-
1
-
-
0036135946
-
Molecular monitoring of succession of bacterial communities in human neonates
-
Favier CF, Vaughan EE, De Vos WM, Akkermans AD. 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68:219-226. http://dx.doi.org/10.1128/AEM .68.1.219-226.2002.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 219-226
-
-
Favier, C.F.1
Vaughan, E.E.2
De Vos, W.M.3
Akkermans, A.D.4
-
2
-
-
8744316858
-
Insights into the taxonomy, genetics and physiology of bifidobacteria
-
Ventura M, van Sinderen D, Fitzgerald GF, Zink R. 2004. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie Van Leeuwenhoek 86:205-223. http://dx.doi.org/10.1023/B:ANTO.0000047930.11029.ec.
-
(2004)
Antonie Van Leeuwenhoek
, vol.86
, pp. 205-223
-
-
Ventura, M.1
van Sinderen, D.2
Fitzgerald, G.F.3
Zink, R.4
-
3
-
-
84861011960
-
Diversity of bifidobacteria within the infant gut microbiota
-
Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M. 2012. Diversity of bifidobacteria within the infant gut microbiota. PLoS One 7:e36957. http://dx.doi.org/10.1371/journal.pone.0036957.
-
(2012)
PLoS One
, vol.7
-
-
Turroni, F.1
Peano, C.2
Pass, D.A.3
Foroni, E.4
Severgnini, M.5
Claesson, M.J.6
Kerr, C.7
Hourihane, J.8
Murray, D.9
Fuligni, F.10
Gueimonde, M.11
Margolles, A.12
De Bellis, G.13
O'Toole, P.W.14
van Sinderen, D.15
Marchesi, J.R.16
Ventura, M.17
-
4
-
-
57749113201
-
The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome
-
Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA. 2008. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc. Natl. Acad. Sci. U. S. A. 105:18964-18969. http://dx .doi.org/10.1073/pnas.0809584105.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 18964-18969
-
-
Sela, D.A.1
Chapman, J.2
Adeuya, A.3
Kim, J.H.4
Chen, F.5
Whitehead, T.R.6
Lapidus, A.7
Rokhsar, D.S.8
Lebrilla, C.B.9
German, J.B.10
Price, N.P.11
Richardson, P.M.12
Mills, D.A.13
-
5
-
-
78650609691
-
Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging
-
Turroni F, Bottacini F, Foroni E, Mulder I, Kim JH, Zomer A, Sanchez B, Bidossi A, Ferrarini A, Giubellini V, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Fitzgerald GF, Mills D, Margolles A, Kelly D, van Sinderen D, Ventura M. 2010. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl. Acad. Sci. U. S. A. 107:19514-19519. http://dx.doi.org /10.1073/pnas.1011100107.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 19514-19519
-
-
Turroni, F.1
Bottacini, F.2
Foroni, E.3
Mulder, I.4
Kim, J.H.5
Zomer, A.6
Sanchez, B.7
Bidossi, A.8
Ferrarini, A.9
Giubellini, V.10
Delledonne, M.11
Henrissat, B.12
Coutinho, P.13
Oggioni, M.14
Fitzgerald, G.F.15
Mills, D.16
Margolles, A.17
Kelly, D.18
van Sinderen, D.19
Ventura, M.20
more..
-
6
-
-
0023520958
-
Only the nose knows
-
Levitt MD. 1987. Only the nose knows. Gastroenterology 93:1437-1438.
-
(1987)
Gastroenterology
, vol.93
, pp. 1437-1438
-
-
Levitt, M.D.1
-
7
-
-
84863990011
-
Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon
-
Ze X, Duncan SH, Louis P, Flint HJ. 2012. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6:1535-1543. http://dx.doi.org/10.1038/ismej.2012.4.
-
(2012)
ISME J.
, vol.6
, pp. 1535-1543
-
-
Ze, X.1
Duncan, S.H.2
Louis, P.3
Flint, H.J.4
-
8
-
-
0030479827
-
Contribution of a neopullulanase, a pullulanase, and an alpha-glucosidase to growth of Bacteroides thetaiotaomicron on starch
-
D'Elia JN, Salyers AA. 1996. Contribution of a neopullulanase, a pullulanase, and an alpha-glucosidase to growth of Bacteroides thetaiotaomicron on starch. J. Bacteriol. 178:7173-7179.
