Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

[1]  Dennis Vitkup,et al.  Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling , 2019, Nature Methods.

[2]  Randall J. Platt,et al.  Transcriptional recording by CRISPR spacer acquisition from RNA , 2018, Nature.

[3]  Harris H. Wang,et al.  Multiplex recording of cellular events over time on CRISPR biological tape , 2017, Science.

[4]  Christian Munck,et al.  Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment , 2017, Front. Microbiol..

[5]  J. Hoch.  A Life in Bacillus subtilis Signal Transduction. , 2017, Annual Review of Microbiology.

[6]  E. Koonin,et al.  Evolutionary Genomics of Defense Systems in Archaea and Bacteria. , 2017, Annual review of microbiology.

[7]  M. Sommer,et al.  Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut , 2017, Front. Cell. Infect. Microbiol..

[8]  N. Gulyaeva.  Molecular mechanisms of neuroplasticity: An expanding universe , 2017, Biochemistry (Moscow).

[9]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[10]  George M. Church,et al.  Molecular recordings by directed CRISPR spacer acquisition , 2016, Science.

[11]  A. K. Singh,et al.  Mobile genes in the human microbiome are structured from global to individual scales , 2016, Nature.

[12]  E. Charpentier,et al.  Adaptation in CRISPR-Cas Systems. , 2016, Molecular cell.

[13]  Christophe Dessimoz,et al.  Inferring Horizontal Gene Transfer , 2015, PLoS Comput. Biol..

[14]  Asaf Levy,et al.  CRISPR adaptation biases explain preference for acquisition of foreign DNA , 2015, Nature.

[15]  Tami D. Lieberman,et al.  Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes , 2015, bioRxiv.

[16]  Laurie E. Comstock,et al.  Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut , 2014, mBio.

[17]  Ole Lund,et al.  In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.

[18]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[19]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[20]  Sarah L. Westcott,et al.  Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform , 2013, Applied and Environmental Microbiology.

[21]  M. Muniesa,et al.  Shiga Toxin 2-Encoding Bacteriophages in Human Fecal Samples from Healthy Individuals , 2013, Applied and Environmental Microbiology.

[22]  Rotem Sorek,et al.  CRISPR-mediated adaptive immune systems in bacteria and archaea. , 2013, Annual review of biochemistry.

[23]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[24]  Jesús García-Martínez,et al.  CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli , 2013, RNA biology.

[25]  Christine L. Sun,et al.  Strong bias in the bacterial CRISPR elements that confer immunity to phage , 2013, Nature Communications.

[26]  A. P. Williams,et al.  The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. , 2013, The Lancet. Infectious diseases.

[27]  N. Goddard,et al.  Competition Between Conjugation and M13 Phage Infection in Escherichia coli in the Absence of Selection Pressure: A Kinetic Study , 2012, G3: Genes | Genomes | Genetics.

[28]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[29]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[30]  U. Qimron,et al.  Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli , 2012, Nucleic acids research.

[31]  Konstantin Severinov,et al.  Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system , 2012, Nature Communications.

[32]  Otto X. Cordero,et al.  Ecology drives a global network of gene exchange connecting the human microbiome , 2011, Nature.

[33]  M. Touchon,et al.  CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection , 2011, Journal of bacteriology.

[34]  D. Mazel,et al.  Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of Escherichia coli Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery , 2010, Journal of bacteriology.

[35]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010, Bioinform..

[36]  G. Michel,et al.  Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota , 2010, Nature.

[37]  Olivier Tenaillon,et al.  The population genetics of commensal Escherichia coli , 2010, Nature Reviews Microbiology.

[38]  Pascal Lapierre,et al.  Estimating the size of the bacterial pan-genome. , 2009, Trends in genetics : TIG.

[39]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[40]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[41]  P. Gajer,et al.  The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates , 2008, Journal of bacteriology.

[42]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[43]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[44]  R. J. Martinez,et al.  Horizontal Gene Transfer of PIB-Type ATPases among Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface Soils , 2006, Applied and Environmental Microbiology.

[45]  Dominique L. Monnet,et al.  In Vivo Transfer of the vanA Resistance Gene from an Enterococcus faecium Isolate of Animal Origin to an E. faecium Isolate of Human Origin in the Intestines of Human Volunteers , 2006, Antimicrobial Agents and Chemotherapy.

[46]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Christopher M Thomas,et al.  Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria , 2005, Nature Reviews Microbiology.

[48]  Jeffrey P Townsend,et al.  Monitoring and modeling horizontal gene transfer , 2004, Nature Biotechnology.

[49]  Herbert Schmidt,et al.  Pathogenicity Islands in Bacterial Pathogenesis , 2004, Clinical Microbiology Reviews.

[50]  John Yen,et al.  Introduction , 2004, CACM.

[51]  H. Vlamakis,et al.  Evidence for Extensive Resistance Gene Transfer amongBacteroides spp. and among Bacteroides and Other Genera in the Human Colon , 2001, Applied and Environmental Microbiology.

[52]  V. de Lorenzo,et al.  Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria , 1990, Journal of bacteriology.

[53]  A. Pühler,et al.  A Broad Host Range Mobilization System for In Vivo Genetic Engineering: Transposon Mutagenesis in Gram Negative Bacteria , 1983, Bio/Technology.

[54]  D. E. Bradley,et al.  Specification of surface mating systems among conjugative drug resistance plasmids in Escherichia coli K-12 , 1980, Journal of bacteriology.

[55]  D. Helinski,et al.  Unidirectional replication of the P-group plasmid RK2. , 1977, Biochimica et biophysica acta.

[56]  T. S. Dhillon,et al.  Studies on bacteriophage distribution: virulent and temperate bacteriophage content of mammalian feces , 1976, Applied and environmental microbiology.

[57]  R. Sykes,et al.  Properties of an R Factor from Pseudomonas aeruginosa , 1971 .