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1. Full Text Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
by Walker, Bruce J and Abeel, Thomas and Shea, Terrance and Priest, Margaret and Abouelliel, Amr and Sakthikumar, Sharadha and Cuomo, Christina A and Zeng, Qiandong and Wortman, Jennifer and Young, Sarah K and Earl, Ashlee M
PLoS ONE, ISSN 1932-6203, 11/2014, Volume 9, Issue 11, p. e112963
Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day.... 
MYCOBACTERIUM-TUBERCULOSIS | READ ALIGNMENT | PROTEIN-A | MULTIDISCIPLINARY SCIENCES | SEQUENCE | DRAFT ASSEMBLIES | EPIDEMIOLOGY | Genetic Variation | Genome, Bacterial | Algorithms | Bacteria - classification | Molecular Sequence Data | Software | Bacteria - genetics | Sequence Analysis, DNA - methods | Automation | Integrated software | Genomics | Data processing | Genomes | Gene sequencing | Streptococcus infections | Freeware | Microorganisms | Tuberculosis | Production methods | Bacteria | Inserts | Assemblies | Bioinformatics
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2. Full Text Ecology and genomics of Bacillus subtilis
by Earl, Ashlee M and Losick, Richard and Kolter, Roberto
Trends in Microbiology, ISSN 0966-842X, 2008, Volume 16, Issue 6, pp. 269 - 275
Bacillus subtilis is a remarkably diverse bacterial species that is capable of growth within many environments. Recent microarray-based comparative genomic... 
Internal Medicine | LIFE-CYCLE | NATURAL-POPULATIONS | MOSAIC STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | GASTROINTESTINAL-TRACT | ESCHERICHIA-COLI | SEQUENCE | GENETIC EXCHANGE | MICROBIOLOGY | GLUTAMIC ACID PRODUCTION | MASTER REGULATOR | BIOFILM FORMATION | Genome, Bacterial | Nucleic Acid Hybridization | Bacillus subtilis - physiology | Bacillus subtilis - growth & development | Oligonucleotide Array Sequence Analysis | Species Specificity | Bacillus subtilis - classification | Genomics | Bacterial Proteins - genetics | Bacterial Proteins - metabolism | Ecology | Bacillus subtilis - genetics | Evolutionary biology
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3. Full Text Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal
by Cohen, Keira A and Abeel, Thomas and Manson McGuire, Abigail and Desjardins, Christopher A and Munsamy, Vanisha and Shea, Terrance P and Walker, Bruce J and Bantubani, Nonkqubela and Almeida, Deepak V and Alvarado, Lucia and Chapman, Sinéad B and Mvelase, Nomonde R and Duffy, Eamon Y and Fitzgerald, Michael G and Govender, Pamla and Gujja, Sharvari and Hamilton, Susanna and Howarth, Clinton and Larimer, Jeffrey D and Maharaj, Kashmeel and Pearson, Matthew D and Priest, Margaret E and Zeng, Qiandong and Padayatchi, Nesri and Grosset, Jacques and Young, Sarah K and Wortman, Jennifer and Mlisana, Koleka P and O'Donnell, Max R and Birren, Bruce W and Bishai, William R and Pym, Alexander S and Earl, Ashlee M
PLoS Medicine, ISSN 1549-1277, 09/2015, Volume 12, Issue 9, p. e1001880
Background The continued advance of antibiotic resistance threatens the treatment and control of many infectious diseases. This is exemplified by the largest... 
