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Acquisition and Long-term Carriage of Multidrug-Resistant Organisms in US International Travelers.
Published in:
Open Forum Infectious Diseases, 2020, v. 7, n. 12, p. 1, doi. 10.1093/ofid/ofaa543
By:
- Worby, Colin J;
- Earl, Ashlee M;
- Turbett, Sarah E;
- Becker, Margaret;
- Rao, Sowmya R;
- Oliver, Elizabeth;
- Walker, Allison Taylor;
- Walters, Maroya;
- Kelly, Paul;
- Leung, Daniel T;
- Knouse, Mark;
- Hagmann, Stefan H F;
- Ryan, Edward T;
- LaRocque, Regina C
Publication type:
Article
Fatal Nosocomial MDR TB Identified through Routine Genetic Analysis and Whole-Genome Sequencing.
Published in:
2015
By:
- Williams, O. Martin;
- Abeel, Thomas;
- Casali, Nicola;
- Cohen, Keira;
- Pym, Alex S.;
- Mungall, Sarah B.;
- Desjardins, Christopher A.;
- Banerjee, Anindo;
- Drobniewski, Francis;
- Earl, Ashlee M.;
- Cooke, Graham S.
Publication type:
Art Reproduction
QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data.
Published in:
BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-6486-3
By:
- Anyansi, Christine;
- Keo, Arlin;
- Walker, Bruce J.;
- Straub, Timothy J.;
- Manson, Abigail L.;
- Earl, Ashlee M.;
- Abeel, Thomas
Publication type:
Article
Analysis of Deinococcus radiodurans's Transcriptional Response to Ionizing Radiation and Desiccation Reveals Novel Proteins That Contribute to Extreme Radioresistance.
Published in:
Genetics, 2004, v. 168, n. 1, p. 21, doi. 10.1534/genetics.104.029249
By:
- Tanaka, Masashi;
- Earl, Ashlee M.;
- Howell, Heather A.;
- Mie-Jung Park;
- Eisen, Jonathan A.;
- Peterson, Scott N.;
- Battista, John R.
Publication type:
Article
Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations.
Published in:
Genetics, 2004, v. 166, n. 2, p. 661, doi. 10.1534/genetics.166.2.661
By:
- Kim, Mandy;
- Wolff, Erika;
- Huang, Tiffany;
- Garibyan, Lilit;
- Earl, Ashlee M.;
- Battista, John R.;
- Miller, Jeffrey H.
Publication type:
Article
Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.67310
By:
- Peijun Ma;
- He, Lorrie L.;
- Pironti, Alejandro;
- Laibinis, Hannah H.;
- Ernst, Christoph M.;
- Manson, Abigail L.;
- Bhattacharyya, Roby P.;
- Earl, Ashlee M.;
- Livny, Jonathan;
- Hung, Deborah T.
Publication type:
Article
Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30272-0
By:
- Zheng, Erica J.;
- Andrews, Ian W.;
- Grote, Alexandra T.;
- Manson, Abigail L.;
- Alcantar, Miguel A.;
- Earl, Ashlee M.;
- Collins, James J.
Publication type:
Article
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25484-9
By:
- Bronson, Ryan A.;
- Gupta, Chhavi;
- Manson, Abigail L.;
- Nguyen, Jan A.;
- Bahadirli-Talbott, Asli;
- Parrish, Nicole M.;
- Earl, Ashlee M.;
- Cohen, Keira A.
Publication type:
Article
The global dissemination of hospital clones of Enterococcus faecium.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00868-0
By:
- van Hal, Sebastiaan J.;
- Willems, Rob J. L.;
- Gouliouris, Theodore;
- Ballard, Susan A.;
- Coque, Teresa M.;
- Hammerum, Anette M.;
- Hegstad, Kristin;
- Westh, Hendrik T.;
- Howden, Benjamin P.;
- Malhotra-Kumar, Surbhi;
- Werner, Guido;
- Yanagihara, Katsunori;
- Earl, Ashlee M.;
- Raven, Katherine E.;
- Corander, Jukka;
- Bowden, Rory;
- Enterococcal Group;
- Pinholt, Mette;
- Loens, Katherine;
- Xavier, Basil B.
