-
1
-
-
84922735613
-
Extensive strain-level copy-number variation across human gut Microbiome species
-
Greenblum S, Carr R, Borenstein E. 2015. Extensive strain-level copy-number variation across human gut Microbiome species. Cell 160: 583-594. https://doi.org/10.1016/j.cell.2014.12.038.
-
(2015)
Cell
, vol.160
, pp. 583-594
-
-
Greenblum, S.1
Carr, R.2
Borenstein, E.3
-
2
-
-
84871732071
-
Genomic variation landscape of the human gut micro-biome
-
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. 2013. Genomic variation landscape of the human gut micro-biome. Nature 493:45-50. https://doi.org/10.1038/nature11711.
-
(2013)
Nature
, vol.493
, pp. 45-50
-
-
Schloissnig, S.1
Arumugam, M.2
Sunagawa, S.3
Mitreva, M.4
Tap, J.5
Zhu, A.6
Waller, A.7
Mende, D.R.8
Kultima, J.R.9
Martin, J.10
Kota, K.11
Sunyaev, S.R.12
Weinstock, G.M.13
Bork, P.14
-
3
-
-
84943606160
-
ConStrains identifies microbial strains in metagenomic datasets
-
Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D. 2015. ConStrains identifies microbial strains in metagenomic datasets. Nat Biotech-nol 33:1045-1052. https://doi.org/10.1038/nbt.3319.
-
(2015)
Nat Biotech-Nol
, vol.33
, pp. 1045-1052
-
-
Luo, C.1
Knight, R.2
Siljander, H.3
Knip, M.4
Xavier, R.J.5
Gevers, D.6
-
4
-
-
84861571695
-
-
Springer Science and Business Media, New York, NY
-
Hagedorn C, Blanch AR, Harwood VJ. 2011. Microbial source tracking: methods, applications, and case studies. Springer Science and Business Media, New York, NY.
-
(2011)
Microbial Source Tracking: Methods, Applications, and Case Studies
-
-
Hagedorn, C.1
Blanch, A.R.2
Harwood, V.J.3
-
5
-
-
84891630221
-
Microbial source tracking markers for detection of fecal contamination in environmental waters: Relationships between pathogens and human health outcomes
-
Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A. 2014. Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes. FEMS Microbiol Rev 38:1-40. https://doi.org/10.1111/1574-6976.12031.
-
(2014)
FEMS Microbiol Rev
, vol.38
, pp. 1-40
-
-
Harwood, V.J.1
Staley, C.2
Badgley, B.D.3
Borges, K.4
Korajkic, A.5
-
6
-
-
84865323065
-
Tracking a hospital outbreak ofcarbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing
-
NISC Comparative Sequencing Program Group
-
Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Segre JA, NISC Comparative Sequencing Program Group. 2012. Tracking a hospital outbreak ofcarbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4:148ra116-148ra116. https://doi.org/10.1126/scitranslmed.3004129.
-
(2012)
Sci Transl Med
, vol.4
, pp. 148ra116-148ra116
-
-
Snitkin, E.S.1
Zelazny, A.M.2
Thomas, P.J.3
Stock, F.4
Henderson, D.K.5
Palmore, T.N.6
Segre, J.A.7
-
7
-
-
75649084906
-
Evolution of MRSA during hospital transmission and intercontinental spread
-
Harris SR, Feil EJ, Holden MTG, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD. 2010. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327:469-474. https://doi.org/10.1126/science.1182395.
-
(2010)
Science
, vol.327
, pp. 469-474
-
-
Harris, S.R.1
Feil, E.J.2
Holden, M.3
Quail, M.A.4
Nickerson, E.K.5
Chantratita, N.6
Gardete, S.7
Tavares, A.8
Day, N.9
Lindsay, J.A.10
Edgeworth, J.D.11
De Lencastre, H.12
Parkhill, J.13
Peacock, S.J.14
Bentley, S.D.15
-
8
-
-
85014751056
-
-
Federal Bureau Investigation, Washington, DC
-
Federal Bureau Investigation. 2016. Amerithrax or anthrax investigation. Federal Bureau Investigation, Washington, DC. https://www.fbi.gov/history/famous-cases/amerithrax-or-anthrax-investigation.
