-
1
-
-
84879677733
-
Genome of the red alga Porphyridium purpureum
-
Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber AP, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zauner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. 2013. Genome of the red alga Porphyridium purpureum. Nature Communications 4:1941 DOI 10.1038/ncomms2931.
-
(2013)
Nature Communications
, vol.4
, pp. 1941
-
-
Bhattacharya, D.1
Price, D.C.2
Chan, C.X.3
Qiu, H.4
Rose, N.5
Ball, S.6
Weber, A.P.7
Arias, M.C.8
Henrissat, B.9
Coutinho, P.M.10
Krishnan, A.11
Zauner, S.12
Morath, S.13
Hilliou, F.14
Egizi, A.15
Perrineau, M.M.16
Yoon, H.S.17
-
2
-
-
56249098614
-
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
-
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kröger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jézéquel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, Von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456:239-244 DOI 10.1038/nature07410.
-
(2008)
Nature
, vol.456
, pp. 239-244
-
-
Bowler, C.1
Allen, A.E.2
Badger, J.H.3
Grimwood, J.4
Jabbari, K.5
Kuo, A.6
Maheswari, U.7
Martens, C.8
Maumus, F.9
Otillar, R.P.10
Rayko, E.11
Salamov, A.12
Vandepoele, K.13
Beszteri, B.14
Gruber, A.15
Heijde, M.16
Katinka, M.17
Mock, T.18
Valentin, K.19
Verret, F.20
Berges, J.A.21
Brownlee, C.22
Cadoret, J.P.23
Chiovitti, A.24
Choi, C.J.25
Coesel, S.26
De Martino, A.27
Detter, J.C.28
Durkin, C.29
Falciatore, A.30
Fournet, J.31
Haruta, M.32
Huysman, M.J.33
Jenkins, B.D.34
Jiroutova, K.35
Jorgensen, R.E.36
Joubert, Y.37
Kaplan, A.38
Kröger, N.39
Kroth, P.G.40
La Roche, J.41
Lindquist, E.42
Lommer, M.43
Martin-Jézéquel, V.44
Lopez, P.J.45
Lucas, S.46
Mangogna, M.47
McGinnis, K.48
Medlin, L.K.49
Montsant, A.50
Oudot-Le Secq, M.P.51
Napoli, C.52
Obornik, M.53
Parker, M.S.54
Petit, J.L.55
Porcel, B.M.56
Poulsen, N.57
Robison, M.58
Rychlewski, L.59
Rynearson, T.A.60
Schmutz, J.61
Shapiro, H.62
Siaut, M.63
Stanley, M.64
Sussman, M.R.65
Taylor, A.R.66
Vardi, A.67
Von Dassow, P.68
Vyverman, W.69
Willis, A.70
Wyrwicz, L.S.71
Rokhsar, D.S.72
Weissenbach, J.73
Armbrust, E.V.74
Green, B.R.75
Van de Peer, Y.76
Grigoriev, I.V.77
more..
-
3
-
-
58249119586
-
Extended Newick: it is time for a standard representation of phylogenetic networks
-
Cardona G, Rossello F, Valiente G. 2008. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics 9:532 DOI 10.1186/1471-2105-9-532.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 532
-
-
Cardona, G.1
Rossello, F.2
Valiente, G.3
-
4
-
-
83755229582
-
Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution
-
Chan CX, Reyes-Prieto A, Bhattacharya D. 2011a. Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution. PLoS ONE 6:e29138 DOI 10.1371/journal.pone.0029138.
-
(2011)
PLoS ONE
, vol.6
-
-
Chan, C.X.1
Reyes-Prieto, A.2
Bhattacharya, D.3
-
5
-
-
79951774451
-
Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes
-
Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D. 2011b. Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Current Biology 21:328-333 DOI 10.1016/j.cub.2011.01.037.
-
(2011)
Current Biology
, vol.21
, pp. 328-333
-
-
Chan, C.X.1
Yang, E.C.2
Banerjee, T.3
Yoon, H.S.4
Martone, P.T.5
Estevez, J.M.6
Bhattacharya, D.7
-
6
-
-
84870564943
-
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
-
Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Syme-onidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Korenỳ L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492:59-65 DOI 10.1038/nature11681.
-
(2012)
Nature
, vol.492
, pp. 59-65
-
-
Curtis, B.A.1
Tanifuji, G.2
Burki, F.3
Gruber, A.4
Irimia, M.5
Maruyama, S.6
Arias, M.C.7
Ball, S.G.8
Gile, G.H.9
Hirakawa, Y.10
Hopkins, J.F.11
Kuo, A.12
Rensing, S.A.13
Schmutz, J.14
Syme-onidi, A.15
Elias, M.16
Eveleigh, R.J.17
Herman, E.K.18
Klute, M.J.19
Nakayama, T.20
Oborník, M.21
Reyes-Prieto, A.22
Armbrust, E.V.23
Aves, S.J.24
Beiko, R.G.25
Coutinho, P.26
Dacks, J.B.27
Durnford, D.G.28
Fast, N.M.29
Green, B.R.30
Grisdale, C.J.31
Hempel, F.32
Henrissat, B.33
Höppner, M.P.34
Ishida, K.35
Kim, E.36
Korenỳ, L.37
Kroth, P.G.38
Liu, Y.39
Malik, S.B.40
Maier, U.G.41
McRose, D.42
Mock, T.43
Neilson, J.A.44
Onodera, N.T.45
Poole, A.M.46
Pritham, E.J.47
Richards, T.A.48
Rocap, G.49
Roy, S.W.50
Sarai, C.51
Schaack, S.52
Shirato, S.53
Slamovits, C.H.54
Spencer, D.F.55
Suzuki, S.56
Worden, A.Z.57
Zauner, S.58
Barry, K.59
Bell, C.60
Bharti, A.K.61
Crow, J.A.62
Grimwood, J.63
Kramer, R.64
Lindquist, E.65
Lucas, S.66
Salamov, A.67
McFadden, G.I.68
Lane, C.E.69
Keeling, P.J.70
Gray, M.W.71
Grigoriev, I.V.72
Archibald, J.M.73
more..