Publication type:
Article
Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.
Published in:
PLoS Neglected Tropical Diseases, 2016, v. 10, n. 1, p. 1, doi. 10.1371/journal.pntd.0004332
By:
- Winglee, Kathryn;
- Manson McGuire, Abigail;
- Maiga, Mamoudou;
- Abeel, Thomas;
- Shea, Terrance;
- Desjardins, Christopher A.;
- Diarra, Bassirou;
- Baya, Bocar;
- Sanogo, Moumine;
- Diallo, Souleymane;
- Earl, Ashlee M.;
- Bishai, William R.
Publication type:
Article
SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings.
Published in:
Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae328
By:
- Urhan, Aysun;
- Cosma, Bianca-Maria;
- Earl, Ashlee M;
- Manson, Abigail L;
- Abeel, Thomas
Publication type:
Article
Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization.
Published in:
International Journal of Mycobacteriology, 2016, v. 5, n. 1, p. 66, doi. 10.1016/j.ijmyco.2015.12.001
By:
- Velayati, Ali Akbar;
- Abeel, Thomas;
- Shea, Terrance;
- Konstantinovich Zhavnerko, Gennady;
- Birren, Bruce;
- Cassell, Gail H.;
- Earl, Ashlee M.;
- Hoffner, Sven;
- Farnia, Parissa
Publication type:
Article
Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains.
Published in:
Frontiers in Immunology, 2019, p. N.PAG, doi. 10.3389/fimmu.2019.00195
By:
- Ramaiah, Arunachalam;
- Nayak, Soumya;
- Rakshit, Srabanti;
- Manson, Abigail L.;
- Abeel, Thomas;
- Shanmugam, Sivakumar;
- Sahoo, Pravat Nalini;
- John, Anto Jesuraj Uday Kumar;
- Sundaramurthi, Jagadish Chandrabose;
- Narayanan, Sujatha;
- D'Souza, George;
- von Hoegen, Paul;
- Ottenhoff, Tom H. M.;
- Swaminathan, Soumya;
- Earl, Ashlee M.;
- Vyakarnam, Annapurna
Publication type:
Article
StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02630-0
By:
- van Dijk, Lucas R.;
- Walker, Bruce J.;
- Straub, Timothy J.;
- Worby, Colin J.;
- Grote, Alexandra;
- Schreiber IV, Henry L.;
- Anyansi, Christine;
- Pickering, Amy J.;
- Hultgren, Scott J.;
- Manson, Abigail L.;
- Abeel, Thomas;
- Earl, Ashlee M.
Publication type:
Article
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement.
Published in:
PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0112963
By:
- Walker, Bruce J.;
- Abeel, Thomas;
- Shea, Terrance;
- Priest, Margaret;
- Abouelliel, Amr;
- Sakthikumar, Sharadha;
- Cuomo, Christina A.;
- Zeng, Qiandong;
- Wortman, Jennifer;
- Young, Sarah K.;
- Earl, Ashlee M.
Publication type:
Article
The Success of Acinetobacter Species; Genetic, Metabolic and Virulence Attributes.
Published in:
PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0046984
By:
- Peleg, Anton Y.;
- de Breij, Anna;
- Adams, Mark D.;
- Cerqueira, Gustavo M.;
- Mocali, Stefano;
- Galardini, Marco;
- Nibbering, Peter H.;
- Earl, Ashlee M.;
- Ward, Doyle V.;
- Paterson, David L.;
- Seifert, Harald;
- Dijkshoorn, Lenie
Publication type:
Article
The "Most Wanted" Taxa from the Human Microbiome for Whole Genome Sequencing.
Published in:
PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0041294
By:
- Fodor, Anthony A.;
- DeSantis, Todd Z.;
- Wylie, Kristine M.;
- Badger, Jonathan H.;
- Yuzhen Ye;
- Hepburn, Theresa;
- Ping Hu;
- Sodergren, Erica;
- Liolios, Konstantinos;
- Huot-Creasy, Heather;
- Birren, Bruce W.;
- Earl, Ashlee M.
