-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
22744458161
-
Gene discovery in the Acanthamoeba castellanii genome
-
Anderson IJ, Watkins RF, Samuelson J, Spencer DF, Majoros WH, Gray MW, Loftus BJ (2005) Gene discovery in the Acanthamoeba castellanii genome. Protist 156:203-214
-
(2005)
Protist
, vol.156
, pp. 203-214
-
-
Anderson, I.J.1
Watkins, R.F.2
Samuelson, J.3
Spencer, D.F.4
Majoros, W.H.5
Gray, M.W.6
Loftus, B.J.7
-
3
-
-
21144441817
-
Lateral gene transfer in eukaryotes
-
Andersson JO (2005) Lateral gene transfer in eukaryotes. Cell Mol Life Sci 62:1182-1197
-
(2005)
Cell Mol Life Sci
, vol.62
, pp. 1182-1197
-
-
Andersson, J.O.1
-
4
-
-
0036550477
-
Evolutionary analyses of the small subunit of glutamate synthase: Gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers
-
Andersson JO, Roger AJ (2002) Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers. Eukaryot Cell 1:304-310
-
(2002)
Eukaryot Cell
, vol.1
, pp. 304-310
-
-
Andersson, J.O.1
Roger, A.J.2
-
5
-
-
2942620629
-
Evolution of glutamate dehydrogenase genes: Evidence for lateral gene transfer within and between prokaryotes and eukaryotes
-
Andersson JO, Roger AJ (2003) Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evol Biol 3:14
-
(2003)
BMC Evol Biol
, vol.3
, pp. 14
-
-
Andersson, J.O.1
Roger, A.J.2
-
7
-
-
0037458124
-
Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes
-
Andersson JO, Sjögren ÅM, Davis LAM, Embley TM, Roger AJ (2003) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 13:94-104
-
(2003)
Curr Biol
, vol.13
, pp. 94-104
-
-
Andersson, J.O.1
Sjögren, Å.M.2
Davis, L.A.M.3
Embley, T.M.4
Roger, A.J.5
-
8
-
-
10344246580
-
Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids
-
Andersson JO, Sarchfield SW, Roger AJ (2005) Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol Biol Evol 22:85-90
-
(2005)
Mol Biol Evol
, vol.22
, pp. 85-90
-
-
Andersson, J.O.1
Sarchfield, S.W.2
Roger, A.J.3
-
9
-
-
0038714278
-
Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans
-
Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci USA 100:7678-7683
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 7678-7683
-
-
Archibald, J.M.1
Rogers, M.B.2
Toop, M.3
Ishida, K.4
Keeling, P.J.5
-
10
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497-3500
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
11
-
-
0032404453
-
You are what you eat: A gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes
-
Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14:307-311
-
(1998)
Trends Genet
, vol.14
, pp. 307-311
-
-
Doolittle, W.F.1
-
13
-
-
0037471694
-
How big is the iceberg of which organellar genes in nuclear genomes are but the tip?
-
Doolittle WF, Boucher Y, Nesbø CL, Douady CJ, Andersson JO, Roger AJ (2002) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans R Soc Lond B Biol Sci 358:39-58
-
(2002)
Philos Trans R Soc Lond B Biol Sci
, vol.358
, pp. 39-58
-
-
Doolittle, W.F.1
Boucher, Y.2
Nesbø, C.L.3
Douady, C.J.4
Andersson, J.O.5
Roger, A.J.6
-
14
-
-
18344395923
-
The genome of the social amoeba Dictyostelium discoideum
-
Eichinger L, Pachebat JA, Glöckner G, Rajandream M-A, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N , Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57
-
(2005)
Nature
, vol.435
, pp. 43-57
-
-
Eichinger, L.1
Pachebat, J.A.2
Glöckner, G.3
Rajandream, M.-A.4
Sucgang, R.5
Berriman, M.6
Song, J.7
Olsen, R.8
Szafranski, K.9
Xu, Q.10
Tunggal, B.11
Kummerfeld, S.12
Madera, M.13
Konfortov, B.A.14
Rivero, F.15
Bankier, A.T.16
Lehmann, R.17
Hamlin, N.18
Davies, R.19
Gaudet, P.20
Fey, P.21
Pilcher, K.22
Chen, G.23
Saunders, D.24
Sodergren, E.25
Davis, P.26
Kerhornou, A.27
Nie, X.28
Hall, N.29
Anjard, C.30
Hemphill, L.31
Bason, N.32
Farbrother, P.33
Desany, B.34
Just, E.35
Morio, T.36
Rost, R.37
Churcher, C.38
Cooper, J.39
Haydock, S.40
Van Driessche, N.41
Cronin, A.42
Goodhead, I.43
Muzny, D.44
Mourier, T.45
Pain, A.46
Lu, M.47
Harper, D.48
Lindsay, R.49
Hauser, H.50
James, K.51
Quiles, M.52
Madan Babu, M.53
Saito, T.54
Buchrieser, C.55
Wardroper, A.56
Felder, M.57
Thangavelu, M.58
Johnson, D.59
Knights, A.60
Loulseged, H.61
Mungall, K.62
Oliver, K.63
Price, C.64
Quail, M.A.65
Urushihara, H.66
Hernandez, J.67
Rabbinowitsch, E.68
Steffen, D.69
Sanders, M.70
Ma, J.71
Kohara, Y.72
Sharp, S.73
Simmonds, M.74
Spiegler, S.75
Tivey, A.76
Sugano, S.77
White, B.78
Walker, D.79
Woodward, J.80
Winckler, T.81
Tanaka, Y.82
Shaulsky, G.83
Schleicher, M.84
Weinstock, G.85
Rosenthal, A.86
Cox, E.C.87
Chisholm, R.L.88
Gibbs, R.89
Loomis, W.F.90
Platzer, M.91
Kay, R.R.92
Williams, J.93
Dear, P.H.94
Noegel, A.A.95
Barrell, B.96
Kuspa, A.97
more..
