Publications

2020

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential.
Moser KA, Drábek EF, Dwivedi A, Stucke EM, Crabtree J, Dara A, Shah Z, Adams M, Li T, Rodrigues PT, Koren S, Phillippy AM, Munro JB, Ouattara A, Sparklin BC, Dunning Hotopp JC, Lyke KE, Sadzewicz L, Tallon LJ, Spring MD, Jongsakul K, Lon C, Saunders DL, Ferreira MU, Nyunt MM, Laufer MK, Travassos MA, Sauerwein RW, Takala-Harrison S, Fraser CM, Sim BKL, Hoffman SL, Plowe CV, Silva JC.
Genome Med. 12(1):6. doi: 10.1186/s13073-019-0708-9.
PMID: 31915075

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.
Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC.
Microb Genom. 6(1). doi: 10.1099/mgen.0.000320.
PMID: 31851607

Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples.
Shah Z, Adams M, Moser KA, Shrestha B, Stucke EM, Laufer MK, Serre D, Silva JC, Takala-Harrison S.
Malar J. 19(1):135. doi: 10.1186/s12936-020-03195-8.
PMID: 32228559

Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression.
Sa JM, Cannon MV, Caleon RL, Wellems TE, Serre D.
PLoS Biol. 18(5):e3000711. doi: 10.1371/journal.pbio.3000711. [Epub ahead of print]
PMID: 32365102

2019

Candida albicans quorum-sensing molecule farnesol modulates staphyloxanthin production and activates the thiol-based oxidative-stress response in Staphylococcus aureus.
Vila T, Kong EF, Ibrahim A, Piepenbrink K, Shetty AC, McCracken C, Bruno V, Jabra-Rizk MA.
Virulence. 10(1):625-642. doi:10.1080/21505594.2019.1635418.
PMID: 31280653

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.
Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC.
Microb Genom. 6(1). doi: 10.1099/mgen.0.000320.
PMID: 31851607

Using Core Genome Alignments To Assign Bacterial Species.
Chung M, Munro JB, Tettelin H, Dunning Hotopp JC.
mSystems.3(6). pii: e00236-18. doi: 10.1128/mSystems.00236-18. eCollection 2018 Nov-Dec.
PMID: 30534598

Multispecies Transcriptomics Data Set of Brugia malayi, Its Wolbachia Endosymbiont wBm, and Aedes aegypti across the B. malayi Life Cycle.
Chung M, Teigen L, Libro S, Bromley RE, Kumar N, Sadzewicz L, Tallon LJ, Foster JM, Michalski ML, Dunning Hotopp JC.
Microbiol Resour Announc. 7(18). pii: e01306-18. doi: 10.1128/MRA.01306-18. eCollection 2018 Nov.
PMID: 30533772

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics.
Chung M, Teigen LE, Libro S, Bromley RE, Olley D, Kumar N, Sadzewicz L, Tallon LJ, Mahurkar A, Foster JM, Michalski ML, Dunning Hotopp JC.
mSystems. 4(6). pii: e00596-19. doi: 10.1128/mSystems.00596-19.
PMID: 31796568

Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae.
Gasser MT, Chung M, Bromley RE, Nadendla S, Dunning Hotopp JC.
Microbiol Resour Announc. 8(43). pii: e01136-19. doi: 10.1128/MRA.01136-19.
PMID: 31649084

Genomic and Phenotypic Diversity among Ten Laboratory Isolates of Pseudomonas aeruginosa PAO1.
Chandler CE, Horspool AM, Hill PJ, Wozniak DJ, Schertzer JW, Rasko DA, Ernst RK.
J Bacteriol. 201(5). pii: e00595-18. doi: 10.1128/JB.00595-18. Print 2019 Mar 1.
PMID: 30530517

Genome and Functional Characterization of Colonization Factor Antigen I- and CS6-Encoding Heat-Stable Enterotoxin-Only Enterotoxigenic Escherichia coli Reveals Lineage and Geographic Variation.
Hazen TH, Nagaraj S, Sen S, Permala-Booth J, Del Canto F, Vidal R, Barry EM, Bitoun JP, Chen WH, Tennant SM, Rasko DA.
mSystems. 4(1). pii: e00329-18. doi: 10.1128/mSystems.00329-18. eCollection 2019 Jan-Feb.
PMID: 30944874