-
(2016)
Amerithrax Or Anthrax Investigation
-
-
-
9
-
-
84864425353
-
Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking
-
McGhee GC, Sundin GW. 2012. Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking. PLoS One 7:e41706. https://doi.org/10.1371/journal.pone.0041706.
-
(2012)
Plos One
, vol.7
-
-
McGhee, G.C.1
Sundin, G.W.2
-
10
-
-
84904841142
-
Validation of high throughput sequencing and microbial forensics applications
-
Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA, Murch RS, Sajantila A, Schmedes SE, Ternus KL, Turner SD, Minot S. 2014. Validation of high throughput sequencing and microbial forensics applications. Invest Genet 5:9.
-
(2014)
Invest Genet
, vol.5
, pp. 9
-
-
Budowle, B.1
Connell, N.D.2
Bielecka-Oder, A.3
Colwell, R.R.4
Corbett, C.R.5
Fletcher, J.6
Forsman, M.7
Kadavy, D.R.8
Markotic, A.9
Morse, S.A.10
Murch, R.S.11
Sajantila, A.12
Schmedes, S.E.13
Ternus, K.L.14
Turner, S.D.15
Minot, S.16
-
11
-
-
0035182670
-
Database-driven multi locus sequence typing (MLST) of bacterial pathogens
-
Chan MS, Maiden MC, Spratt BG. 2001. Database-driven multi locus sequence typing (MLST) of bacterial pathogens. Bioinformatics 17: 1077-1083. https://doi.org/10.1093/bioinformatics/17.11.1077.
-
(2001)
Bioinformatics
, vol.17
, pp. 1077-1083
-
-
Chan, M.S.1
Maiden, M.C.2
Spratt, B.G.3
-
12
-
-
0032904916
-
Principles and applications of methods for DNA-based typing of microbial organisms
-
Olive DM, Bean P. 1999. Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37: 1661-1669.
-
(1999)
J Clin Microbiol
, vol.37
, pp. 1661-1669
-
-
Olive, D.M.1
Bean, P.2
-
13
-
-
84930239113
-
Whole-genome sequencing in outbreak analysis
-
Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. 2015. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev 28:541-563. https://doi.org/10.1128/CMR.00075-13.
-
(2015)
Clin Microbiol Rev
, vol.28
, pp. 541-563
-
-
Gilchrist, C.A.1
Turner, S.D.2
Riley, M.F.3
Petri, W.A.4
Hewlett, E.L.5
-
15
-
-
84936942726
-
Unusual biology across a group comprising more than 15% Of domain Bacteria
-
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF. 2015. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523: 208-211. https://doi.org/10.1038/nature14486.
-
(2015)
Nature
, vol.523
, pp. 208-211
-
-
Brown, C.T.1
Hug, L.A.2
Thomas, B.C.3
Sharon, I.4
Castelle, C.J.5
Singh, A.6
Wilkins, M.J.7
Wrighton, K.C.8
Williams, K.H.9
Banfield, J.F.10
-
16
-
-
84992418589
-
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
-
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. 2016. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 7:13219. https://doi.org/10.1038/ncomms13219.
-
(2016)
Nat Commun
, vol.7
, pp. 13219
-
-
Anantharaman, K.1
Brown, C.T.2
Hug, L.A.3
Sharon, I.4
Castelle, C.J.5
Probst, A.J.6
Thomas, B.C.7
Singh, A.8
Wilkins, M.J.9
Karaoz, U.10
Brodie, E.L.11
Williams, K.H.12
Hubbard, S.S.13
Banfield, J.F.14
-
17
-
-
85014796072
-
-
2 December, bioRxiv
-
Lee ST, Kahn SA, Delmont TO, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM. 2 December 2016. High-resolution tracking of microbial colonization in fecal microbiota transplantation experiments via metagenome-assembled genomes. bioRxiv. http://biorxiv.org/content/early/2016/12/02/090993.