Publication type:
Article
Whole Genome Characterization of the Mechanisms of Daptomycin Resistance in Clinical and Laboratory Derived Isolates of Staphylococcus aureus.
Published in:
PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0028316
By:
- Peleg, Anton Y.;
- Miyakis, Spiros;
- Ward, Doyle V.;
- Earl, Ashlee M.;
- Rubio, Aileen;
- Cameron, David R.;
- Pillai, Satish;
- Moellering, Jr., Robert C.;
- Eliopoulos, George M.
Publication type:
Article
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections.
Published in:
BMC Microbiology, 2021, v. 21, n. 1, p. 1, doi. 10.1186/s12866-021-02106-4
By:
- Straub, Timothy J.;
- Chou, Wen-Chi;
- Manson, Abigail L.;
- Schreiber IV, Henry L.;
- Walker, Bruce J.;
- Desjardins, Christopher A.;
- Chapman, Sinéad B.;
- Kaspar, Kerrie L.;
- Kahsai, Orsalem J.;
- Traylor, Elizabeth;
- Dodson, Karen W.;
- Hullar, Meredith A. J.;
- Hultgren, Scott J.;
- Khoo, Christina;
- Earl, Ashlee M.
Publication type:
Article
Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants.
Published in:
BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-3152-x
By:
- Dehoux, Pierre;
- Marvaud, Jean Christophe;
- Abouelleil, Amr;
- Earl, Ashlee M.;
- Lambert, Thierry;
- Dauga, Catherine
Publication type:
Article
ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database.
Published in:
PLoS ONE, 2019, v. 14, n. 10, p. 1, doi. 10.1371/journal.pone.0223364
By:
- Reis-Cunha, João L.;
- Bartholomeu, Daniella C.;
- Manson, Abigail L.;
- Earl, Ashlee M.;
- Cerqueira, Gustavo C.
Publication type:
Article
Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery.
Published in:
Molecular Systems Biology, 2022, v. 18, n. 9, p. 1, doi. 10.15252/msb.202211081
By:
- Wong, Felix;
- Krishnan, Aarti;
- Zheng, Erica J;
- Stärk, Hannes;
- Manson, Abigail L;
- Earl, Ashlee M;
- Jaakkola, Tommi;
- Collins, James J
Publication type:
Article
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.
Published in:
Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad050
By:
- Yorki, Sosie;
- Shea, Terrance;
- Cuomo, Christina A;
- Walker, Bruce J;
- LaRocque, Regina C;
- Manson, Abigail L;
- Earl, Ashlee M;
- Worby, Colin J
Publication type:
Article
Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster.
Published in:
Nature Communications, 2014, v. 5, n. 11, p. 5411, doi. 10.1038/ncomms6411
By:
- Valentino, Michael D.;
- McGuire, Abigail Manson;
- Rosch, Jason W.;
- Bispo, Paulo J. M.;
- Burnham, Corinna;
- Sanfilippo, Christine M.;
- Carter, Robert A.;
- Zegans, Michael E.;
- Beall, Bernard;
- Earl, Ashlee M.;
- Tuomanen, Elaine I.;
- Morris, Timothy W.;
- Haas, Wolfgang;
- Gilmore, Michael S.
Publication type:
Article
Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream.
Published in:
Science Translational Medicine, 2019, v. 11, n. 487, p. N.PAG, doi. 10.1126/scitranslmed.aat8418
By:
- Van Tyne, Daria;
- Manson, Abigail L.;
- Huycke, Mark M.;
- Karanicolas, John;
- Earl, Ashlee M.;
- Gilmore, Michael S.
Publication type:
Article
Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections.
Published in:
Science Translational Medicine, 2017, v. 9, n. 382, p. 1, doi. 10.1126/scitranslmed.aaf1283
By:
- Schreiber IV, Henry L.;
- Conover, Matt S.;
- Wen-Chi Chou;
- Hibbing, Michael E.;
- Manson, Abigail L.;
- Dodson, Karen W.;
- Hannan, Thomas J.;
- Roberts, Pacita L.;
- Stapleton, Ann E.;
- Hooton, Thomas M.;
- Livny, Jonathan;
- Earl, Ashlee M.;
- Hultgren, Scott J.