-
(1996)
J. Bacteriol
, vol.178
, pp. 7173-7179
-
-
D'Elia, J.N.1
Salyers, A.A.2
-
9
-
-
79952765513
-
Substrate- driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch
-
Scott KP, Martin JC, Chassard C, Clerget M, Potrykus J, Campbell G, Mayer CD, Young P, Rucklidge G, Ramsay AG, Flint HJ. 2011. Substrate- driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch. Proc. Natl. Acad. Sci. U. S. A. 108(Suppl 1):S4672-S4679. http://dx.doi.org/10.1073/pnas .1000091107.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. S4672-S4679
-
-
Scott, K.P.1
Martin, J.C.2
Chassard, C.3
Clerget, M.4
Potrykus, J.5
Campbell, G.6
Mayer, C.D.7
Young, P.8
Rucklidge, G.9
Ramsay, A.G.10
Flint, H.J.11
-
10
-
-
79960845066
-
Genomics and ecological overview of the genus Bifidobacterium
-
Turroni F, van Sinderen D, Ventura M. 2010. Genomics and ecological overview of the genus Bifidobacterium. Int. J. Food Microbiol. 149:37-44. http://dx.doi.org/10.1016/j.ijfoodmicro.2010.12.010.
-
(2010)
Int. J. Food Microbiol.
, vol.149
, pp. 37-44
-
-
Turroni, F.1
van Sinderen, D.2
Ventura, M.3
-
11
-
-
78751580602
-
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
-
Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ. 2011. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5:220- 230. http://dx.doi.org/10.1038/ismej.2010.118.
-
(2011)
ISME J.
, vol.5
, pp. 220- 230
-
-
Walker, A.W.1
Ince, J.2
Duncan, S.H.3
Webster, L.M.4
Holtrop, G.5
Ze, X.6
Brown, D.7
Stares, M.D.8
Scott, P.9
Bergerat, A.10
Louis, P.11
McIntosh, F.12
Johnstone, A.M.13
Lobley, G.E.14
Parkhill, J.15
Flint, H.J.16
-
12
-
-
0032731669
-
In vitro utilization of amylopectin and high-amylose maize (amylomaize) starch granules by human colonic bacteria
-
Wang X, Conway PL, Brown IL, Evans AJ. 1999. In vitro utilization of amylopectin and high-amylose maize (amylomaize) starch granules by human colonic bacteria. Appl. Environ. Microbiol. 65:4848-4854.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 4848-4854
-
-
Wang, X.1
Conway, P.L.2
Brown, I.L.3
Evans, A.J.4
-
13
-
-
54949084244
-
Characterization of ApuB, an extracellular type II amylopullulanase from Bifidobacterium breve UCC2003
-
O'Connell Motherway M, Fitzgerald GF, Neirynck S, Ryan S, Steidler L, van Sinderen D. 2008. Characterization of ApuB, an extracellular type II amylopullulanase from Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 74:6271-6279. http://dx.doi.org/10.1128/AEM.01169-08.
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 6271-6279
-
-
O'Connell Motherway, M.1
Fitzgerald, G.F.2
Neirynck, S.3
Ryan, S.4
Steidler, L.5
van Sinderen, D.6
-
14
-
-
84866895877
-
Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria
-
Ventura M, Turroni F, O'Connell Motherway M, MacSharry J, van Sinderen D. 2012. Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria. Trends Microbiol. 20:467-476. http: //dx.doi.org/10.1016/j.tim.2012.07.002.
-
(2012)
Trends Microbiol.
, vol.20
, pp. 467-476
-
-
Ventura, M.1
Turroni, F.2
O'Connell Motherway, M.3
MacSharry, J.4
van Sinderen, D.5
-
15
-
-
0034931508
-
Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA)
-
Ventura M, Elli M, Reniero R, Zink R. 2001. Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA). FEMS Microbiol. Ecol. 36:113-121. http://dx.doi.org/10.1111/j.1574-6941.2001.tb00831.x.
-
(2001)
FEMS Microbiol. Ecol.
, vol.36
, pp. 113-121
-
-
Ventura, M.1
Elli, M.2
Reniero, R.3
Zink, R.4
-
17
-
-
3042615882
-
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
-
Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S. 2004. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14:1147-1159. http://dx.doi.org/10.1101/gr.1917404.
