-
1
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355-9.
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
Deboy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
2
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007;14:169-81.
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
-
3
-
-
84879343905
-
Control of pathogens and pathobionts by the gut microbiota
-
Kamada N, Chen GY, Inohara N, Nunez G. Control of pathogens and pathobionts by the gut microbiota. Nat Immunol. 2013;14:685-90.
-
(2013)
Nat Immunol
, vol.14
, pp. 685-690
-
-
Kamada, N.1
Chen, G.Y.2
Inohara, N.3
Nunez, G.4
-
4
-
-
84966861852
-
Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study
-
Milani C, Ticinesi A, Gerritsen J, Nouvenne A, Lugli GA, Mancabelli L, Turroni F, Duranti S, Mangifesta M, Viappiani A, et al. Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. Sci Rep. 2016;6:25945.
-
(2016)
Sci Rep
, vol.6
, pp. 25945
-
-
Milani, C.1
Ticinesi, A.2
Gerritsen, J.3
Nouvenne, A.4
Lugli, G.A.5
Mancabelli, L.6
Turroni, F.7
Duranti, S.8
Mangifesta, M.9
Viappiani, A.10
-
5
-
-
84861708688
-
Metagenomics of human microbiome: beyond 16 s rDNA
-
Gosalbes MJ, Abellan JJ, Durban A, Perez-Cobas AE, Latorre A, Moya A. Metagenomics of human microbiome: beyond 16 s rDNA. Clin Microbiol Infect. 2012;18 Suppl 4:47-9.
-
(2012)
Clin Microbiol Infect
, vol.18
, pp. 47-49
-
-
Gosalbes, M.J.1
Abellan, J.J.2
Durban, A.3
Perez-Cobas, A.E.4
Latorre, A.5
Moya, A.6
-
6
-
-
84880286399
-
Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol
-
Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martin R, Gueimonde M, van Sinderen D, et al. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One. 2013;8:e68739.
-
(2013)
PLoS One
, vol.8
-
-
Milani, C.1
Hevia, A.2
Foroni, E.3
Duranti, S.4
Turroni, F.5
Lugli, G.A.6
Sanchez, B.7
Martin, R.8
Gueimonde, M.9
van Sinderen, D.10
-
7
-
-
67549119095
-
Microbiomic analysis of the bifidobacterial population in the human distal gut
-
Turroni F, Marchesi JR, Foroni E, Gueimonde M, Shanahan F, Margolles A, van Sinderen D, Ventura M. Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME J. 2009;3:745-51.
-
(2009)
ISME J
, vol.3
, pp. 745-751
-
-
Turroni, F.1
Marchesi, J.R.2
Foroni, E.3
Gueimonde, M.4
Shanahan, F.5
Margolles, A.6
van Sinderen, D.7
Ventura, M.8
-
8
-
-
84943327494
-
Exploring vertical transmission of bifidobacteria from mother to child
-
Milani C, Mancabelli L, Lugli GA, Duranti S, Turroni F, Ferrario C, Mangifesta M, Viappiani A, Ferretti P, Gorfer V, et al. Exploring vertical transmission of bifidobacteria from mother to child. Appl Environ Microbiol. 2015;81:7078-87.
-
(2015)
Appl Environ Microbiol
, vol.81
, pp. 7078-7087
-
-
Milani, C.1
Mancabelli, L.2
Lugli, G.A.3
Duranti, S.4
Turroni, F.5
Ferrario, C.6
Mangifesta, M.7
Viappiani, A.8
Ferretti, P.9
Gorfer, V.10
-
9
-
-
0031761561
-
Sequence analysis of bacterial DNA in the colon of an Andean mummy
-
Ubaldi M, Luciani S, Marota I, Fornaciari G, Cano RJ, Rollo F. Sequence analysis of bacterial DNA in the colon of an Andean mummy. Am J Phys Anthropol. 1998;107:285-95.