-
(2016)
High-Resolution Tracking of Microbial Colonization in Fecal Microbiota Transplantation Experiments via Metagenome-Assembled Genomes
-
-
Lee, S.T.1
Kahn, S.A.2
Delmont, T.O.3
Hubert, N.A.4
Morrison, H.G.5
Antonopoulos, D.A.6
Rubin, D.T.7
Eren, A.M.8
-
18
-
-
84988871268
-
Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill
-
Dombrowski N, Donaho JA, Gutierrez T, Seitz KW, Teske AP, Baker BJ. 2016. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nat Microbiol 1:16057. https://doi.org/10.1038/nmicrobiol.2016.57.
-
(2016)
Nat Microbiol
, vol.1
, pp. 16057
-
-
Dombrowski, N.1
Donaho, J.A.2
Gutierrez, T.3
Seitz, K.W.4
Teske, A.P.5
Baker, B.J.6
-
19
-
-
84920644670
-
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
-
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. 2014. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:87. https://doi.org/10.1186/s12915-014-0087-z.
-
(2014)
BMC Biol
, vol.12
, pp. 87
-
-
Salter, S.J.1
Cox, M.J.2
Turek, E.M.3
Calus, S.T.4
Cookson, W.O.5
Moffatt, M.F.6
Turner, P.7
Parkhill, J.8
Loman, N.J.9
Walker, A.W.10
-
20
-
-
80052301430
-
Bayesian community-wide culture-independent microbial source tracking
-
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. 2011. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761-763. https://doi.org/10.1038/nmeth.1650.
-
(2011)
Nat Methods
, vol.8
, pp. 761-763
-
-
Knights, D.1
Kuczynski, J.2
Charlson, E.S.3
Zaneveld, J.4
Mozer, M.C.5
Collman, R.G.6
Bushman, F.D.7
Knight, R.8
Kelley, S.T.9
-
21
-
-
84887301559
-
Reconstructing the microbial diversity and function of Pre-Agricultural Tallgrass prairie soils in the United States
-
Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. 2013. Reconstructing the microbial diversity and function of Pre-Agricultural Tallgrass prairie soils in the United States. Science 342:621-624. https://doi.org/10.1126/science.1243768.
-
(2013)
Science
, vol.342
, pp. 621-624
-
-
Fierer, N.1
Ladau, J.2
Clemente, J.C.3
Leff, J.W.4
Owens, S.M.5
Pollard, K.S.6
Knight, R.7
Gilbert, J.A.8
McCulley, R.L.9
-
22
-
-
84897492912
-
Tackling soil diversity with the assembly of large, complex metagenomes
-
Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT. 2014. Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111:4904-4909. https://doi.org/10.1073/pnas.1402564111.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 4904-4909
-
-
Howe, A.C.1
Jansson, J.K.2
Malfatti, S.A.3
Tringe, S.G.4
Tiedje, J.M.5
Brown, C.T.6
-
23
-
-
20444395757
-
Abundance and diversity of viruses in six Delaware soils
-
Williamson KE, Radosevich M, Wommack KE. 2005. Abundance and diversity of viruses in six Delaware soils. Appl Environ Microbiol 71: 3119-3125. https://doi.org/10.1128/AEM.71.63119-3125.2005.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 3119-3125
-
-
Williamson, K.E.1
Radosevich, M.2
Wommack, K.E.3
-
24
-
-
84995468063
-
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
-
Butterfield C, Zhou L, Andeer P, Spaulding S, Thomas B, Andrea S, Hettich R, Suttle K, Probst A, Tringe S, Northen T, Pan C, Banfield J. 2016. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 4:e2687.
-
(2016)
Peerj
, vol.4
-
-
Butterfield, C.1
Zhou, L.2
Eer, P.3
Spaulding, S.4
Thomas, B.5
Rea, S.6
Hettich, R.7
Suttle, K.8
Probst, A.9
Tringe, S.10
Northen, T.11
Pan, C.12
Banfield, J.13
-
25
-
-
33846555715
-
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
-
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81-91. https://doi.org/10.1099/ijs.0.64483-0.
