2021

• Topçuoğlu BD, Lapp Z, Sovacool KL, Snitkin E, Wiens J, Schloss PD. mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. J Open Source Softw. 2021;6(61):3073. PMCID: PMC8372219

• Sansom SE, Benedict E, Thiede SN, Hota B, Aroutcheva A, Payne D, Zawitz C, Snitkin ES, Green SJ, Weinstein RA, Popovich KJ. Genomic Update of Phenotypic Prediction Rule for Methicillin-Resistant Staphylococcus aureus (MRSA) USA300 Discloses Jail Transmission Networks with Increased Resistance. Microbiol Spectr. 2021 Jul 21;e0037621. PMID: 34287060

• Popovich KJ*, Thiede SN*, Zawitz C, Aroutcheva A, Payne D, Janda W, Schoeny M, Green SJ, Snitkin ES, Weinstein RA. Genomic Epidemiology of MRSA During Incarceration at a Large Inner-City Jail. Clin Infect Dis. 2021 Jan 4; PMID: 33395473

• Miles-Jay A, Young VB, Pamer EG, Savidge TC, Kamboj M, Garey KW, Snitkin ES. A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains. Microb Genom. 2021 Jun;7(6). PMID: 34180789

• Lapp Z, Han JH, Wiens J, Goldstein EJC, Lautenbach E, Snitkin ES. Patient and Microbial Genomic Factors Associated with Carbapenem-Resistant Klebsiella pneumoniae Extraintestinal Colonization and Infection. mSystems. 2021 Mar 16;6(2). PMID: 33727393

• Lapp Z, Crawford R, Miles-Jay A, Pirani A, Trick WE, Weinstein RA, Hayden MK, Snitkin ES*, Lin MY*. Regional spread of blaNDM-1-containing Klebsiella pneumoniae ST147 in post-acute care facilities. Clin Infect Dis. 2021 May 17; PMID: 33999991

• Crawford RD, Snitkin ES. cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets. BMC Bioinformatics. 2021 Feb 15;22(1):70. PMCID: PMC7885345

• Anderson MT, Brown AN, Pirani A, Smith SN, Photenhauer AL, Sun Y, Snitkin ES, Bachman MA, Mobley HLT. Replication Dynamics for Six Gram-Negative Bacterial Species during Bloodstream Infection. mBio. 2021 Jul 6;e0111421. PMID: 34225485

• Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning. Trends Microbiol. 2021 Jan 14; PMID: 3345584

2020

• Steinberg HD, Snitkin ES. Homologous Recombination in Clostridioides difficile Mediates Diversification of Cell Surface Features and Transport Systems. mSphere. 2020 Nov 18;5(6). PMCID: PMC7677006

• Saund K, Snitkin ES. Hogwash: three methods for genome-wide association studies in bacteria. Microb Genom. 2020 Nov;6(11). PMCID: PMC7725327

• Wang J, Foxman B, Pirani A, Lapp Z, Mody L, Snitkin E. Application of combined genomic and transfer analyses to identify factors mediating regional spread of antibiotic resistant bacterial lineages. Clin Infect Dis. 2020 Apr 2

• Wang J, Cassone M, Gibson K, Lansing B, Mody L, Snitkin ES*, Rao K.* Gut microbiota features on nursing home admission are associated with subsequent acquisition of antibiotic resistant organism colonization. Clin Infect Dis. 2020 Jun 1

• Saund K, Rao K, Young VB, Snitkin ES. Genetic Determinants of Trehalose Utilization Are Not Associated With Severe Clostridium difficile Infection Outcome. Open Forum Infect Dis. 2020 Jan;7(1):ofz548

• Saund K*, Lapp Z*, Thiede SN*, Pirani A, Snitkin ES. prewas: data pre-processing for more informative bacterial GWAS. Microb Genom. 2020 May;6(5)

• Porter NT, Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, Martens EC. Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. Nat Microbiol. 2020 Jun 29

• Popovich KJ, Green SJ, Okamoto K, Rhee Y, Hayden MK, Schoeny M, Snitkin ES, Weinstein RA. MRSA transmission in ICUs: Genomic analysis of patients, their environments and healthcare workers. Clin Infect Dis. 2020 Jun 6

• Hawken SE, Hayden MK, Lolans K, Yelin RD, Weinstein RA, Lin MY, Snitkin ES. Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp)-positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH). Infect Control Hosp Epidemiol. 2020 Jun 23;1–7

