7248 KB]

Woo, H. J., C. Yu, K. Kumar, B. Gold, and J. Reifman. Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism. BMC Genomics. 2016 August 30; 17:695. [PDF 2650 KB]

Hang, J., V. Desai, N. Zavaljevski, Y. Yang, X. Lin, R. V. Satya, L. J. Martinez, J. M. Blaylock, R. G. Jarman, S. J. Thomas, and R. A. Kuschner. 16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles. Microbiome. 2014 September 16; 2:31. [PDF 2454 KB]

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 1983 KB]

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 315 KB]

Kumar, K., V. Desai, L. Cheng, M. Khitrov, D. Grover, R. V. Satya, C. Yu, N. Zavaljevski, and J. Reifman. AGeS: a software system for microbial genome sequence annotation. PLOS ONE. 2011 March; 6(3):e17469. [PDF 439 KB]

Yu, C., N. Zavaljevski, V. Desai, and J. Reifman. Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases. Proteins. 2009 February 1; 74:449-460. [PDF 321 KB]

Yu, C., N. Zavaljevski, V. Desai, S. Johnson, F. J. Stevens, and J. Reifman. The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. BMC Bioinformatics. 2008 January 29; 9:52. [PDF 545 KB]

Yu, C., and P. A. Wilson. A tool for creating and parallelizing bioinformatics pipelines. Proceedings of the HPCMP Users Group Conference. Pittsburgh, PA. 2007 June 18-22; 417-420. [PDF 769 KB]

Yu, C., N. Zavaljevski, F. J. Stevens, K. Yackovich, and J. Reifman. Classifying noisy protein sequence data: a case study of immunoglobulin light chains. Bioinformatics. 2005 June; 21(1):i495-501. [PDF 97 KB]

Chen, D., D. Hua, X. Cheng, and J. Reifman. Gene selection for multiclass prediction of microarray data. Proceedings of the IEEE Computer Society Bioinformatics Conference. Stanford, CA. 2003 August 11-14; 492-495. [PDF 994 KB]

Zavaljevski, N., F. J. Stevens, and J. Reifman. Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions. Bioinformatics. 2002 May; 18(5):689-696. [PDF 115 KB]

Reifman, J., N. Zavaljevski, and F. J. Stevens. Support vector machines for protein functional classification. Proceedings of the International Conference on Bioinformatics. Bangkok, Thailand. 2002 February 6-8; O-BH-02. [PDF 123 KB]