-
(2007)
Int J Syst Evol Microbiol
, vol.57
, pp. 81-91
-
-
Goris, J.1
Konstantinidis, K.T.2
Klappenbach, J.A.3
Coenye, T.4
Vandamme, P.5
Tiedje, J.M.6
-
26
-
-
84863507534
-
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
-
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649. https://doi.org/10.1093/bioinformatics/bts199.
-
(2012)
Bioinformatics
, vol.28
, pp. 1647-1649
-
-
Kearse, M.1
Moir, R.2
Wilson, A.3
Stones-Havas, S.4
Cheung, M.5
Sturrock, S.6
Buxton, S.7
Cooper, A.8
Markowitz, S.9
Duran, C.10
Thierer, T.11
Ashton, B.12
Meintjes, P.13
Drummond, A.14
-
27
-
-
84941368240
-
Growth dynamics of gut microbiota in health and disease inferred from single metag-enomic samples
-
Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier RJ, Elinav E, Segal E. 2015. Growth dynamics of gut microbiota in health and disease inferred from single metag-enomic samples. Science 349:1101-1106. https://doi.org/10.1126/science.aac4812.
-
(2015)
Science
, vol.349
, pp. 1101-1106
-
-
Korem, T.1
Zeevi, D.2
Suez, J.3
Weinberger, A.4
Avnit-Sagi, T.5
Pompan-Lotan, M.6
Matot, E.7
Jona, G.8
Harmelin, A.9
Cohen, N.10
Sirota-Madi, A.11
Thaiss, C.A.12
Pevsner-Fischer, M.13
Sorek, R.14
Xavier, R.J.15
Elinav, E.16
Segal, E.17
-
29
-
-
84875921666
-
A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4
-
Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ-m, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ. 2013. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309:1502-1510. https://doi.org/10.1001/jama.2013.3231.
-
(2013)
JAMA
, vol.309
, pp. 1502-1510
-
-
Loman, N.J.1
Constantinidou, C.2
Christner, M.3
Rohde, H.4
Jz-M, C.5
Quick, J.6
Weir, J.C.7
Quince, C.8
Smith, G.P.9
Betley, J.R.10
Aepfelbacher, M.11
Pallen, M.J.12
-
30
-
-
0036774995
-
Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States
-
Hoffmaster AR, Fitzgerald CC, Ribot E, Mayer LW, Popovic T. 2002. Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States. Emerg Infect Dis 8:1111-1116. https://doi.org/10.3201/eid0810.020394.
-
(2002)
Emerg Infect Dis
, vol.8
, pp. 1111-1116
-
-
Hoffmaster, A.R.1
Fitzgerald, C.C.2
Ribot, E.3
Mayer, L.W.4
Popovic, T.5
-
31
-
-
79953172949
-
Bacillus anthracis comparative genome analysis in support of the Ameri-thrax investigation
-
Box: Downloaded from mbio.asm.org on March 8, 2017-Published by mbio.asm.org Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, Keim PS, Fraser-Liggett CM, Ravel J. 2011. Bacillus anthracis comparative genome analysis in support of the Ameri-thrax investigation. Proc Natl Acad Sci U S A 108:5027-5032. https://doi.org/10.1073/pnas.1016657108.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 5027-5032
-
-
Rasko, D.A.1
Worsham, P.L.2
Abshire, T.G.3
Stanley, S.T.4
Bannan, J.D.5
Wilson, M.R.6
Langham, R.J.7
Decker, R.S.8
Jiang, L.9
Read, T.D.10
Phillippy, A.M.11
Salzberg, S.L.12
Pop, M.13
Van Ert, M.N.14
Kenefic, L.J.15
Keim, P.S.16
Fraser-Liggett, C.M.17
Ravel, J.18
-
32
-
-
0033607184
-
Calibrating bacterial evolution
-
Ochman H, Elwyn S, Moran NA. 1999. Calibrating bacterial evolution. Proc Natl Acad Sci U S A 96:12638-12643. https://doi.org/10.1073/pnas.96.22.12638.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 12638-12643
-
-
Ochman, H.1
Elwyn, S.2
Moran, N.A.3
-
33
-
-
0037849904
-
Stress-induced mutagenesis in bacteria
-
Bjedov I, Tenaillon O, Gerard B, Souza V, Denamur E, Radman M, Taddei F, Matic I. 2003. Stress-induced mutagenesis in bacteria. Science 300: 1404-1409. https://doi.org/10.1126/science.1082240.