Publication type:
Article
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
Published in:
Genome Biology, 2012, v. 13, n. 3, p. 1, doi. 10.1186/gb-2012-13-3-r23
By:
- Giannoukos, Georgia;
- Ciulla, Dawn M.;
- Huang, Katherine;
- Haas, Brian J.;
- Izard, Jacques;
- Levin, Joshua Z.;
- Livny, Jonathan;
- Earl, Ashlee M.;
- Gevers, Dirk;
- Ward, Doyle V.;
- Nusbaum, Chad;
- Birren1, Bruce W.;
- Gnirke1, Andreas
Publication type:
Article
Reply to Lee and Howden.
Published in:
Clinical Infectious Diseases, 2018, v. 66, n. 1, p. 160, doi. 10.1093/cid/cix751
By:
- Manson, Abigail L.;
- Abeel, Thomas;
- Galagan, James;
- Sundaramurthi, Jagadish Chandrabose;
- Shanmugam, Siva Kumar;
- Palaniyandi, Kannan;
- Narayanan, Sujatha;
- Swaminathan, Soumya;
- Earl, Ashlee M.
Publication type:
Article
Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics.
Published in:
Clinical Infectious Diseases, 2017, v. 64, n. 11, p. 1494, doi. 10.1093/cid/cix169
By:
- Manson, Abigail L.;
- Abeel, Thomas;
- Galagan, James E.;
- Sundaramurthi, Jagadish Chandrabose;
- Salazar, Alex;
- Gehrmann, Thies;
- Shanmugam, Siva Kumar;
- Palaniyandi, Kannan;
- Narayanan, Sujatha;
- Swaminathan, Soumya;
- Earl, Ashlee M.
Publication type:
Article
Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection.
Published in:
Clinical Infectious Diseases, 2024, v. 78, n. 1, p. 31, doi. 10.1093/cid/ciad507
By:
- Roach, David J;
- Sridhar, Sushmita;
- Oliver, Elizabeth;
- Rao, Sowmya R;
- Slater, Damien M;
- Hwang, Wontae;
- Vater, Kian Hutt;
- Dinesh, Anupama;
- Qadri, Firdausi;
- Chisti, Mohammod J;
- Pierce, Virginia M;
- Turbett, Sarah E;
- Bhattacharyya, Roby P;
- Worby, Colin J;
- Earl, Ashlee M;
- LaRocque, Regina C;
- Harris, Jason B
Publication type:
Article
Correction: Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1.
Published in:
2006
By:
- Harris, Dennis R.;
- Tanaka, Masashi;
- Saveliev, Sergei V.;
- Jolivet, Edmond;
- Earl, Ashlee M.;
- Cox, Michael M.;
- Battista, John R.
Publication type:
Correction Notice
Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1.
Published in:
PLoS Biology, 2004, v. 2, n. 10, p. 1629, doi. 10.1371/journal.pbio.0020304
By:
- Harris, Dennis R.;
- Tanaka, Masashi;
- Saveliev, Sergei V.;
- Jolivet, Edmond;
- Earl, Ashlee M.;
- Cox, Michael M.;
- Battista, John R.
Publication type:
Article
Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1.
Published in:
PLoS Biology, 2004, v. 2, n. 9, p. 1, doi. 10.1371/journal.pbio.0020304
By:
- Harris, Dennis R;
- Tanaka, Masashi;
- Saveliev, Sergei V;
- Jolivet, Edmond;
- Earl, Ashlee M;
- Cox, Michael M;
- Battista, John R
Publication type:
Article
Structure, function and diversity of the healthy human microbiome.
