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SNIT: SNP identification for strain typing.
Vijaya Satya R, Zavaljevski N, Reifman J. Vijaya Satya R, et al. Source Code Biol Med. 2011 Sep 8;6:14. doi: 10.1186/1751-0473-6-14. Source Code Biol Med. 2011. PMID: 21902825 Free PMC article.
A high-throughput pipeline for the design of real-time PCR signatures.
Vijaya Satya R, Kumar K, Zavaljevski N, Reifman J. Vijaya Satya R, et al. BMC Bioinformatics. 2010 Jun 23;11:340. doi: 10.1186/1471-2105-11-340. BMC Bioinformatics. 2010. PMID: 20573238 Free PMC article.
In silico microarray probe design for diagnosis of multiple pathogens.
Vijaya Satya R, Zavaljevski N, Kumar K, Bode E, Padilla S, Wasieloski L, Geyer J, Reifman J. Vijaya Satya R, et al. BMC Genomics. 2008 Oct 21;9:496. doi: 10.1186/1471-2164-9-496. BMC Genomics. 2008. PMID: 18940003 Free PMC article.
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays.
Vijaya Satya R, Zavaljevski N, Kumar K, Reifman J. Vijaya Satya R, et al. BMC Bioinformatics. 2008 Apr 10;9:185. doi: 10.1186/1471-2105-9-185. BMC Bioinformatics. 2008. PMID: 18402679 Free PMC article.
An efficient algorithm for Perfect Phylogeny Haplotyping.
Vijayasatya R, Mukherjee A. Vijayasatya R, et al. Proc IEEE Comput Syst Bioinform Conf. 2005:103-10. doi: 10.1109/csb.2005.12. Proc IEEE Comput Syst Bioinform Conf. 2005. PMID: 16447968
Thermodynamic basis for the emergence of genomes during prebiotic evolution.
Woo HJ, Vijaya Satya R, Reifman J. Woo HJ, et al. Among authors: vijaya satya r. PLoS Comput Biol. 2012 May;8(5):e1002534. doi: 10.1371/journal.pcbi.1002534. Epub 2012 May 31. PLoS Comput Biol. 2012. PMID: 22693440 Free PMC article.
An optimal algorithm for perfect phylogeny haplotyping.
Vijayasatya R, Mukherjee A. Vijayasatya R, et al. J Comput Biol. 2006 May;13(4):897-928. doi: 10.1089/cmb.2006.13.897. J Comput Biol. 2006. PMID: 16761918
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.
Razavi P, Li BT, Brown DN, Jung B, Hubbell E, Shen R, Abida W, Juluru K, De Bruijn I, Hou C, Venn O, Lim R, Anand A, Maddala T, Gnerre S, Vijaya Satya R, Liu Q, Shen L, Eattock N, Yue J, Blocker AW, Lee M, Sehnert A, Xu H, Hall MP, Santiago-Zayas A, Novotny WF, Isbell JM, Rusch VW, Plitas G, Heerdt AS, Ladanyi M, Hyman DM, Jones DR, Morrow M, Riely GJ, Scher HI, Rudin CM, Robson ME, Diaz LA Jr, Solit DB, Aravanis AM, Reis-Filho JS. Razavi P, et al. Among authors: vijaya satya r. Nat Med. 2019 Dec;25(12):1928-1937. doi: 10.1038/s41591-019-0652-7. Epub 2019 Nov 25. Nat Med. 2019. PMID: 31768066 Free PMC article. Clinical Trial.
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