-
(2003)
Science
, vol.300
, pp. 1404-1409
-
-
Bjedov, I.1
Tenaillon, O.2
Gerard, B.3
Souza, V.4
Denamur, E.5
Radman, M.6
Taddei, F.7
Matic, I.8
-
34
-
-
76949094947
-
The population genetics of commensal Escherichia coli
-
Tenaillon O, Skurnik D, Picard B, Denamur E. 2010. The population genetics of commensal Escherichia coli. Nat Rev Microbiol 8:207-217. https://doi.org/10.1038/nrmicro2298.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 207-217
-
-
Tenaillon, O.1
Skurnik, D.2
Picard, B.3
Denamur, E.4
-
35
-
-
84930626863
-
Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche
-
Rosen MJ, Davison M, Bhaya D, Fisher DS. 2015. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science348:1019-1023. https://doi.org/10.1126/science.aaa4456.
-
(2015)
Science348
, pp. 1019-1023
-
-
Rosen, M.J.1
Davison, M.2
Bhaya, D.3
Fisher, D.S.4
-
36
-
-
83055186603
-
Ecology drives a global network of gene exchange connecting the human microbiome
-
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244. https://doi.org/10.1038/nature10571.
-
(2011)
Nature
, vol.480
, pp. 241-244
-
-
Smillie, C.S.1
Smith, M.B.2
Friedman, J.3
Cordero, O.X.4
David, L.A.5
Alm, E.J.6
-
37
-
-
3242753673
-
Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria
-
Schleheck D, Knepper TP, Fischer K, Cook AM. 2004. Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria. Appl Environ Microbiol 70:4053-4063. https://doi.org/10.1128/AEM.70.7.4053-4063.2004.
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 4053-4063
-
-
Schleheck, D.1
Knepper, T.P.2
Fischer, K.3
Cook, A.M.4
-
38
-
-
3843150551
-
Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles
-
Friedman R, Drake JW, Hughes AL. 2004. Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles. Genetics 167:1507-1512. https://doi.org/10.1534/genetics.104.026344.
-
(2004)
Genetics
, vol.167
, pp. 1507-1512
-
-
Friedman, R.1
Drake, J.W.2
Hughes, A.L.3
-
39
-
-
33644630612
-
Comparisons of dN/dS are time dependent for closely related bacterial genomes
-
Rocha EPC, Smith JM, Hurst LD, Holden MTG, Cooper JE, Smith NH, Feil EJ. 2006. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol 239:226-235. https://doi.org/10.1016/j.jtbi.2005.08.037.
-
(2006)
J Theor Biol
, vol.239
, pp. 226-235
-
-
Rocha, E.1
Smith, J.M.2
Hurst, L.D.3
Holden, M.4
Cooper, J.E.5
Smith, N.H.6
Feil, E.J.7
-
41
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420-1428. https://doi.org/10.1093/bioinformatics/bts174.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.2
Yiu, S.M.3
Chin, F.Y.L.4
-
42
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. https://doi.org/10.1186/1471-2105-11-119.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
43
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42:D199-D205. https://doi.org/10.1093/nar/gkt1076.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
44
-
-
34347388470
-
UniRef: Comprehensive and non-redundant UniProt reference clusters
-
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23:1282-1288. https://doi.org/10.1093/bioinformatics/btm098.
-
(2007)
Bioinformatics
, vol.23
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
45
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461. https://doi.org/10.1093/bioinformatics/btq461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
46
-
-
84890037468
-
Infernal 1.1:100-fold faster RNA homology searches
-
Nawrocki EP, Eddy SR. 2013. Infernal 1.1:100-fold faster RNA homology searches. Bioinformatics 29:2933-2935. https://doi.org/10.1093/bioinformatics/btt509.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
48
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR. 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955-964. https://doi.org/10.1093/nar/25.5.0955.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
49
-
-
85006276920
-
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development
-
Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. 2015. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 4:e05477. https://doi.org/10.7554/eLife.05477.