-
(2004)
Genome Res.
, vol.14
, pp. 1147-1159
-
-
Chevreux, B.1
Pfisterer, T.2
Drescher, B.3
Driesel, A.J.4
Muller, W.E.5
Wetter, T.6
Suhai, S.7
-
18
-
-
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. http://dx.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
-
19
-
-
0027399530
-
Identification of protein coding regions by database similarity search
-
Gish W, States DJ. 1993. Identification of protein coding regions by database similarity search. Nat. Genet. 3:266-272.
-
(1993)
Nat. Genet.
, vol.3
, pp. 266-272
-
-
Gish, W.1
States, D.J.2
-
20
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
21
-
-
0033635022
-
Artemis: sequence visualization and annotation
-
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945. http://dx.doi.org/10.1093/bioinformatics/16.10.944.
-
(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
-
22
-
-
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.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
23
-
-
75549086595
-
REBASE-a database for DNA restriction and modification: enzymes, genes and genomes
-
Roberts RJ, Vincze T, Posfai J, Macelis D. 2010. REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 38:D234-D236. http://dx.doi.org/10.1093/nar/gkp874.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D234-D236
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
26
-
-
42449107363
-
annot8r: GO, EC and KEGG annotation of EST datasets
-
Schmid R, Blaxter ML. 2008. annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics 9:180. http://dx.doi.org/10.1186/1471 -2105-9-180.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 180
-
-
Schmid, R.1
Blaxter, M.L.2
-
27
-
-
33747858422
-
GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
-
Gao F, Zhang CT. 2006. GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res. 34:W686-W691. http://dx.doi.org/10.1093/nar/gkl040.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W686-W691
-
-
Gao, F.1
Zhang, C.T.2
-
28
-
-
0030749594
-
Economic analysis of alternative AD control programmes
-
McInerney J, Kooij D. 1997. Economic analysis of alternative AD control programmes. Vet. Microbiol. 55:113-121.
-
(1997)
Vet. Microbiol.
, vol.55
, pp. 113-121
-
-
McInerney, J.1
Kooij, D.2
-
29
-
-
74249117479
-
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity
-
Ventura M, Turroni F, Zomer A, Foroni E, Giubellini V, Bottacini F, Canchaya C, Claesson MJ, He F, Mantzourani M, Mulas L, Ferrarini A, Gao B, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Gupta RS, Zhang Z, Beighton D, Fitzgerald GF, O'Toole PW, van Sinderen D. 2009. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet. 5:e1000785. http: //dx.doi.org/10.1371/journal.pgen.1000785.
-
(2009)
PLoS Genet.
, vol.5
-
-
Ventura, M.1
Turroni, F.2
Zomer, A.3
Foroni, E.4
Giubellini, V.5
Bottacini, F.6
Canchaya, C.7
Claesson, M.J.8
He, F.9
Mantzourani, M.10
Mulas, L.11
Ferrarini, A.12
Gao, B.13
Delledonne, M.14
Henrissat, B.15
Coutinho, P.16
Oggioni, M.17
Gupta, R.S.18
Zhang, Z.19
Beighton, D.20
Fitzgerald, G.F.21
O'Toole, P.W.22
van Sinderen, D.23
more..
-
30
-
-
84879824186
-
Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon
-
Milani C, Duranti S, Lugli GA, Bottacini F, Strati F, Arioli S, Foroni E, Turroni F, van Sinderen D, Ventura M. 2013. Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon. Appl. Environ. Microbiol. 79:4304-4315. http://dx.doi .org/10.1128/AEM.00984-13.
-
(2013)
Appl. Environ. Microbiol.
, vol.79
, pp. 4304-4315
-
-
Milani, C.1
Duranti, S.2
Lugli, G.A.3
Bottacini, F.4
Strati, F.5
Arioli, S.6
Foroni, E.7
Turroni, F.8
van Sinderen, D.9
Ventura, M.10
-
32
-
-
0037195083
-
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
-
Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. U. S. A. 99:14422-14427. http://dx.doi.org/10.1073/pnas.212527599.