-
(1998)
Am J Phys Anthropol
, vol.107
, pp. 285-295
-
-
Ubaldi, M.1
Luciani, S.2
Marota, I.3
Fornaciari, G.4
Cano, R.J.5
Rollo, F.6
-
10
-
-
0033938753
-
Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman
-
Cano RJ, Tiefenbrunner F, Ubaldi M, Del Cueto C, Luciani S, Cox T, Orkand P, Kunzel KH, Rollo F. Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman. Am J Phys Anthropol. 2000;112:297-309.
-
(2000)
Am J Phys Anthropol
, vol.112
, pp. 297-309
-
-
Cano, R.J.1
Tiefenbrunner, F.2
Ubaldi, M.3
Del Cueto, C.4
Luciani, S.5
Cox, T.6
Orkand, P.7
Kunzel, K.H.8
Rollo, F.9
-
11
-
-
84871194834
-
Insights from characterizing extinct human gut microbiomes
-
Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, et al. Insights from characterizing extinct human gut microbiomes. PLoS One. 2012;7:e51146.
-
(2012)
PLoS One
, vol.7
-
-
Tito, R.Y.1
Knights, D.2
Metcalf, J.3
Obregon-Tito, A.J.4
Cleeland, L.5
Najar, F.6
Roe, B.7
Reinhard, K.8
Sobolik, K.9
Belknap, S.10
-
12
-
-
84925335423
-
Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures
-
Cano RJ, Rivera-Perez J, Toranzos GA, Santiago-Rodriguez TM, Narganes-Storde YM, Chanlatte-Baik L, Garcia-Roldan E, Bunkley-Williams L, Massey SE. Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures. PLoS One. 2014;9:e106833.
-
(2014)
PLoS One
, vol.9
-
-
Cano, R.J.1
Rivera-Perez, J.2
Toranzos, G.A.3
Santiago-Rodriguez, T.M.4
Narganes-Storde, Y.M.5
Chanlatte-Baik, L.6
Garcia-Roldan, E.7
Bunkley-Williams, L.8
Massey, S.E.9
-
13
-
-
84897417984
-
Pathogens and host immunity in the ancient human oral cavity
-
Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, et al. Pathogens and host immunity in the ancient human oral cavity. Nat Genet. 2014;46:336-44.
-
(2014)
Nat Genet
, vol.46
, pp. 336-344
-
-
Warinner, C.1
Rodrigues, J.F.2
Vyas, R.3
Trachsel, C.4
Shved, N.5
Grossmann, J.6
Radini, A.7
Hancock, Y.8
Tito, R.Y.9
Fiddyment, S.10
-
14
-
-
84875759214
-
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
-
Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW, Haak W, Bradshaw CJ, Townsend G, Soltysiak A, Alt KW, et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet. 2013;45:450-5. 455e451.
-
(2013)
Nat Genet
, vol.45
, pp. 450e451-455e451
-
-
Adler, C.J.1
Dobney, K.2
Weyrich, L.S.3
Kaidonis, J.4
Walker, A.W.5
Haak, W.6
Bradshaw, C.J.7
Townsend, G.8
Soltysiak, A.9
Alt, K.W.10
-
16
-
-
0035344143
-
Ancient DNA
-
Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Nat Rev Genet. 2001;2:353-9.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 353-359
-
-
Hofreiter, M.1
Serre, D.2
Poinar, H.N.3
Kuch, M.4
Paabo, S.5
-
18
-
-
0014234390
-
Dermatophytes isolated from an open air public bath
-
Gip L, Aschan-Aberg K. Dermatophytes isolated from an open air public bath. Acta Derm Venereol. 1968;48:246-8.
-
(1968)
Acta Derm Venereol
, vol.48
, pp. 246-248
-
-
Gip, L.1
Aschan-Aberg, K.2
-
19
-
-
80054987989
-
A draft genome of Yersinia pestis from victims of the Black Death
-
Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S, et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011;478:506-10.