Genetic changes associated with the temporal shift in invasive non-typhoidal Salmonella serovars in Bamako Mali.
Bornstein K, Tennant SM, Hazen TH, Sorkin JD, Tapia MD, Sow SO, Onwuchekwa U, Levine MM, Rasko DA.
PLoS Negl Trop Dis. 13(6):e0007297. doi: 10.1371/journal.pntd.0007297. eCollection 2019 Jun.
PMID: 31170153

Comparative genomic analysis and molecular examination of the diversity of enterotoxigenic Escherichia coli isolates from Chile.
Rasko DA, Del Canto F, Luo Q, Fleckenstein JM, Vidal R, Hazen TH.
PLoS Negl Trop Dis. 13(11):e0007828. doi: 10.1371/journal.pntd.0007828. eCollection 2019 Nov.
PMID: 31747410

Conservation and global distribution of non-canonical antigens in Enterotoxigenic Escherichia coli.
Kuhlmann FM, Martin J, Hazen TH, Vickers TJ, Pashos M, Okhuysen PC, Gómez-Duarte OG, Cebelinski E, Boxrud D, Del Canto F, Vidal R, Qadri F, Mitreva M, Rasko DA, Fleckenstein JM.
PLoS Negl Trop Dis. 13(11):e0007825. doi: 10.1371/journal.pntd.0007825. eCollection 2019 Nov.
PMID: 31756188

Examination of 388 Staphylococcus aureus Isolates from Intensive Care Unit Patients.
Adedrian T, Hitchcock S, O'Hara LM, Michalski JM, Johnson JK, Calfee DP, Miller LG, Hazen TH, Rasko DA, Harris AD.
Microbiol Resour Announc. 8(46). pii: e01246-19. doi: 10.1128/MRA.01246-19.
PMID: 31727718

Shigella flexneri Adherence Factor Expression in In Vivo-Like Conditions.
Chanin RB, Nickerson KP, Llanos-Chea A, Sistrunk JR, Rasko DA, Kumar DKV, de la Parra J, Auclair JR, Ding J, Li K, Dogiparthi SK, Kusber BJD, Faherty CS.
mSphere. 4(6). pii: e00751-19. doi: 10.1128/mSphere.00751-19.
PMID: 31722995

The Complete Genome of the Atypical Enteropathogenic Escherichia coli Archetype Isolate E110019 Highlights a Role for Plasmids in Dissemination of the Type III Secreted Effector EspT.
Hazen TH, Rasko DA.
Infect Immun. 87(10). pii: e00412-19. doi: 10.1128/IAI.00412-19. Print 2019 Oct.
PMID: 31358567

Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns.
Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA, Han KT, Hlaing TM, Nyunt MM, Silva JC, Stewart KE, Plowe CV, O'Connor TD, Takala-Harrison S; Artemisinin Resistance Confirmation, Characterization, and Containment (ARC3); Artemisinin Resistance Containment and Elimination (ARCE); Tracking Resistance to Artemisinin Collaboration (TRAC).
Nat Commun. 10(1):2665. doi: 10.1038/s41467-019-10121-3.
PMID: 31209259

A multiplex qPCR approach for detection of pfhrp2 and pfhrp3 gene deletions in multiple strain infections of Plasmodium falciparum.
Schindler T, Deal AC, Fink M, Guirou E, Moser KA, Mwakasungula SM, Mihayo MG, Jongo SA, Chaki PP, Abdulla S, Valverde PCM, Torres K, Bijeri JR, Silva JC, Hoffman SL, Gamboa D, Tanner M, Daubenberger C.
Sci Rep. 9(1):13107. doi: 10.1038/s41598-019-49389-2.
PMID: 31511562

2018

A role for Candida albicans superoxide dismutase enzymes in glucose signaling.
Broxton CN, He B, Bruno VM, Culotta VC.
Biochem Biophys Res Commun. 495(1):814-820. doi: 10.1016/j.bbrc.2017.11.084.
PMID: 29154829

Comparative transcriptomics of Aspergillus fumigatus strains Upon Exposure to Airway Epithelial Cells.
Watkins TN, Liu H, Chung M, Hazen TH, Dunning Hotopp JC, Filler SG, Bruno VM.
Microb Genom. doi: 10.1099/mgen.0.000154.
PMID: 29345613