STRAINS | SOUTH-AFRICA | POPULATION | MEDICINE, GENERAL & INTERNAL | MUTATION-RATE | TRANSMISSION | RIFAMPIN RESISTANCE | HIV | DIVERSITY | INFECTION | ISONIAZID PREVENTIVE THERAPY | Drug resistance in microorganisms | Genetic aspects | Nucleotide sequencing | Mycobacterium tuberculosis | Methods | DNA sequencing | Studies | Datasets | Epidemics | Tuberculosis | Researchers | Antibiotics | Cloning | Genomes | Mutation | Drug resistance | Public health
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4. Full Text Structure, function and diversity of the healthy human microbiome
by Huttenhower, Curtis and Gevers, Dirk and Knight, Rob and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Creasy, Heather H and Earl, Ashlee M and Fitzgerald, Michael G and Fulton, Robert S and Giglio, Michelle G and Hallsworth-Pepin, Kymberlie and Lobos, Elizabeth A and Madupu, Ramana and Magrini, Vincent and Martin, John C and Mitreva, Makedonka and Muzny, Donna M and Sodergren, Erica J and Versalovic, James and Wollam, Aye M and Worley, Kim C and Wortman, Jennifer R and Young, Sarah K and Zeng, Qiandong and Aagaard, Kjersti M and Abolude, Olukemi O and Allen-Vercoe, Emma and Alm, Eric J and Alvarado, Lucia and Andersen, Gary L and Anderson, Scott and Appelbaum, Elizabeth and Arachchi, Harindra M and Armitage, Gary and Arze, Cesar A and Ayvaz, Tulin and Baker, Carl C and Begg, Lisa and Belachew, Tsegahiwot and Bhonagiri, Veena and Bihan, Monika and Blaser, Martin J and Bloom, Toby and Bonazzi, Vivien and Paul Brooks, J and Buck, Gregory A and Buhay, Christian J and Busam, Dana A and Campbell, Joseph L and Canon, Shane R and Cantarel, Brandi L and Chain, Patrick S. G and Chen, I-Min A and Chen, Lei and Chhibba, Shaila and Chu, Ken and Ciulla, Dawn M and Clemente, Jose C and Clifton, Sandra W and Conlan, Sean and Crabtree, Jonathan and Cutting, Mary A and Davidovics, Noam J and Davis, Catherine C and Desantis, Todd Z and Deal, Carolyn and Delehaunty, Kimberley D and Dewhirst, Floyd E and Deych, Elena and Ding, Yan and Dooling, David J and Dugan, Shannon P and Michael Dunne, Wm and Scott Durkin, A and Edgar, Robert C and Erlich, Rachel L and Farmer, Candace N and Farrell, Ruth M and Faust, Karoline and Feldgarden, Michael and Felix, Victor M and Fisher, Sheila and Fodor, Anthony A and Forney, Larry J and Foster, Leslie and Di Francesco, Valentina and Friedman, Jonathan and Friedrich, Dennis C and Fronick, Catrina C and Fulton, Lucinda L and Gao, Hongyu and Garcia, Nathalia and Giannoukos, Georgia and Giblin, Christina and Giovanni, Maria Y and Goldberg, Jonathan M and Goll, Johannes and Gonzalez, Antonio and Griggs, Allison and ... and Human Microbiome Project Consortiu and Human Microbiome Project Consortium and The Human Microbiome Project Consortium and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2012, Volume 486, Issue 7402, pp. 207 - 214
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and... 
IDENTIFICATION | BACTERIA | MULTIDISCIPLINARY SCIENCES | Metagenomics | Health | Humans | Male | Biodiversity | Bacteria - genetics | Young Adult | Phenotype | Ecosystem | Adolescent | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Adult | Female | Metabolic Networks and Pathways - physiology | Metagenome | Microbiota (Symbiotic organisms) | Research | Biological diversity | Microbiology | Disease | Habitats | Taxonomy | Data processing | Skin | Life sciences | Genomes
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5. Full Text Relating the metatranscriptome and metagenome of the human gut
by Eric A. Franzosa and Xochitl C. Morgan and Nicola Segata and Levi Waldron and Joshua Reyes and Ashlee M. Earl and Georgia Giannoukos and Matthew R. Boylan and Dawn Ciulla and Dirk Gevers and Jacques Izard and Wendy S. Garrett and Andrew T. Chan and Curtis Huttenhower
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 06/2014, Volume 111, Issue 22, pp. E2329 - E2338
Although the composition of the human microbiome is now well-studied, the microbiota's >8 million genes and their regulation remain largely uncharacterized.... 
HUMAN MICROBIOME | BACTERIA | ENVIRONMENTS | TWINS | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | COMMUNITIES | SAMPLES | Humans | Specimen Handling - methods | Gastrointestinal Tract - microbiology | Transcriptome - genetics | RNA, Bacterial - analysis | Feces - microbiology | Metagenome - genetics | Mouth - microbiology | Gastrointestinal Tract - physiology | Microbiota - genetics | Saliva - microbiology | DNA, Bacterial - analysis | Gene Expression Regulation, Bacterial | Genomics - methods | PNAS Plus | Biological Sciences
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6. Full Text A framework for human microbiome research