-
(2011)
Nature
, vol.478
, pp. 506-510
-
-
Bos, K.I.1
Schuenemann, V.J.2
Golding, G.B.3
Burbano, H.A.4
Waglechner, N.5
Coombes, B.K.6
McPhee, J.B.7
DeWitte, S.N.8
Meyer, M.9
Schmedes, S.10
-
20
-
-
84880294680
-
Genome-wide comparison of medieval and modern Mycobacterium leprae
-
Schuenemann VJ, Singh P, Mendum TA, Krause-Kyora B, Jager G, Bos KI, Herbig A, Economou C, Benjak A, Busso P, et al. Genome-wide comparison of medieval and modern Mycobacterium leprae. Science. 2013;341:179-83.
-
(2013)
Science
, vol.341
, pp. 179-183
-
-
Schuenemann, V.J.1
Singh, P.2
Mendum, T.A.3
Krause-Kyora, B.4
Jager, G.5
Bos, K.I.6
Herbig, A.7
Economou, C.8
Benjak, A.9
Busso, P.10
-
21
-
-
84955119180
-
The 5300-year-old Helicobacter pylori genome of the Iceman
-
Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, et al. The 5300-year-old Helicobacter pylori genome of the Iceman. Science. 2016;351:162-5.
-
(2016)
Science
, vol.351
, pp. 162-165
-
-
Maixner, F.1
Krause-Kyora, B.2
Turaev, D.3
Herbig, A.4
Hoopmann, M.R.5
Hallows, J.L.6
Kusebauch, U.7
Vigl, E.E.8
Malfertheiner, P.9
Megraud, F.10
-
22
-
-
0028896005
-
The 'Iceman': molecular structure of 5200-year-old skin characterised by Raman spectroscopy and electron microscopy
-
Williams AC, Edwards HG, Barry BW. The 'Iceman': molecular structure of 5200-year-old skin characterised by Raman spectroscopy and electron microscopy. Biochim Biophys Acta. 1995;1246:98-105.
-
(1995)
Biochim Biophys Acta
, vol.1246
, pp. 98-105
-
-
Williams, A.C.1
Edwards, H.G.2
Barry, B.W.3
-
23
-
-
0036771771
-
Otzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps
-
Rollo F, Ubaldi M, Ermini L, Marota I. Otzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proc Natl Acad Sci U S A. 2002;99:12594-9.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 12594-12599
-
-
Rollo, F.1
Ubaldi, M.2
Ermini, L.3
Marota, I.4
-
24
-
-
84863230079
-
New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
-
Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun. 2012;3:698.
-
(2012)
Nat Commun
, vol.3
, pp. 698
-
-
Keller, A.1
Graefen, A.2
Ball, M.3
Matzas, M.4
Boisguerin, V.5
Maixner, F.6
Leidinger, P.7
Backes, C.8
Khairat, R.9
Forster, M.10
-
25
-
-
84907803675
-
Ancient human genomes suggest three ancestral populations for present-day Europeans
-
Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014;513:409-13.
-
(2014)
Nature
, vol.513
, pp. 409-413
-
-
Lazaridis, I.1
Patterson, N.2
Mittnik, A.3
Renaud, G.4
Mallick, S.5
Kirsanow, K.6
Sudmant, P.H.7
Schraiber, J.G.8
Castellano, S.9
Lipson, M.10
-
26
-
-
55149118400
-
An effective method for isolation of DNA from pig faeces and comparison of five different methods
-
Tang JN, Zeng ZG, Wang HN, Yang T, Zhang PJ, Li YL, Zhang AY, Fan WQ, Zhang Y, Yang X, et al. An effective method for isolation of DNA from pig faeces and comparison of five different methods. J Microbiol Methods. 2008;75:432-6.
-
(2008)
J Microbiol Methods
, vol.75
, pp. 432-436
-
-
Tang, J.N.1
Zeng, Z.G.2
Wang, H.N.3
Yang, T.4
Zhang, P.J.5
Li, Y.L.6
Zhang, A.Y.7
Fan, W.Q.8
Zhang, Y.9
Yang, X.10
-
27
-
-
85027920660
-
Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany
-
Lee EJ, Makarewicz C, Renneberg R, Harder M, Krause-Kyora B, Muller S, Ostritz S, Fehren-Schmitz L, Schreiber S, Muller J, et al. Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany. Am J Phys Anthropol. 2012;148:571-9.