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 14422-14427
-
-
Schell, M.A.1
Karmirantzou, M.2
Snel, B.3
Vilanova, D.4
Berger, B.5
Pessi, G.6
Zwahlen, M.C.7
Desiere, F.8
Bork, P.9
Delley, M.10
Pridmore, R.D.11
Arigoni, F.12
-
33
-
-
79960586903
-
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved hostcolonization factor
-
O'Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D. 2011. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved hostcolonization factor. Proc. Natl. Acad. Sci. U. S. A. 108:11217-11222. http: //dx.doi.org/10.1073/pnas.1105380108.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 11217-11222
-
-
O'Connell Motherway, M.1
Zomer, A.2
Leahy, S.C.3
Reunanen, J.4
Bottacini, F.5
Claesson, M.J.6
O'Brien, F.7
Flynn, K.8
Casey, P.G.9
Munoz, J.A.10
Kearney, B.11
Houston, A.M.12
O'Mahony, C.13
Higgins, D.G.14
Shanahan, F.15
Palva, A.16
de Vos, W.M.17
Fitzgerald, G.F.18
Ventura, M.19
O'Toole, P.W.20
van Sinderen, D.21
more..
-
34
-
-
0033990061
-
Flexible sequence similarity searching with the FASTA3 program package
-
Pearson WR. 2000. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132:185-219.
-
(2000)
Methods Mol. Biol.
, vol.132
, pp. 185-219
-
-
Pearson, W.R.1
-
35
-
-
0005924596
-
-
Ph.D. thesis. University of Utrecht, Utrecht, The Netherlands.
-
van Dongen S. 2002. Graph clustering by flow simulation. Ph.D. thesis. University of Utrecht, Utrecht, The Netherlands.
-
(2002)
Graph clustering by flow simulation
-
-
van Dongen, S.1
-
36
-
-
54049108449
-
Multiple sequence alignment using ClustalW and ClustalX
-
Chapter 2:Unit 2.3.
-
Thompson JD, Gibson TJ, Higgins DG. 2002. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics Chapter 2:Unit 2.3. http://dx.doi.org/10.1002/0471250953.bi0203s00.
-
(2002)
Curr. Protoc. Bioinformatics
-
-
Thompson, J.D.1
Gibson, T.J.2
Higgins, D.G.3
-
37
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696- 704. http://dx.doi.org/10.1080/10635150390235520.
-
(2003)
Syst. Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
38
-
-
77952265532
-
Characterization of the serpin-encoding gene of Bifidobacterium breve 210B
-
Turroni F, Foroni E, O'Connell Motherway M, Bottacini F, Giubellini V, Zomer A, Ferrarini A, Delledonne M, Zhang Z, van Sinderen D, Ventura M. 2010. Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Appl. Environ. Microbiol. 76:3206-3219. http: //dx.doi.org/10.1128/AEM.02938-09.
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 3206-3219
-
-
Turroni, F.1
Foroni, E.2
O'Connell Motherway, M.3
Bottacini, F.4
Giubellini, V.5
Zomer, A.6
Ferrarini, A.7
Delledonne, M.8
Zhang, Z.9
van Sinderen, D.10
Ventura, M.11
-
39
-
-
0003903343
-
-
2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
(1989)
Molecular cloning: a laboratory manual
-
-
Sambrook, J.1
Fritsch, E.F.2
Maniatis, T.3
-
40
-
-
83155193029
-
Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative real-time PCR
-
Turroni F, Foroni E, Montanini B, Viappiani A, Strati F, Duranti S, Ferrarini A, Delledonne M, van Sinderen D, Ventura M. 2011. Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative real-time PCR. Appl. Environ. Microbiol. 77:8578-8587. http://dx .doi.org/10.1128/AEM.06352-11.
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 8578-8587
-
-
Turroni, F.1
Foroni, E.2
Montanini, B.3
Viappiani, A.4
Strati, F.5
Duranti, S.6
Ferrarini, A.7
Delledonne, M.8
van Sinderen, D.9
Ventura, M.10
-
41
-
-
67649884743
-
Fast and accurate short read alignment with Burrows- Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25:1754-1760. http://dx.doi .org/10.1093/bioinformatics/btp324.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
42
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol. 11:R106. http://dx.doi.org/10.1186/gb-2010-11 -10-r106.
-
(2010)
Genome Biol.