Iron Restriction Inside Macrophages is an Essential Host Defense Mechanism Against Mucorales.
Andrianaki AM, Kyrmizi I, Thanopoulou K, Baldin C, Drakos E, Soliman SSM, Shetty AC, McCracken C, Akoumianaki T, Stylianou K, Ioannou P, Pontikoglou C, Papadaki HA, Tzardi M, Belle V, Ettiene E, Beauvais A, Samonis G, Kontoyiannis DP, Andreakos E, Bruno VM, Ibrahim AS, Chamilos G.
Nat Commun. 9(1):3333. doi: 10.1038/s41467-018-05820-2.
PMID: 30127354

Inhibition of EGFR signaling protects from Mucormycosis.
Watkins TN, Gebremariam T, Swidergall M, Shetty AC, Graf KT, Alqarihi A, Alkhazraji S, Alsaadi AI, Edwards VL, Filler SG, Ibrahim AS, Bruno VM.
MBio. 9(4). pii: e01384-18. doi: 10.1128/mBio.01384-18.
PMID: 30108171

Targeted Enrichment Outperforms Other Enrichment Techniques and Enables More Multi-Speices RNA-Seq Analyses.
Chung M, Teigen L, Liu H, Libro S, Shetty A, Kumar N, Zhao X, Bromley RE, Tallon LJ, Sadzewicz L, Fraser CM, Rasko DA, Filler SG, Foster JM, Michalski ML, Bruno VM, Dunning Hotopp JC.
Sci Rep. 8(1):13377. doi: 10.1038/s41598-018-31420-7.
PMID: 30190541

Draft Genome Sequences of blaKPC-Containing Enterobacter aerogenes, Citrobacter freundii, and Citrobacter koseri Strains.
Hazen TH, Mettus RT, McElheny CL, Bowler SL, Doi Y, Rasko DA.
Genome Announc. 6(8). pii: e00035-18. doi: 10.1128/genomeA.00035-18.
PMID: 29472325

Diversity among blaKPC-containing plasmids in Escherichia coli and other bacterial species isolated from the same patients.
Hazen TH, Mettus R, McElheny CL, Bowler SL, Nagaraj S, Doi Y, Rasko DA.
Sci Rep. 8(1):10291. doi: 10.1038/s41598-018-28085-7.
PMID: 29980699

Phosphotyrosine-Mediated Regulation of Enterohemorrhagic Escherichia coli Virulence.
Robertson CD, Hazen TH, Kaper JB, Rasko DA, Hansen AM.
MBio. 9(1). pii: e00097-18. doi: 10.1128/mBio.00097-18.
PMID: 29487233

Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances.
Richter TKS, Michalski JM, Zanetti L, Tennant SM, Chen WH, Rasko DA.
mSystems. 3(4). pii: e00047-18. doi: 10.1128/mSystems.00047-18.
PMID: 30057943

A Novel Shigella Proteome Microarray Discriminates Targets of Human Antibody Reactivity following Oral Vaccination and Experimental Challenge.
Ndungo E, Randall A, Hazen TH, Kania DA, Trappl-Kimmons K, Liang X, Barry EM, Kotloff KL, Chakraborty S, Mani S, Rasko DA, Pasetti MF.
mSphere. 3(4). pii: e00260-18. doi: 10.1128/mSphere.00260-18.
PMID: 30068560

Extent and dynamics of polymorphism in the malaria vaccine candidate Plasmodium falciparum reticulocyte-binding protein homologue-5 in Kalifabougou, Mali.
Ouattara A, Tran TM, Doumbo S, Matthew A, Agrawal S, Niangaly A, Nelson-Owens S, Doumtabé D, Tolo Y, Ongoiba A, Takala-Harrison S, Traoré B, Silva JC, Crompton PD, Doumbo OK, Plowe CV.
Am J Trop Med Hyg. 99(1):43-50. doi: 10.4269/ajtmh.17-0737.
PMID: 29848401