-
15
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-178
-
(1998)
Genome Res
, vol.8
, pp. 175-178
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
16
-
-
0000122573
-
PHYLIP - Phylogeny Inference Package (version 3.2)
-
Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics 5:164-166
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
17
-
-
0032949947
-
Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: Evidence for intra- and inter-kingdom gene transfer
-
Figge RM, Schubert M, Brinkmann H, Cerff R (1999) Glyceraldehyde-3- phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer. Mol Biol Evol 16:429-440
-
(1999)
Mol Biol Evol
, vol.16
, pp. 429-440
-
-
Figge, R.M.1
Schubert, M.2
Brinkmann, H.3
Cerff, R.4
-
18
-
-
0030464460
-
SEAVIEW and PHYLO_ WIN: Two graphic tools for sequence alignment and molecular phylogeny
-
Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_ WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-548
-
(1996)
Comput Appl Biosci
, vol.12
, pp. 543-548
-
-
Galtier, N.1
Gouy, M.2
Gautier, C.3
-
19
-
-
20444468864
-
Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae
-
Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4:1102-1115
-
(2005)
Eukaryot Cell
, vol.4
, pp. 1102-1115
-
-
Hall, C.1
Brachat, S.2
Dietrich, F.S.3
-
20
-
-
4744374045
-
Lateral gene transfer and the complex distribution of insertions in eukaryotic enolase
-
Harper JT, Keeling PJ (2004) Lateral gene transfer and the complex distribution of insertions in eukaryotic enolase. Gene 340:227-235
-
(2004)
Gene
, vol.340
, pp. 227-235
-
-
Harper, J.T.1
Keeling, P.J.2
-
21
-
-
5344236782
-
Bacterial endosymbionts of free-living amoebae
-
Horn M, Wagner M (2004) Bacterial endosymbionts of free-living amoebae. J Euk Microbiol 51:509-514
-
(2004)
J Euk Microbiol
, vol.51
, pp. 509-514
-
-
Horn, M.1
Wagner, M.2
-
22
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868-877
-
(1999)
Genome Res
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
23
-
-
21144435581
-
Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum
-
Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS, Kissinger JC (2004) Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol 5:R88
-
(2004)
Genome Biol
, vol.5
-
-
Huang, J.1
Mullapudi, N.2
Lancto, C.A.3
Scott, M.4
Abrahamsen, M.S.5
Kissinger, J.C.6
-
24
-
-
5344236101
-
Genetic and physiological interactions in the amoeba-bacteria symbiosis
-
Jeon KW (2004) Genetic and physiological interactions in the amoeba-bacteria symbiosis. J Eukaryot Microbiol 51:502-508
-
(2004)
J Eukaryot Microbiol
, vol.51
, pp. 502-508
-
-
Jeon, K.W.1
-
25
-
-
0036739501
-
Lateral gene transfers and the evolution of eukaryotes: Theories and data
-
Katz LA (2002) Lateral gene transfers and the evolution of eukaryotes: theories and data. Int J Syst Evol Microbiol 52:1893-1900
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1893-1900
-
-
Katz, L.A.1
-
26
-
-
7444263971
-
A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1α
-
Keeling PJ, Inagaki Y (2004) A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1α. Proc Natl Acad Sci USA 101:15380-15385
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 15380-15385
-
-
Keeling, P.J.1
Inagaki, Y.2
-
27
-
-
0035845578
-
Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase
-
Keeling PJ, Palmer JD (2001) Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc Natl Acad Sci USA 98:10745-10750
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 10745-10750
-
-
Keeling, P.J.1
Palmer, J.D.2
-
28
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709-742
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
29
-
-
8744293062
-
Intracellular proliferation of Legionella pneumophila in Hartmannella vermiformis in aquatic biofilms grown on plasticized polyvinyl chloride
-
Kuiper MW, Wullings BA, Akkermans AD, Beumer RR, van der Kooij D (2004) Intracellular proliferation of Legionella pneumophila in Hartmannella vermiformis in aquatic biofilms grown on plasticized polyvinyl chloride. Appl Environ Microbiol 70:6826-6833