, vol.11
-
-
Anders, S.1
Huber, W.2
-
43
-
-
84879700369
-
Role of sortase-dependent pili of BifidobacteriumbifidumPRL2010in modulating bacterium-host interactions
-
Turroni F, Serafini F, Foroni E, Duranti S, O'Connell Motherway M, Taverniti V, Mangifesta M, Milani C, Viappiani A, Roversi T, Sanchez B, Santoni A, Gioiosa L, Ferrarini A, Delledonne M, Margolles A, Piazza L, Palanza P, Bolchi A, Guglielmetti S, van Sinderen D, Ventura M. 2013. Role of sortase-dependent pili of BifidobacteriumbifidumPRL2010in modulating bacterium-host interactions. Proc. Natl. Acad. Sci. U. S. A. 110:11151-11156. http://dx.doi.org/10.1073/pnas.1303897110.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 11151-11156
-
-
Turroni, F.1
Serafini, F.2
Foroni, E.3
Duranti, S.4
O'Connell Motherway, M.5
Taverniti, V.6
Mangifesta, M.7
Milani, C.8
Viappiani, A.9
Roversi, T.10
Sanchez, B.11
Santoni, A.12
Gioiosa, L.13
Ferrarini, A.14
Delledonne, M.15
Margolles, A.16
Piazza, L.17
Palanza, P.18
Bolchi, A.19
Guglielmetti, S.20
van Sinderen, D.21
Ventura, M.22
more..
-
44
-
-
84893312287
-
A high-fat diet differentially affects the gut metabolism and blood lipids of rats depending on the type of dietary fat and carbohydrate
-
Jurgonski A, Juskiewicz J, Zdunczyk Z. 2014. A high-fat diet differentially affects the gut metabolism and blood lipids of rats depending on the type of dietary fat and carbohydrate. Nutrients 6:616-626. http://dx.doi .org/10.3390/nu6020616.
-
(2014)
Nutrients
, vol.6
, pp. 616-626
-
-
Jurgonski, A.1
Juskiewicz, J.2
Zdunczyk, Z.3
-
45
-
-
0029757175
-
Controlled gene expression systems for Lactococcus lactis with the food-grade inducer nisin
-
de Ruyter PG, Kuipers OP, de Vos WM. 1996. Controlled gene expression systems for Lactococcus lactis with the food-grade inducer nisin. Appl. Environ. Microbiol. 62:3662-3667.
-
(1996)
Appl. Environ. Microbiol.
, vol.62
, pp. 3662-3667
-
-
de Ruyter, P.G.1
Kuipers, O.P.2
de Vos, W.M.3
-
46
-
-
34548746905
-
Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum
-
Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 71:495- 548. http://dx.doi.org/10.1128/MMBR.00005-07.
-
(2007)
Microbiol. Mol. Biol. Rev.
, vol.71
, pp. 495- 548
-
-
Ventura, M.1
Canchaya, C.2
Tauch, A.3
Chandra, G.4
Fitzgerald, G.F.5
Chater, K.F.6
van Sinderen, D.7
-
47
-
-
45749094143
-
Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth
-
Lee JH, Karamychev VN, Kozyavkin SA, Mills D, Pavlov AR, Pavlova NV, Polouchine NN, Richardson PM, Shakhova VV, Slesarev AI, Weimer B, O'Sullivan DJ. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9:247. http://dx.doi.org/10 .1186/1471-2164-9-247.
-
(2008)
BMC Genomics
, vol.9
, pp. 247
-
-
Lee, J.H.1
Karamychev, V.N.2
Kozyavkin, S.A.3
Mills, D.4
Pavlov, A.R.5
Pavlova, N.V.6
Polouchine, N.N.7
Richardson, P.M.8
Shakhova, V.V.9
Slesarev, A.I.10
Weimer, B.11
O'Sullivan, D.J.12
-
48
-
-
0037187437
-
Properties and applications of starch-converting enzymes of the alpha-amylase family
-
van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L. 2002. Properties and applications of starch-converting enzymes of the alpha-amylase family. J. Biotechnol. 94:137-155. http://dx .doi.org/10.1016/S0168-1656(01)00407-2.