A Plasmodium berghei Sporozoite-Based Vaccination Platform Against Human Malaria.
Mendes AM, Machado M, Gonçalves-Rosa N, Reuling IJ, Foquet L, Marques C, Salman AM, Yang ASP, Moser KA, Dwivedi A, Hermsen CC, Jiménez-Díaz B, Viera S, Santos JM, Albuquerque I, Bhatia SN, Bial J, Angulo-Barturen I, Silva JC, Leroux-Roels G, Janse CJ, Khan SM, Mota MM, Sauerwein RW, Prudêncio M.
NPJ Vaccines. 3:33. doi: 10.1038/s41541-018-0068-2.
PMID: 30155278

2017

The aryl hydrocarbon receptor governs epithelial cell invasion during oropharyngeal candidiasis.
Solis NV, Swidergall M, Bruno VM, Gaffen SL, Filler SG.
MBio. 8(2). pii: e00025-17. doi: 10.1128/mBio.00025-17.
PMID: 28325761

New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali.
Dara A, Drábek EF, Travassos MA, Moser KA, Delcher AL, Su Q, Hostelley T, Coulibaly D, Daou M, Dembele A, Diarra I, Kone AK, Kouriba B, Laurens MB, Niangaly A, Traore K, Tolo Y, Fraser CM, Thera MA, Djimde AA, Doumbo OK, Plowe CV, Silva JC.
Genome Med. 9(1):30. doi: 10.1186/s13073-017-0422-4.
PMID: 28351419

Protection against Plasmodium falciparum malaria by PfSPZ Vaccine
Epstein JE, Paolino KM, Richie TL, Sedegah M, Singer A, Ruben AJ, Chakravarty S, Stafford A, Ruck RC, Eappen AG, Li T, Billingsley PF, Manoj A, Silva JC, Moser K, Nielsen R, Tosh D, Cicatelli S, Ganeshan H, Case J, Padilla D, Davidson S, Garver L, Saverino E, Murshedkar T, Gunasekera A, Twomey PS, Reyes S, Moon JE, James ER, Kc N, Li M, Abot E, Belmonte A, Hauns K, Belmonte M, Huang J, Vasquez C, Remich S, Carrington M, Abebe Y, Tillman A, Hickey B, Regules J, Villasante E, Sim BK, Hoffman SL.
JCI Insight. 2(1):e89154. doi: 10.1172/jci.insight.89154.
PMID: 28097230

Transcriptional variation of diverse enteropathogenic Escherichia coli under virulence-inducing conditions.
Hazen TH, Daugherty SC, Shetty AC, Nataro JP, Rasko DA.
mSystems. 2(4). pii: e00024-17. doi: 10.1128/mSystems.00024-17.
PMID: 28766584

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli.
Hazen TH, Michalski J, Luo Q, Shetty AC, Daugherty SC, Fleckenstein JM, Rasko DA.
Sci Rep. 7(1):3513. doi: 10.1038/s41598-017-03489-z.
PMID: 28615618

Analysis of Shigella flexneri Resistance, Biofilm Formation, and Transcriptional Profile in Response to Bile Salts.
Nickerson KP, Chanin RB, Sistrunk JR, Rasko DA, Fink PJ, Barry EM, Nataro JP, Faherty CS.
Infect Immun. 85(6). pii: e01067-16. doi: 10.1128/IAI.01067-16.
PMID: 28348056

Changes in microbiome during and after Travellers Diarrhea: What we know and what we do not.
Rasko DA.
J Travel Med. 24(suppl_1):S52-S56. doi: 10.1093/jtm/tax017.
PMID: 28521002

A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples.
Dara A, Travassos MA, Adams M, Schaffer DeRoo S, Drábek EF, Agrawal S, Laufer MK, Plowe CV, Silva JC.
Malar J. 16(1):343. doi: 10.1186/s12936-017-1976-8.
PMID: 28818101

Analysis of Complete Genome Sequence and Major Surface Antigens of Neorickettsia helminthoeca, Causative Agent of Salmon Poisoning Disease.
Lin M, Bachman K, Cheng Z, Daugherty SC, Nagaraj S, Sengamalay N, Ott S, Godinez A, Tallon LJ, Sadzewicz L, Fraser C, Dunning Hotopp JC, Rikihisa Y.
Microb Biotechnol. 10(4):933-957. doi: 10.1111/1751-7915.12731.
PMID: 28585301