• Davis E, Hicks L, Ali I, Salzman E, Wang J, Snitkin E, Gibson K, Cassone M, Mody L, Foxman B. Epidemiology of Vancomycin-Resistant Enterococcus faecium and Enterococcus faecalis Colonization in Nursing Facilities. Open Forum Infect Dis. 2020 Jan;7(1):ofz553

• Cassone M, Zhu Z, Mantey J, Gibson KE, Perri MB, Zervos MJ, Snitkin ES, Foxman B, Mody L. Interplay Between Patient Colonization and Environmental Contamination With Vancomycin-Resistant Enterococci and Their Association With Patient Health Outcomes in Postacute Care. Open Forum Infect Dis. 2020 Jan;7(1):ofz519.

2019

• Sintsova A, Frick-Cheng AE, Smith S, Pirani A, Subashchandrabose S, Snitkin ES, Mobley H. Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs. Helaine S, Ferguson NM, Westermann A, editors. eLife. 2019 Oct 21;8:e49748

• Popovich KJ, Snitkin ES, Zawitz C, Aroutcheva A, Payne D, Thiede SN, Schoeny M, Green SJ, Hayden MK, Hota B, Weinstein RA. Frequent Methicillin-Resistant Staphylococcus aureus Introductions Into an Inner-city Jail: Indications of Community Transmission Networks. Clin Infect Dis, 2019

• Han JH, Lapp Z, Bushman F, Lautenbach E, Goldstein EJC, Mattei L, Hofstaedter CE, Kim D, Nachamkin I, Garrigan C, Jain T, Bilker W, Wolford HM, Slayton RB, Wise J, Tolomeo P, Snitkin ES. Whole-Genome Sequencing To Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission within and between Regional Long-Term Acute-Care Hospitals. Antimicrobial Agents and Chemotherapy. 2019 Nov 1;63(11):e01622-19. PMID: 3145149

• Mau T, Eckley SS, Bergin IL, Saund K, Villano JS, Vendrov KC, Snitkin ES, Young VB, Yung R. Outbreak of Murine Infection with Clostridium difficile Associated with the Administration of a Pre- and Perinatal Methyl Donor Diet. mSphere. 2019 Apr 24;4(2):e00138-19. PMID: 3089443

• Snitkin ES. Contamination of Hospital Plumbing: A Source or a Sink for Antibiotic-Resistant Organisms? JAMA Netw Open. 2019 Feb 1;2(2):e187660–e187660

• Hughes HY, Odom RT, Michelin AV, Snitkin ES, Sinaii N, Milstone AM, Henderson DK, Palmore TN. A retrospective cohort study of antibiotic exposure and vancomycin-resistant Enterococcus recolonization. Infection Control & Hospital Epidemiology. 2019;1–6

2018

• Eaton K, Pirani A, Snitkin ES, Reproducibility Project: Cancer Biology. Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota. eLife. 2018 Oct 3;7:e34364

• Martin RM, Cao J, Wu W, Zhao L, Manthei DM, Pirani A, Snitkin E, Malani PN, Rao K, Bachman MA. Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients. mSystems. 2018 Jun 26;PMCID: PMC6020474

• Forsyth VS, Armbruster CE, Smith SN, Pirani A, Springman AC, Walters MS, Nielubowicz GR, Himpsl SD, Snitkin ES, Mobley HLT. Rapid Growth of Uropathogenic Escherichia coli during Human Urinary Tract Infection. mBio. 2018 May 2;9(2):e00186-18. PMID: 2951107

• Hawken SE, Snitkin ES. Genomic epidemiology of multidrug-resistant Gram-negative organisms. Ann N Y Acad Sci. 2018 Mar 31; PMID: 29604079

2017

• 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 , 2017

• Wang J, Foxman B, Mody L, Snitkin ES. Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms. PNAS. 2017 Sep 26;114(39):10467–10472. PMID: 28900004

• Snitkin ES, Won S, Pirani A, Lapp Z, Weinstein RA, Lolans K, Hayden MK. Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak. Science Translational Medicine. 2017 Nov 22;9(417):eaan0093.

• 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.

2016

• 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;

2015

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

2014

• 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.

2013

• 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.

2012

• 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.

2011

• 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.

2010

• 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

2009

• 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.

2008

• 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.

2006

• 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.

2005

• 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