-
(2002)
J. Biotechnol.
, vol.94
, pp. 137-155
-
-
van der Maarel, M.J.1
van der Veen, B.2
Uitdehaag, J.C.3
Leemhuis, H.4
Dijkhuizen, L.5
-
49
-
-
84863871551
-
Microbial degradation of complex carbohydrates in the gut
-
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. 2012. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3:289- 306. http://dx.doi.org/10.4161/gmic.19897.
-
(2012)
Gut Microbes
, vol.3
, pp. 289- 306
-
-
Flint, H.J.1
Scott, K.P.2
Duncan, S.H.3
Louis, P.4
Forano, E.5
-
50
-
-
33747360729
-
Screening for and identification of starch-, amylopectin-, and pullulan-degrading activities in bifidobacterial strains
-
Ryan SM, Fitzgerald GF, van Sinderen D. 2006. Screening for and identification of starch-, amylopectin-, and pullulan-degrading activities in bifidobacterial strains. Appl. Environ. Microbiol. 72:5289-5296. http: //dx.doi.org/10.1128/AEM.00257-06.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5289-5296
-
-
Ryan, S.M.1
Fitzgerald, G.F.2
van Sinderen, D.3
-
51
-
-
84875850627
-
Metabolism of oligosaccharides and starch in lactobacilli: a review
-
Ganzle MG, Follador R. 2012. Metabolism of oligosaccharides and starch in lactobacilli: a review. Front. Microbiol. 3:340. http://dx.doi.org/10.3389 /fmicb.2012.00340.
-
(2012)
Front. Microbiol.
, vol.3
, pp. 340
-
-
Ganzle, M.G.1
Follador, R.2
-
52
-
-
33644877904
-
MetaCyc: a multiorganism database of metabolic pathways and enzymes
-
Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD. 2006. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 34:D511-D516. http://dx.doi.org/10.1093 /nar/gkj128.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D511-D516
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
Hopkinson, R.4
Ingraham, J.5
Kaipa, P.6
Krummenacker, M.7
Paley, S.8
Pick, J.9
Rhee, S.Y.10
Tissier, C.11
Zhang, P.12
Karp, P.D.13
-
53
-
-
84863738705
-
Analysis of predicted carbohydrate transport systems encoded by Bifidobacterium bifidum PRL2010
-
Turroni F, Strati F, Foroni E, Serafini F, Duranti S, van Sinderen D, Ventura M. 2012. Analysis of predicted carbohydrate transport systems encoded by Bifidobacterium bifidum PRL2010. Appl. Environ. Microbiol. 78:5002-5012. http://dx.doi.org/10.1128/AEM.00629-12.
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 5002-5012
-
-
Turroni, F.1
Strati, F.2
Foroni, E.3
Serafini, F.4
Duranti, S.5
van Sinderen, D.6
Ventura, M.7
-
54
-
-
80052194287
-
Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium
-
Foroni E, Serafini F, Amidani D, Turroni F, He F, Bottacini F, O'Connell Motherway M, Viappiani A, Zhang Z, Rivetti C, van Sinderen D, Ventura M. 2011. Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium. Microb. Cell Fact. 10(Suppl 1):S16. http://dx.doi.org/10.1186/1475-2859 -10-S1-S16.
-
(2011)
Microb. Cell Fact.
, vol.10
-
-
Foroni, E.1
Serafini, F.2
Amidani, D.3
Turroni, F.4
He, F.5
Bottacini, F.6
O'Connell Motherway, M.7
Viappiani, A.8
Zhang, Z.9
Rivetti, C.10
van Sinderen, D.11
Ventura, M.12
-
55
-
-
62149124800
-
Exploring the diversity of the bifidobacterial population in the human intestinal tract
-
Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, Merusi P, Cagnasso P, Bizzarri B, de'Angelis GL, Shanahan F, van Sinderen D, Ventura M. 2009. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl. Environ. Microbiol. 75:1534- 1545. http://dx.doi.org/10.1128/AEM.02216-08.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 1534-1545
-
-
Turroni, F.1
Foroni, E.2
Pizzetti, P.3
Giubellini, V.4
Ribbera, A.5
Merusi, P.6
Cagnasso, P.7
Bizzarri, B.8
de'Angelis, G.L.9
Shanahan, F.10
van Sinderen, D.11
Ventura, M.12
-
56
-
-
0344683235
-
-
8th ed. National Academies Press, Washington, DC.