-
(2015)
Elife
, vol.4
-
-
Raveh-Sadka, T.1
Thomas, B.C.2
Singh, A.3
Firek, B.4
Brooks, B.5
Castelle, C.J.6
Sharon, I.7
Baker, R.8
Good, M.9
Morowitz, M.J.10
Banfield, J.F.11
-
50
-
-
0038356405
-
A tribute to Claude Shannon (1916-2001)and a plea for more rigorous use of species richness, species diversity and the "Shannon-Wiener" index
-
Spellerberg IF, Fedor PJ. 2003. A tribute to Claude Shannon (1916-2001)and a plea for more rigorous use of species richness, species diversity and the "Shannon-Wiener" index. Glob Ecol Biogeogr 12:177-179.
-
(2003)
Glob Ecol Biogeogr
, vol.12
, pp. 177-179
-
-
Spellerberg, I.F.1
Fedor, P.J.2
-
51
-
-
84859210032
-
Fast gapped-read alignment with Bow-tie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bow-tie 2. Nat Methods 9:357-359. https://doi.org/10.1038/nmeth.1923.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
52
-
-
67650735586
-
ABACAS: Algorithm-based automatic contiguation ofassembled sequences
-
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. 2009. ABACAS: algorithm-based automatic contiguation ofassembled sequences. Bioinformatics 25:1968-1969. https://doi.org/10.1093/bioinformatics/btp347.
-
(2009)
Bioinformatics
, vol.25
, pp. 1968-1969
-
-
Assefa, S.1
Keane, T.M.2
Otto, T.D.3
Newbold, C.4
Berriman, M.5
-
53
-
-
68549115571
-
Reordering contigs of draft genomes using the Mauve aligner
-
Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. 2009. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 25:2071-2073. https://doi.org/10.1093/bioinformatics/btp356.
-
(2009)
Bioinformatics
, vol.25
, pp. 2071-2073
-
-
Rissman, A.I.1
Mau, B.2
Biehl, B.S.3
Darling, A.E.4
Glasner, J.D.5
Perna, N.T.6
-
54
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. https://doi.org/10.1093/nar/gkh340.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
55
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. https://doi.org/10.1093/bioinformatics/btl446.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
56
-
-
26944478553
-
Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: General implications and practical use in endodontic antimicrobial therapy
-
Horz HP, Vianna ME, Gomes BPFA, Conrads G. 2005. Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J Clin Microbiol 43:5332-5337. https://doi.org/10.1128/JCM.43.10.5332-5337.2005.
-
(2005)
J Clin Microbiol
, vol.43
, pp. 5332-5337
-
-
Horz, H.P.1
Vianna, M.E.2
Gomes, B.3
Conrads, G.4
-
57
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
1000 Genome Project Data Processing Subgroup
-
Box: Downloaded from mbio.asm.org on March 8, 2017-Published by mbio.asm.org Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. https://doi.org/10.1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
58
-
-
85007014992
-
-
Broad Institute, Cambridge, MA
-
Broad Institute. 2009. Picard Tools. Broad Institute, Cambridge, MA. http://broadinstitute.github.io/picard/.
-
(2009)
Picard Tools
-
-
-
59
-
-
69949122158
-
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples
-
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. 2009. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25:2283-2285. https://doi.org/10.1093/bioinformatics/btp373.
-
(2009)
Bioinformatics
, vol.25
, pp. 2283-2285
-
-
Koboldt, D.C.1
Chen, K.2
Wylie, T.3
Larson, D.E.4
McLellan, M.D.5
Mardis, E.R.6
Weinstock, G.M.7
Wilson, R.K.8
Ding, L.9
-
60
-
-
84917686994
-
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
-
Deatherage DE, Barrick JE. 2014. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol 1151:165-188. https://doi.org/10.1007/978-1-4939-0554-6_12.
-
(2014)
Methods Mol Biol
, vol.1151
, pp. 165-188
-
-
Deatherage, D.E.1
Barrick, J.E.2
|