-
(2012)
Am J Phys Anthropol
, vol.148
, pp. 571-579
-
-
Lee, E.J.1
Makarewicz, C.2
Renneberg, R.3
Harder, M.4
Krause-Kyora, B.5
Muller, S.6
Ostritz, S.7
Fehren-Schmitz, L.8
Schreiber, S.9
Muller, J.10
-
28
-
-
84855295457
-
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
-
Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2012;40:e3.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kircher, M.1
Sawyer, S.2
Meyer, M.3
-
29
-
-
77956285690
-
Illumina sequencing library preparation for highly multiplexed target capture and sequencing
-
Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010; 2010:pdb prot5448.
-
(2010)
Cold Spring Harb Protoc
, vol.2010
-
-
Meyer, M.1
Kircher, M.2
-
30
-
-
84961231203
-
MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
-
Epub 2016 Mar 1
-
Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation. FEMS Microbiol Lett. 2016;363(7). doi:10.1093/femsle/fnw049. Epub 2016 Mar 1.
-
(2016)
FEMS Microbiol Lett
, vol.363
, Issue.7
-
-
Lugli, G.A.1
Milani, C.2
Mancabelli, L.3
van Sinderen, D.4
Ventura, M.5
-
31
-
-
84860771820
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455-77.
-
(2012)
J Comput Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
-
32
-
-
79960421225
-
mapDamage: testing for damage patterns in ancient DNA sequences
-
Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics. 2011;27:2153-5.
-
(2011)
Bioinformatics
, vol.27
, pp. 2153-2155
-
-
Ginolhac, A.1
Rasmussen, M.2
Gilbert, M.T.3
Willerslev, E.4
Orlando, L.5
-
33
-
-
77956193448
-
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
-
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5:e11147.
-
(2010)
PLoS One
, vol.5
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
34
-
-
77952299957
-
Prodigal: prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;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
-
35
-
-
84855167751
-
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
-
Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012;28:125-6.
-
(2012)
Bioinformatics
, vol.28
, pp. 125-126
-
-
Zhao, Y.1
Tang, H.2
Ye, Y.3
-
36
-
-
0030854739
-
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955-64.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
37
-
-
34250665888
-
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
-
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100-8.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rodland, E.A.3
Staerfeldt, H.H.4
Rognes, T.5
Ussery, D.W.6
-
38
-
-
84891782659
-
Pfam: the protein families database
-
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222-30.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
Heger, A.7
Hetherington, K.8
Holm, L.9
Mistry, J.10
-
39
-
-
0033635022
-
Artemis: sequence visualization and annotation
-
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16:944-5.
-
(2000)
Bioinformatics
, vol.16
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Rice, P.5
Rajandream, M.A.6
Barrell, B.7
-
40
-
-
84856571322
-
PGAP: pan-genomes analysis pipeline
-
Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. PGAP: pan-genomes analysis pipeline. Bioinformatics. 2012;28:416-8.
-
(2012)
Bioinformatics
, vol.28
, pp. 416-418
-
-
Zhao, Y.1
Wu, J.2
Yang, J.3
Sun, S.4
Xiao, J.5
Yu, J.6
-
41
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575-84.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
42
-
-
0037100671
-
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059-66.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
43
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947-8.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
44
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106:19126-31.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 19126-19131
-
-
Richter, M.1
Rossello-Mora, R.2
-
45
-
-
77955038643
-
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
-
Csuros M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26:1910-2.
