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  • Hawken SE, Washer LL, Williams CL, Newton DW, Snitkin ES. Genomic investigation of a putative endoscope-associated carbapenem resistant Enterobacter cloacae outbreak reveals a wide diversity of circulating strains and resistance mutations. Clin Infect Dis. Accepted.
  • Wang J, Foxman B, Mody L, Snitkin ES. A network of microbial and antibiotic interactions drive colonization and infection with multi-drug resistant organisms. Proc. Natl. Acad. Sci. Accepted.
  • Snitkin ES, Won S, Pirani A, Lapp Z, Weinstein RA, Lolans K, Hayden MK. Integrated genomic and patient transfer network analysis of a regional outbreak of bla-KPC Klebsiella pneumoniae. Sci Transl Med. Accepted.
  • Popovich KJ, Snitkin ES, Hota B, Green SJ, Pirani A, Aroutcheva A, Weinstein RA. Genomic and Epidemiological Evidence for Community Origins of Hospital-Onset Methicillin-Resistant Staphylococcus aureus Bloodstream Infections. J Infect Dis. 2017 May 9; PMID: 28486667
  • Popovich KJ, Snitkin ES. Whole Genome Sequencing—Implications for Infection Prevention and Outbreak Investigations. Curr Infect Dis Rep. 2017 Apr 1;19(4):15.


  • Popovich KJ, Snitkin E, Green SJ, Aroutcheva A, Hayden MK, Hota B, Weinstein RA. Genomic Epidemiology of USA300 Methicillin-Resistant Staphylococcus aureus in an Urban Community. Clin Infect Dis. 2016 Jan 1;


  • Snitkin ES, Segre JA. Pseudomonas aeruginosa adaptation to human hosts. Nat Genet. 2015 Jan;47(1):2–3.


  • Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai Y-C, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med. 2014 Sep 17;6(254):126–254.


  • Snitkin ES, Zelazny A, Gupta J, Palmore TN, Murray PR, Segre JA. Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment. Genome Res. 2013 Jul;23(7):1155–62.
  • Yang JY, Brooks S, Meyer JA, Blakesley RR, Zelazny AM, Segre JA*, Snitkin ES*. Pan-PCR, a Computational Method for Designing Bacterium-Typing Assays Based on Whole-Genome Sequence Data. J. Clin. Microbiol. 2013 Mar 1;51(3):752–8.


  • Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Segre JA. Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing. Sci Transl Med. 2012 Aug 22;4(148):148ra116–148ra116.


  • Snitkin ES, Zelazny AM, Montero CI, Stock F, Mijares L, Murray PR, Segre JA. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii. Proc. Natl. Acad. Sci. U.S.A. 2011 Aug 16;108(33):13758–63.
  • Snitkin ES, Segrè D. Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes. PLoS Genet. 2011 Feb 10;7(2):e1001294.


  • Grice EA, Snitkin ES, Yockey LJ, Bermudez DM, NISC Comparative Sequencing Program, Liechty KW, Segre JA. Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response. Proceedings of the National Academy of Sciences. 2010;107(33):14799 –14804


  • Mazumdar V, Snitkin ES, Amar S, Segre D. Metabolic Network Model of a Human Oral Pathogen. J. Bacteriol. 2009 Jan 1;191(1):74–90.
  • Linghu B, Snitkin E, Hu Z, Xia Y, DeLisi C. Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biology. 2009;10(9):R91.


  • Snitkin ES, Segrè D. Optimality criteria for the prediction of metabolic fluxes in yeast mutants. Genome Informatics 2008 - Proceedings of the 8th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2008). Zeuten Lake, Berlin, Germany; 2008. p. 123–34.
  • Snitkin E, Dudley A, Janse D, Wong K, Church G, Segre D. Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biol. 2008;9(9):R140.
  • Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics. 2008;9:119.
  • Hu Z, Snitkin ES, DeLisi C. VisANT: an integrative framework for networks in systems biology. Brief. Bioinform. 2008 Jul 1;9(4):317–25.


  • Snitkin ES*, Gustafson AM*, Mellor J, Wu J, DeLisi C. Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics. 2006;7:420.
  • Gustafson A*, Snitkin E*, Parker S, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics. 2006;7(1):265.


  • Wisniewski H-G, Snitkin ES, Mindrescu C, Sweet MH, Vilcek J. TSG-6 protein binding to glycosaminoglycans: formation of stable complexes with hyaluronan and binding to chondroitin sulfates. J. Biol. Chem. 2005 Apr 15;280(15):14476–84.

* Co-first or co-corresponding author