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 6826-6833
-
-
Kuiper, M.W.1
Wullings, B.A.2
Akkermans, A.D.3
Beumer, R.R.4
Van Der Kooij, D.5
-
30
-
-
23044437168
-
What tangled web: Barriers to rampant horizontal gene transfer
-
Kurland CG (2005) What tangled web: barriers to rampant horizontal gene transfer. Bioessays 27:741-747
-
(2005)
Bioessays
, vol.27
, pp. 741-747
-
-
Kurland, C.G.1
-
31
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, Linton LM, Birren B, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
-
32
-
-
14544294428
-
The genome of the protist parasite Entamoeba histolytica
-
Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillén N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433:865-868
-
(2005)
Nature
, vol.433
, pp. 865-868
-
-
Loftus, B.1
Anderson, I.2
Davies, R.3
Alsmark, U.C.M.4
Samuelson, J.5
Amedeo, P.6
Roncaglia, P.7
Berriman, M.8
Hirt, R.P.9
Mann, B.J.10
Nozaki, T.11
Suh, B.12
Pop, M.13
Duchene, M.14
Ackers, J.15
Tannich, E.16
Leippe, M.17
Hofer, M.18
Bruchhaus, I.19
Willhoeft, U.20
Bhattacharya, A.21
Chillingworth, T.22
Churcher, C.23
Hance, Z.24
Harris, B.25
Harris, D.26
Jagels, K.27
Moule, S.28
Mungall, K.29
Ormond, D.30
Squares, R.31
Whitehead, S.32
Quail, M.A.33
Rabbinowitsch, E.34
Norbertczak, H.35
Price, C.36
Wang, Z.37
Guillén, N.38
Gilchrist, C.39
Stroup, S.E.40
Bhattacharya, S.41
Lohia, A.42
Foster, P.G.43
Sicheritz-Ponten, T.44
Weber, C.45
Singh, U.46
Mukherjee, C.47
El-Sayed, N.M.48
Petri Jr., W.A.49
Clark, C.G.50
Embley, T.M.51
Barrell, B.52
Fraser, C.M.53
Hall, N.54
more..
-
33
-
-
77956803013
-
Induction of synchronous encystment (differentiation) in Acanthamoeba sp.
-
Prescott DM (ed) Academic Press, New York
-
Neff RJ, Ray SA, Benton WF, Wilborn M (1964) Induction of synchronous encystment (differentiation) in Acanthamoeba sp. In: Prescott DM (ed) Methods in cell physiology, Vol I. Academic Press, New York, pp 55-83
-
(1964)
Methods in Cell Physiology
, vol.1
, pp. 55-83
-
-
Neff, R.J.1
Ray, S.A.2
Benton, W.F.3
Wilborn, M.4
-
34
-
-
0034800187
-
Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer
-
Qian Q, Keeling PJ (2001) Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer. Protist 152:193-201
-
(2001)
Protist
, vol.152
, pp. 193-201
-
-
Qian, Q.1
Keeling, P.J.2
-
35
-
-
0035827328
-
Microbial genes in the human genome: Lateral transfer or gene loss?
-
Salzberg SL, White O, Peterson J, Eisen JA (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292:1903-1906
-
(2001)
Science
, vol.292
, pp. 1903-1906
-
-
Salzberg, S.L.1
White, O.2
Peterson, J.3
Eisen, J.A.4
-
36
-
-
21544481142
-
Structure of bacterial tubulin BtubA/B: Evidence for horizontal gene transfer
-
Schlieper D, Oliva MA, Andreu JM, Löwe J (2005) Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer. Proc Natl Acad Sci USA 102:9170-9175
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 9170-9175
-
-
Schlieper, D.1
Oliva, M.A.2
Andreu, J.M.3
Löwe, J.4
-
37
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
39
-
-
12544255323
-
The real 'kingdoms' of eukaryotes
-
Simpson AG, Roger AJ (2004) The real 'kingdoms' of eukaryotes. Curr Biol 14:R693-R696
-
(2004)
Curr Biol
, vol.14
-
-
Simpson, A.G.1
Roger, A.J.2
-
40
-
-
0035927649
-
Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates
-
Stanhope MJ, Lupas A, Italia MJ, Koretke KK, Volker C, Brown JR (2001) Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411:940-944
-
(2001)
Nature
, vol.411
, pp. 940-944
-
-
Stanhope, M.J.1
Lupas, A.2
Italia, M.J.3
Koretke, K.K.4
Volker, C.5
Brown, J.R.6
-
41
-
-
0037069362
-
Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment
-
Zardoya R, Ding X, Kitagawa Y, Chrispeels MJ (2002) Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment. Proc Natl Acad Sci USA 99:14893-14896
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 14893-14896
-
-
Zardoya, R.1
Ding, X.2
Kitagawa, Y.3
Chrispeels, M.J.4
|