-
(2010)
Bioinformatics
, vol.26
, pp. 1910-1912
-
-
Csuros, M.1
-
47
-
-
84976869393
-
VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on
-
Chen L, Zheng D, Liu B, Yang J, Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on. Nucleic Acids Res. 2016;44:D694-7.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. D694-D697
-
-
Chen, L.1
Zheng, D.2
Liu, B.3
Yang, J.4
Jin, Q.5
-
48
-
-
84891763855
-
The carbohydrate-active enzymes database (CAZy) in 2013
-
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490-5.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D490-D495
-
-
Lombard, V.1
Golaconda Ramulu, H.2
Drula, E.3
Coutinho, P.M.4
Henrissat, B.5
-
49
-
-
84891774001
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2014;42:D459-71.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D459-D471
-
-
Caspi, R.1
Altman, T.2
Billington, R.3
Dreher, K.4
Foerster, H.5
Fulcher, C.A.6
Holland, T.A.7
Keseler, I.M.8
Kothari, A.9
Kubo, A.10
-
50
-
-
80052549504
-
Integrative analysis of environmental sequences using MEGAN4
-
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011;21:1552-60.
-
(2011)
Genome Res
, vol.21
, pp. 1552-1560
-
-
Huson, D.H.1
Mitra, S.2
Ruscheweyh, H.J.3
Weber, N.4
Schuster, S.C.5
-
51
-
-
84907716417
-
Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans
-
Scales BS, Dickson RP, LiPuma JJ, Huffnagle GB. Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans. Clin Microbiol Rev. 2014;27:927-48.
-
(2014)
Clin Microbiol Rev
, vol.27
, pp. 927-948
-
-
Scales, B.S.1
Dickson, R.P.2
LiPuma, J.J.3
Huffnagle, G.B.4
-
52
-
-
84875825207
-
Pseudomonas fluorescens can induce and divert the human beta-defensin-2 secretion in intestinal epithelial cells to enhance its virulence
-
Madi A, Alnabhani Z, Leneveu C, Mijouin L, Feuilloley M, Connil N. Pseudomonas fluorescens can induce and divert the human beta-defensin-2 secretion in intestinal epithelial cells to enhance its virulence. Arch Microbiol. 2013; 195:189-195.
-
(2013)
Arch Microbiol
, vol.195
, pp. 189-195
-
-
Madi, A.1
Alnabhani, Z.2
Leneveu, C.3
Mijouin, L.4
Feuilloley, M.5
Connil, N.6
-
53
-
-
84862181304
-
Ancient DNA studies: new perspectives on old samples
-
Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol. 2012;44:21.
-
(2012)
Genet Sel Evol
, vol.44
, pp. 21
-
-
Rizzi, E.1
Lari, M.2
Gigli, E.3
De Bellis, G.4
Caramelli, D.5
-
54
-
-
14044262978
-
Genomic insights that advance the species definition for prokaryotes
-
Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A. 2005;102:2567-72.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2567-2572
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
55
-
-
84928583669
-
Genomic analyses of Clostridium perfringens isolates from five toxinotypes
-
Hassan KA, Elbourne LD, Tetu SG, Melville SB, Rood JI, Paulsen IT. Genomic analyses of Clostridium perfringens isolates from five toxinotypes. Res Microbiol. 2015;166:255-63.
-
(2015)
Res Microbiol
, vol.166
, pp. 255-263
-
-
Hassan, K.A.1
Elbourne, L.D.2
Tetu, S.G.3
Melville, S.B.4
Rood, J.I.5
Paulsen, I.T.6
-
56
-
-
84952876173
-
Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs
-
Scales BS, Erb-Downward JR, Huffnagle IM, LiPuma JJ, Huffnagle GB. Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs. BMC Genomics. 2015;16:1032.
-
(2015)
BMC Genomics
, vol.16
, pp. 1032
-
-
Scales, B.S.1
Erb-Downward, J.R.2
Huffnagle, I.M.3
LiPuma, J.J.4
Huffnagle, G.B.5
-
57
-
-
33746747586
-
Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
-
Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, et al. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res. 2006;16:1031-40.
