Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement
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Published in PloS one (19.11.2014)
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Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc
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Published in Cell host & microbe (10.08.2016)
Published in Cell host & microbe (10.08.2016)
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Tracing the Enterococci from Paleozoic Origins to the Hospital
Lebreton, François, Manson, Abigail L., Saavedra, Jose T., Straub, Timothy J., Earl, Ashlee M., Gilmore, Michael S.
Published in Cell (18.05.2017)
Published in Cell (18.05.2017)
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Clinically relevant mutations in core metabolic genes confer antibiotic resistance
Lopatkin, Allison J, Bening, Sarah C, Manson, Abigail L, Stokes, Jonathan M, Kohanski, Michael A, Badran, Ahmed H, Earl, Ashlee M, Cheney, Nicole J, Yang, Jason H, Collins, James J
Published in Science (American Association for the Advancement of Science) (19.02.2021)
Published in Science (American Association for the Advancement of Science) (19.02.2021)
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Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus
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
Published in PloS one (06.01.2012)
Published in PloS one (06.01.2012)
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Relating the metatranscriptome and metagenome of the human gut
Franzosa, Eric A, Morgan, Xochitl C, Segata, Nicola, Waldron, Levi, Reyes, Joshua, Earl, Ashlee M, Giannoukos, Georgia, Boylan, Matthew R, Ciulla, Dawn, Gevers, Dirk, Izard, Jacques, Garrett, Wendy S, Chan, Andrew T, Huttenhower, Curtis
Published in Proceedings of the National Academy of Sciences - PNAS (03.06.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (03.06.2014)
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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Haas, Brian J, Gevers, Dirk, Earl, Ashlee M, Feldgarden, Mike, Ward, Doyle V, Giannoukos, Georgia, Ciulla, Dawn, Tabbaa, Diana, Highlander, Sarah K, Sodergren, Erica, Methé, Barbara, DeSantis, Todd Z, Petrosino, Joseph F, Knight, Rob, Birren, Bruce W
Published in Genome research (01.03.2011)
Published in Genome research (01.03.2011)
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Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
Kostic, Aleksandar D, Gevers, Dirk, Pedamallu, Chandra Sekhar, Michaud, Monia, Duke, Fujiko, Earl, Ashlee M, Ojesina, Akinyemi I, Jung, Joonil, Bass, Adam J, Tabernero, Josep, Baselga, José, Liu, Chen, Shivdasani, Ramesh A, Ogino, Shuji, Birren, Bruce W, Huttenhower, Curtis, Garrett, Wendy S, Meyerson, Matthew
Published in Genome research (01.02.2012)
Published in Genome research (01.02.2012)
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SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings
Urhan, Aysun, Cosma, Bianca-Maria, Earl, Ashlee M, Manson, Abigail L, Abeel, Thomas
Published in Bioinformatics (Oxford, England) (03.06.2024)
Published in Bioinformatics (Oxford, England) (03.06.2024)
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The success of acinetobacter species; genetic, metabolic and virulence attributes
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
Published in PloS one (29.10.2012)
Published in PloS one (29.10.2012)
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Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae
Ernst, Christoph M, Braxton, Julian R, Rodriguez-Osorio, Carlos A, Zagieboylo, Anna P, Li, Li, Pironti, Alejandro, Manson, Abigail L, Nair, Anil V, Benson, Maura, Cummins, Kaelyn, Clatworthy, Anne E, Earl, Ashlee M, Cosimi, Lisa A, Hung, Deborah T
Published in Nature medicine (01.05.2020)
Published in Nature medicine (01.05.2020)
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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
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, Birren, Bruce W, Gnirke, Andreas
Published in Genome Biology (01.01.2012)
Published in Genome Biology (01.01.2012)
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Ecology and genomics of Bacillus subtilis
Earl, Ashlee M, Losick, Richard, Kolter, Roberto
Published in Trends in microbiology (Regular ed.) (01.06.2008)
Published in Trends in microbiology (Regular ed.) (01.06.2008)
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Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies
Zheng, Erica J, Andrews, Ian W, Grote, Alexandra T, Manson, Abigail L, Alcantar, Miguel A, Earl, Ashlee M, Collins, James J
Published in Nature communications (09.05.2022)
Published in Nature communications (09.05.2022)
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Colon Cancer-Associated Fusobacterium nucleatum May Originate From the Oral Cavity and Reach Colon Tumors via the Circulatory System
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
Published in Frontiers in cellular and infection microbiology (07.08.2020)
Published in Frontiers in cellular and infection microbiology (07.08.2020)
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