by Methé, Barbara A and Nelson, Karen E and Pop, Mihai and Creasy, Heather H and Giglio, Michelle G and Huttenhower, Curtis and Gevers, Dirk and Petrosino, Joseph F and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Earl, Ashlee M and Fitzgerald, Michael G and Fulton, Robert S and Hallsworth-Pepin, Kymberlie and Lobos, Elizabeth A and Madupu, Ramana and Magrini, Vincent and Martin, John C and Mitreva, Makedonka and Muzny, Donna M and Sodergren, Erica J and Versalovic, James and Wollam, Aye M and Worley, Kim C and Wortman, Jennifer R and Young, Sarah K and Zeng, Qiandong and Aagaard, Kjersti M and Abolude, Olukemi O and Allen-Vercoe, Emma and Alm, Eric J and Alvarado, Lucia and Andersen, Gary L and Anderson, Scott and Appelbaum, Elizabeth and Arachchi, Harindra M and Armitage, Gary and Arze, Cesar A and Ayvaz, Tulin and Baker, Carl C and Begg, Lisa and Belachew, Tsegahiwot and Bhonagiri, Veena and Bihan, Monika and Blaser, Martin J and Bloom, Toby and Bonazzi, Vivien R and Brooks, Paul and Buck, Gregory A and Buhay, Christian J and Busam, Dana A and Campbell, Joseph L and Canon, Shane R and Cantarel, Brandi L and Chain, Patrick S and Chen, I-Min A and Chen, Lei and Chhibba, Shaila and Chu, Ken and Ciulla, Dawn M and Clemente, Jose C and Clifton, Sandra W and Conlan, Sean and Crabtree, Jonathan and Cutting, Mary A and Davidovics, Noam J and Davis, Catherine C and Desantis, Todd Z and Deal, Carolyn and Delehaunty, Kimberley D and Dewhirst, Floyd E and Deych, Elena and Ding, Yan and Dooling, David J and Dugan, Shannon P and Michael Dunne, W and Scott Durkin, A and Edgar, Robert C and Erlich, Rachel L and Farmer, Candace N and Farrell, Ruth M and Faust, Karoline and Feldgarden, Michael and Felix, Victor M and Fisher, Sheila and Fodor, Anthony A and Forney, Larry and Foster, Leslie and Di Francesco, Valentina and Friedman, Jonathan and Friedrich, Dennis C and Fronick, Catrina C and Fulton, Lucinda L and Gao, Hongyu and Garcia, Nathalia and Giannoukos, Georgia and Giblin, Christina and Giovanni, Maria Y and Goldberg, Jonathan M and ... and Human Microbiome Project Consortiu and Human Microbiome Project Consortium and The Human Microbiome Project Consortium and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2012, Volume 486, Issue 7402, pp. 215 - 221
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The... 
MULTIDISCIPLINARY SCIENCES | CATALOG | Young Adult | Reference Standards | Humans | Adolescent | Metagenomics - methods | RNA, Ribosomal, 16S - genetics | Adult | Female | Male | Statistics as Topic | Bacteria - genetics | Metagenome | Genetic research | Microbiological research | Genomes | Research | Microbiota (Symbiotic organisms) | Studies | Medicine | Microbiology | Publications | Taxonomy | Genomics | Data processing | Manuscripts
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7. Full Text Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of staphylococcus aureus
by Peleg, Anton Y and Miyakis, Spiros and Ward, Doyle V and Earl, Ashlee M and Rubio, Aileen and Cameron, David R and Pillai, Satish and Moellering Jr, Robert C and Eliopoulos, George M
PLoS ONE, ISSN 1932-6203, 01/2012, Volume 7, Issue 1, p. e28316
Background: Daptomycin remains one of our last-line anti-staphylococcal agents. This study aims to characterize the genetic evolution to daptomycin resistance... 
METHICILLIN-RESISTANT | STRAINS | NONSUSCEPTIBILITY | ALIGNMENT | BACTEREMIA | MULTIDISCIPLINARY SCIENCES | IN-VIVO | SUSCEPTIBILITY | VANCOMYCIN-INTERMEDIATE | PHENOTYPE | POLYMORPHISM | Staphylococcus aureus - genetics | Staphylococcus aureus - isolation & purification | Humans | Cell Wall - chemistry | Patients | Sequence Analysis, DNA | Microbial Sensitivity Tests | Daptomycin - pharmacology | Laboratories, Hospital | Cell Wall - drug effects | Models, Biological | Cell Wall - metabolism | Lipid Metabolism - drug effects | Anti-Bacterial Agents - pharmacology | Staphylococcal Infections - microbiology | Genome, Bacterial - drug effects | Drug Resistance, Bacterial - genetics | Staphylococcus aureus - drug effects | Daptomycin - therapeutic use | Phosphates | Drug resistance in microorganisms | Genomics | Physiological aspects | Lipids | Genomes | Disease susceptibility | Genetic aspects | Nucleotide sequencing | Cardiolipin | Staphylococcus aureus | DNA sequencing | Laboratories | Genes | Biological evolution | Daptomycin | Diacylglycerol | Biosynthesis | Phospholipids | Kinases | Medical schools | Gene sequencing | Genotype & phenotype | Glycerol-3-phosphate | Phosphatidylglycerol | Pathogens | Cell walls | Mortality | Glycerol | Staphylococcus infections | Membrane composition | Exposure | RNA polymerase | Electron microscopy | CDP-diacylglycerol | Infectious diseases | Antibiotics | Mutation | Evolution & development
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