Association of a Novel Mutation in the Plasmodium falciparum Chloroquine Resistance Transporter With Decreased Piperaquine Sensitivity.
Agrawal S, Moser KA, Morton L, Cummings MP, Parihar A, Dwivedi A, Shetty AC, Drabek EF, Jacob CG, Henrich PP, Parobek CM, Jongsakul K, Huy R, Spring MD, Lanteri CA, Chaorattanakawee S, Lon C, Fukuda MM, Saunders DL, Fidock DA, Lin JT, Juliano JJ, Plowe CV, Silva JC, Takala-Harrison S.
J Infect Dis. 216(4):468-476. doi: 10.1093/infdis/jix334.
PMID: 28931241

Draft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb.
Chung M, Small ST, Serre D, Zimmerman PA, Dunning Hotopp JC.
Pathog Dis. 75(9). doi: 10.1093/femspd/ftx115.
PMID: 29099918

Aligner Optimization Increases Accuracy and Decreases Compute Times in Multi-Species Sequence Data* (note title change).
Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC.
Microb Genom. 3(9):e000122. doi: 10.1099/mgen.0.000122.
PMID: 29114401

Characterization of a large antibiotic resistance plasmid found in enteropathogenic Escherichia coli strain B171 and its relatedness to plasmids of diverse E. coli.
Hazen TH, Michalski J, Nagaraj S, Okeke IN, Rasko DA.
Antimicrob Agents Chemother. 61(9). pii: e00995-17. doi: 10.1128/AAC.00995-17.
PMID: 28674052

2016

Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples.
Kumar N, Lin M, Zhao X, Ott S, Santana-Cruz I, Daugherty S, Rikihisa Y, Sadzewicz L, Tallon LJ, Fraser CM, Dunning Hotopp JC.
Sci Rep. 6:34850. doi: 10.1038/srep34850.
PMID: 27713560

The genome of Onchocerca volvulus, agent of river blindness.
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S.
Nat Microbiol. 2:16216. doi: 10.1038/nmicrobiol.2016.216.
PMID: 27869790

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.
Chibucos MC, Soliman S, Gebremariam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O'Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart SR, Skory CD, Ibrahim AS, Bruno VM.
Nat Commun. 7:12218. doi: 10.1038/ncomms12218.
PMID: 27447865

IL-17 Receptor Signaling in Oral Epithelial Cells Is Critical for Protection against Oropharyngeal Candidiasis.
Conti HR, Bruno VM, Childs EE, Daugherty S, Hunter JP, Mengesha BG, Saevig DL, Hendricks MR, Coleman BM, Brane L, Solis N, Cruz JA, Verma AH, Garg AV, Hise AG, Richardson JP, Naglik JR, Filler SG, Kolls JK, Sinha S, Gaffen SL.
Cell Host Microbe. 20(5):606-617. doi: 10.1016/j.chom.2016.10.001. Epub 2016 Oct 27.
PMID: 27923704

Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection.
Sistrunk JR, Nickerson KP, Chanin RB, Rasko DA, Faherty CS.
Clin Microbiol Rev. 29(4):819-36. doi: 10.1128/CMR.00031-16.
PMID: 27464994

Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics.
Hazen TH, Leonard SR, Lampel KA, Lacher DW, Maurelli AT, Rasko DA.
Infect Immun. 84(8):2362-2371. doi: 10.1128/IAI.00350-16. Print 2016 Aug.
PMID: 27271741

Genomic diversity of EPEC associated with clinical presentations of differing severity.
Hazen TH, Donnenberg MS, Panchalingam S, Antonio M, Hossain A, Mandomando I, Ochieng JB, Ramamurthy T, Tamboura B, Qureshi S, Quadri F, Zaidi A, Kotloff KL, Levine MM, Barry EM, Kaper JB, Rasko DA, Nataro JP.
Nat Microbiol. 1:15014. doi: 10.1038/nmicrobiol.2015.14.
PMID: 27571975

2015

Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.
Takala-Harrison S, Jacob CG, Arze C, Cummings MP, Silva JC, Dondorp AM, Fukuda MM, Hien TT, Mayxay M, Noedl H, Nosten F, Kyaw MP, Nhien NT, Imwong M, Bethell D, Se Y, Lon C, Tyner SD, Saunders DL, Ariey F, Mercereau-Puijalon O, Menard D, Newton PN, Khanthavong M, Hongvanthong B, Starzengruber P, Fuehrer HP, Swoboda P, Khan WA, Phyo AP, Nyunt MM, Nyunt MH, Brown TS, Adams M, Pepin CS, Bailey J, Tan JC, Ferdig MT, Clark TG, Miotto O, MacInnis B, Kwiatkowski DP, White NJ, Ringwald P, Plowe CV. 2015.
PMID:25180241

Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype.
Brown TS, Jacob CG, Silva JC, Takala-Harrison S, Djimdé A, Dondorp AM, Fukuda M, Noedl H, Nyunt MM, Kyaw MP, Mayxay M, Hien TT, Plowe CV, Cummings MP. 2015.
Infect Genet Evol. 30:318-22. doi: 10.1016/j.meegid.2014.12.010. Epub 2014 Dec 13.
PMID: 25514047

Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection.
Sahl JW, Sistrunk JR, Fraser CM, Hine E, Baby N, Begum Y, Luo Q, Sheikh A, Qadri F, Fleckenstein JM, Rasko DA. 2015.
MBio. 6(3):e00501. doi: 10.1128/mBio.00501-15
PMID: 26060273

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates.
Hazen TH, Daugherty SC, Shetty A, Mahurkar AA, White O, Kaper JB, Rasko DA. 2015.
Front Microbiol., 6:569. doi: 10.3389/fmicb.2015.00569.
PMID:26124752

Diarrhea, bacteremia and multiorgan dysfunction due to an extraintestinal pathogenic Escherichia coli strain with enteropathogenic E. coli genes.
Kessler R, Nisa S, Hazen TH, Horneman A, Amoroso A, Rasko DA, Donnenberg MS. 2015.
Pathog Dis. 73(8):ftv076. doi: 10.1093/femspd/ftv076.
PMID:26410828

Comparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids.
Hazen TH, Kaper JB, Nataro JP, Rasko DA. 2015.
Infect Immun. 83(10):4103-17. doi: 10.1128/IAI.00769-15.
PMID:26238712

Transcriptomic analysis of vulvovaginal candidiasis identifies a role for the NLRP3 inflammasome.
Bruno VM, Shetty AC, Yano J, Fidel PL Jr, Noverr MC, Peters BM. 2015.
MBio. 6(2). pii: e00182-15. doi: 10.1128/mBio.00182-15.
PMID:25900651

New signaling pathways govern the host response to C. albicans infection in various niches.
Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM. 2015.
Genome Res. 25(5):679-89. doi: 10.1101/gr.187427.114.
PMID:25858952

The genome sequence of four isolates from the family Lichtheimiaceae.
Chibucos MC, Etienne KA, Orvis J, Lee H, Daugherty S, Lockhart SR, Ibrahim AS, Bruno VM. 2015.
Pathog Dis. 73(5). pii: ftv024. doi: 10.1093/femspd/ftv024.
PMID:25857734

Candida albicans adapts to host copper during infection by swapping metal cofactors for superoxide dismutase.
Li CX, Gleason JE, Zhang SX, Bruno VM, Cormack BP, Culotta VC. 2015.
Proc Natl Acad Sci USA. 112(38):E5336-42. doi: 10.1073/pnas.1513447112.
PMID:26351691

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis.
Shelburne SA, Ajami NJ, Chibucos MC, Beird HC, Tarrand J, Galloway-Peña J, Albert N, Chemaly RF, Ghantoji SS, Marsh L, Pemmaraju N, Andreeff M, Shpall EJ, Wargo JA, Rezvani K, Alousi A, Bruno VM, Futreal PA, Petrosino JF, Kontoyiannis DP.
PLoS One. 2015. 10(11):e0139851. doi: 10.1371/journal.pone.0139851.
PMID: 26556047

Designing malaria vaccines to circumvent antigen variability.
Ouattara A, Barry AE, Dutta S, Remarque EJ, Beeson JG, Plowe CV.
Vaccine. 2015. 33(52):7506-12. doi: 10.1016/j.vaccine.2015.09.110. Epub 2015 Nov 1.
PMID: 26475447

2014

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.
J. Crabtree, S. Agrawal, A. Mahurkar, G.S. Myers, D.A. Rasko and O. White. 2014.
Bioinformatics. 30(21):3125-7.
PMID: 25075113

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.
Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC. 2014.
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