-
(2006)
Genome Res
, vol.16
, pp. 1031-1040
-
-
Myers, G.S.1
Rasko, D.A.2
Cheung, J.K.3
Ravel, J.4
Seshadri, R.5
DeBoy, R.T.6
Ren, Q.7
Varga, J.8
Awad, M.M.9
Brinkac, L.M.10
-
58
-
-
0029837467
-
DNA relatedness among Pseudomonas strains isolated from natural mineral waters and proposal of Pseudomonas veronii sp. n. ov
-
Elomari M, Coroler L, Hoste B, Gillis M, Izard D, Leclerc H. DNA relatedness among Pseudomonas strains isolated from natural mineral waters and proposal of Pseudomonas veronii sp. nov. Int J Syst Bacteriol. 1996;46:1138-44.
-
(1996)
Int J Syst Bacteriol
, vol.46
, pp. 1138-1144
-
-
Elomari, M.1
Coroler, L.2
Hoste, B.3
Gillis, M.4
Izard, D.5
Leclerc, H.6
-
59
-
-
0032950921
-
The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages
-
Nakayama K, Kanaya S, Ohnishi M, Terawaki Y, Hayashi T. The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol Microbiol. 1999;31:399-419.
-
(1999)
Mol Microbiol
, vol.31
, pp. 399-419
-
-
Nakayama, K.1
Kanaya, S.2
Ohnishi, M.3
Terawaki, Y.4
Hayashi, T.5
-
60
-
-
70349962990
-
Pseudomonas extremaustralis sp. n. ov., a Poly(3-hydroxybutyrate) producer isolated from an antarctic environment
-
Lopez NI, Pettinari MJ, Stackebrandt E, Tribelli PM, Potter M, Steinbuchel A, Mendez BS. Pseudomonas extremaustralis sp. nov., a Poly(3-hydroxybutyrate) producer isolated from an antarctic environment. Curr Microbiol. 2009;59:514-9.
-
(2009)
Curr Microbiol
, vol.59
, pp. 514-519
-
-
Lopez, N.I.1
Pettinari, M.J.2
Stackebrandt, E.3
Tribelli, P.M.4
Potter, M.5
Steinbuchel, A.6
Mendez, B.S.7
-
62
-
-
0031726607
-
Virulence genes of Clostridium perfringens
-
Rood JI. Virulence genes of Clostridium perfringens. Annu Rev Microbiol. 1998;52:333-60.
-
(1998)
Annu Rev Microbiol
, vol.52
, pp. 333-360
-
-
Rood, J.I.1
-
63
-
-
74649086747
-
The occurrence of cpb2-toxigenic Clostridium perfringens and the possible role of the beta2-toxin in enteric disease of domestic animals, wild animals and humans
-
van Asten AJ, Nikolaou GN, Grone A. The occurrence of cpb2-toxigenic Clostridium perfringens and the possible role of the beta2-toxin in enteric disease of domestic animals, wild animals and humans. Vet J. 2010;183:135-40.
-
(2010)
Vet J
, vol.183
, pp. 135-140
-
-
van Asten, A.J.1
Nikolaou, G.N.2
Grone, A.3
-
64
-
-
84962508839
-
Clostridium perfringens enterotoxin: action, genetics, and translational applications
-
Freedman JC, Shrestha A, McClane BA. Clostridium perfringens enterotoxin: action, genetics, and translational applications. Toxins. 2016;8(3):73. doi:10. 3390/toxins8030073.
-
(2016)
Toxins
, vol.8
, Issue.3
, pp. 73
-
-
Freedman, J.C.1
Shrestha, A.2
McClane, B.A.3
-
65
-
-
79952808907
-
Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxinantitoxin modules
-
Georgiades K, Raoult D. Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxinantitoxin modules. PLoS One. 2011;6:e17962.
-
(2011)
PLoS One
, vol.6
-
-
Georgiades, K.1
Raoult, D.2
-
66
-
-
14244266086
-
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes
-
Pandey DP, Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 2005;33:966-76.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 966-976
-
-
Pandey, D.P.1
Gerdes, K.2
|