-
National Research Council. 2011. Guide for the care and use of laboratory animals, 8th ed. National Academies Press, Washington, DC.
-
(2011)
Guide for the care and use of laboratory animals
-
-
-
57
-
-
84892801172
-
Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective
-
Turroni F, Ventura M, Butto LF, Duranti S, O'Toole PW, O'Connell Motherway M, van Sinderen D. 2014. Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective. Cell. Mol. Life Sci. 71:183-203. http://dx.doi.org/10 .1007/s00018-013-1318-0.
-
(2014)
Cell. Mol. Life Sci.
, vol.71
, pp. 183-203
-
-
Turroni, F.1
Ventura, M.2
Butto, L.F.3
Duranti, S.4
O'Toole, P.W.5
O'Connell Motherway, M.6
van Sinderen, D.7
-
58
-
-
83755174215
-
Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria
-
Imam S, Chen Z, Roos DS, Pohlschroder M. 2011. Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria. PLoS One 6:e28919. http://dx.doi.org/10.1371/journal.pone .0028919.
-
(2011)
PLoS One
, vol.6
-
-
Imam, S.1
Chen, Z.2
Roos, D.S.3
Pohlschroder, M.4
-
59
-
-
84857128238
-
Bifidobacterial surface-exopolysaccharide facilitates commensal- host interaction through immune modulation and pathogen protection
-
Fanning S, Hall LJ, Cronin M, Zomer A, MacSharry J, Goulding D, O'Connell Motherway M, Shanahan F, Nally K, Dougan G, van Sinderen D. 2012. Bifidobacterial surface-exopolysaccharide facilitates commensal- host interaction through immune modulation and pathogen protection. Proc. Natl. Acad. Sci. U. S. A. 109:2108-2113. http://dx.doi.org /10.1073/pnas.1115621109.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 2108-2113
-
-
Fanning, S.1
Hall, L.J.2
Cronin, M.3
Zomer, A.4
MacSharry, J.5
Goulding, D.6
O'Connell Motherway, M.7
Shanahan, F.8
Nally, K.9
Dougan, G.10
van Sinderen, D.11
-
60
-
-
84891110585
-
Genomic overview and biological functions of exopolysaccharide biosynthesis in Bifidobacterium spp
-
Hidalgo-Cantabrana C, Sanchez B, Milani C, Ventura M, Margolles A, Ruas-Madiedo P. 2014. Genomic overview and biological functions of exopolysaccharide biosynthesis in Bifidobacterium spp. Appl. Environ. Microbiol. 80:9-18. http://dx.doi.org/10.1128/AEM.02977-13.
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 9-18
-
-
Hidalgo-Cantabrana, C.1
Sanchez, B.2
Milani, C.3
Ventura, M.4
Margolles, A.5
Ruas-Madiedo, P.6
-
61
-
-
82955205923
-
Ability of Bifidobacterium breve to grow on different types of milk: exploring the metabolism of milk through genome analysis
-
Turroni F, Foroni E, Serafini F, Viappiani A, Montanini B, Bottacini F, Ferrarini A, Bacchini PL, Rota C, Delledonne M, Ottonello S, van Sinderen D, Ventura M. 2011. Ability of Bifidobacterium breve to grow on different types of milk: exploring the metabolism of milk through genome analysis. Appl. Environ. Microbiol. 77:7408-7417. http://dx.doi .org/10.1128/AEM.05336-11.
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 7408-7417
-
-
Turroni, F.1
Foroni, E.2
Serafini, F.3
Viappiani, A.4
Montanini, B.5
Bottacini, F.6
Ferrarini, A.7
Bacchini, P.L.8
Rota, C.9
Delledonne, M.10
Ottonello, S.11
van Sinderen, D.12
Ventura, M.13
-
62
-
-
0017178414
-
Bifidobacteria in the intestinal tract of infants: an in-vitro study
-
Bullen CL, Tearle PV. 1976. Bifidobacteria in the intestinal tract of infants: an in-vitro study. J. Med. Microbiol. 9:335-344. http://dx.doi.org /10.1099/00222615-9-3-335.
-
(1976)
J. Med. Microbiol.
, vol.9
, pp. 335-344
-
-
Bullen, C.L.1
Tearle, P.V.2
|