-
7
-
-
84923245137
-
SICLE: a high-throughput tool for extracting evolution-ary relationships from phylogenetic trees
-
ArXiv preprint. arXiv:1303.5785.
-
DeBlasio D, Wisecaver J. 2013. SICLE: a high-throughput tool for extracting evolution-ary relationships from phylogenetic trees. ArXiv preprint. arXiv:1303.5785.
-
(2013)
-
-
DeBlasio, D.1
Wisecaver, J.2
-
8
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27:401-410 DOI 10.2307/2412923.
-
(1978)
Systematic Zoology
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
9
-
-
47249160614
-
The origin of plastids
-
Howe CJ, Barbrook AC, Nisbet RE, Lockhart PJ, Larkum AW. 2008. The origin of plastids. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 363:2675-2685 DOI 10.1098/rstb.2008.0050.
-
(2008)
Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences
, vol.363
, pp. 2675-2685
-
-
Howe, C.J.1
Barbrook, A.C.2
Nisbet, R.E.3
Lockhart, P.J.4
Larkum, A.W.5
-
10
-
-
0015197890
-
Optimum binary search trees
-
Knuth DE. 1971. Optimum binary search trees. Acta Informatica 1:14-25 DOI 10.1007/BF00264289.
-
(1971)
Acta Informatica
, vol.1
, pp. 14-25
-
-
Knuth, D.E.1
-
11
-
-
40049106345
-
PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas
-
Moustafa A, Bhattacharya D. 2008. PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evolutionary Biology 8:6 DOI 10.1186/1471-2148-8-6.
-
(2008)
BMC Evolutionary Biology
, vol.8
, pp. 6
-
-
Moustafa, A.1
Bhattacharya, D.2
-
12
-
-
1042304216
-
APE: analyses of phylogenetics and evolution in R language
-
Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290 DOI 10.1093/bioinformatics/btg412.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
13
-
-
84857242898
-
Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants
-
Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JA, Lang BF, Burger G, Steiner JM, Löffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MC, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D. 2012. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335:843-847 DOI 10.1126/science.1213561.
-
(2012)
Science
, vol.335
, pp. 843-847
-
-
Price, D.C.1
Chan, C.X.2
Yoon, H.S.3
Yang, E.C.4
Qiu, H.5
Weber, A.P.6
Schwacke, R.7
Gross, J.8
Blouin, N.A.9
Lane, C.10
Reyes-Prieto, A.11
Durnford, D.G.12
Neilson, J.A.13
Lang, B.F.14
Burger, G.15
Steiner, J.M.16
Löffelhardt, W.17
Meuser, J.E.18
Posewitz, M.C.19
Ball, S.20
Arias, M.C.21
Henrissat, B.22
Coutinho, P.M.23
Rensing, S.A.24
Symeonidi, A.25
Doddapaneni, H.26
Green, B.R.27
Rajah, V.D.28
Boore, J.29
Bhattacharya, D.30
more..
-
15
-
-
84867364321
-
phytools: an R package for phylogenetic comparative biology (and other things)
-
Revell LJ. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217-223 DOI 10.1111/j.2041-210X.2011.00169.x.
-
(2012)
Methods in Ecology and Evolution
, vol.3
, pp. 217-223
-
-
Revell, L.J.1
-
16
-
-
0037291976
-
Taxon sampling, bioinformatics, and phylogenomics
-
Rosenberg MS, Kumar S. 2003. Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124 DOI 10.1080/10635150390132894.
-
(2003)
Systematic Biology
, vol.52
, pp. 119-124
-
-
Rosenberg, M.S.1
Kumar, S.2
-
17
-
-
77952490857
-
Phylogenomics with incomplete taxon coverage: the limits to inference
-
Sanderson MJ, McMahon MM, Steel M. 2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 10:155 DOI 10.1186/1471-2148-10-155.
-
(2010)
BMC Evolutionary Biology
, vol.10
, pp. 155
-
-
Sanderson, M.J.1
McMahon, M.M.2
Steel, M.3
-
18
-
-
80052858002
-
Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer
-
Stiller JW. 2011. Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evolutionary Biology 11:259 DOI 10.1186/1471-2148-11-259.
-
(2011)
BMC Evolutionary Biology
, vol.11
, pp. 259
-
-
Stiller, J.W.1
|