Published in:
Nature, 2012, v. 486, n. 7402, p. 207, doi. 10.1038/nature11234
By:
- Huttenhower, Curtis;
- Gevers, Dirk;
- Knight, Rob;
- Abubucker, Sahar;
- Badger, Jonathan H.;
- Chinwalla, Asif T.;
- Creasy, Heather H.;
- Earl, Ashlee M.;
- FitzGerald, Michael G.;
- Fulton, Robert S.;
- Giglio, Michelle G.;
- Hallsworth-Pepin, Kymberlie;
- Lobos, Elizabeth A.;
- Madupu, Ramana;
- Magrini, Vincent;
- Martin, John C.;
- Mitreva, Makedonka;
- Muzny, Donna M.;
- Sodergren, Erica J.;
- Versalovic, James
Publication type:
Article
A framework for human microbiome research.
Published in:
Nature, 2012, v. 486, n. 7402, p. 215, doi. 10.1038/nature11209
By:
- Methé, Barbara A.;
- Nelson, Karen E.;
- Pop, Mihai;
- Creasy, Heather H.;
- Giglio, Michelle G.;
- Huttenhower, Curtis;
- Gevers, Dirk;
- Petrosino, Joseph F.;
- Abubucker, Sahar;
- Badger, Jonathan H.;
- Chinwalla, Asif T.;
- Earl, Ashlee M.;
- FitzGerald, Michael G.;
- Fulton, Robert S.;
- Hallsworth-Pepin, Kymberlie;
- Lobos, Elizabeth A.;
- Madupu, Ramana;
- Magrini, Vincent;
- Martin, John C.;
- Mitreva, Makedonka
Publication type:
Article
Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data.
Published in:
Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.01925
By:
- Anyansi, Christine;
- Straub, Timothy J.;
- Manson, Abigail L.;
- Earl, Ashlee M.;
- Abeel, Thomas
Publication type:
Article
Colon Cancer-Associated Fusobacterium nucleatum May Originate From the Oral Cavity and Reach Colon Tumors via the Circulatory System.
Published in:
Frontiers in Cellular & Infection Microbiology, 2020, v. 10, p. N.PAG, doi. 10.3389/fcimb.2020.00400
By:
- Abed, Jawad;
- Maalouf, Naseem;
- Manson, Abigail L.;
- Earl, Ashlee M.;
- Parhi, Lishay;
- Emgård, Johanna E. M.;
- Klutstein, Michael;
- Tayeb, Shay;
- Almogy, Gideon;
- Atlan, Karine A.;
- Chaushu, Stella;
- Israeli, Eran;
- Mandelboim, Ofer;
- Garrett, Wendy S.;
- Bachrach, Gilad
Publication type:
Article
Utility of Mycobacterium tuberculosis Genome Sequencing Snapshots to Assess Transmission Dynamics Over Time.
Published in:
Journal of Infectious Diseases, 2024, v. 229, n. 5, p. 1493, doi. 10.1093/infdis/jiad515
By:
- Yuen, Courtney M;
- Huang, Chuan-Chin;
- Millones, Ana Karina;
- Calderon, Roger I;
- Manson, Abigail L;
- Jimenez, Judith;
- Contreras, Carmen;
- Earl, Ashlee M;
- Becerra, Mercedes C;
- Lecca, Leonid;
- Murray, Megan B
Publication type:
Article
Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium.
Published in:
2018
By:
- Lebreton, François;
- Valentino, Michael D;
- Schaufler, Katharina;
- Earl, Ashlee M;
- Cattoir, Vincent;
- Gilmore, Michael S
Publication type:
journal article
Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics.
Published in:
Frontiers in Microbiology, 2020, v. 10, p. 1, doi. 10.3389/fmicb.2019.03019
By:
- Bachmann, Nathan L.;
- Salamzade, Rauf;
- Manson, Abigail L.;
- Whittington, Richard;
- Sintchenko, Vitali;
- Earl, Ashlee M.;
- Marais, Ben J.
Publication type:
Article
Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges.
Published in:
Genome Medicine, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13073-019-0660-8
By:
- Cohen, Keira A.;
- Manson, Abigail L.;
- Desjardins, Christopher A.;
- Abeel, Thomas;
- Earl, Ashlee M.
Publication type:
Article

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