-
1
-
-
80053125482
-
Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes
-
10.1016/j.protis
-
Katz LA, Grant JR, Parfrey LW, Gant A, Kelly CJ, Anderson OR, Molestina RE, Nerad T: Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes. Protist 2011, 162(5):762-773. 10.1016/j.protis.2011.05.002.
-
(2011)
Protist
, vol.162
, Issue.5
, pp. 762-773
-
-
Katz, L.A.1
Grant, J.R.2
Parfrey, L.W.3
Gant, A.4
Kelly, C.J.5
Anderson, O.R.6
Molestina, R.E.7
Nerad, T.8
-
2
-
-
84861386206
-
Collodictyon-an ancient lineage in the tree of eukaryotes
-
Zhao S, Burki F, Brate J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K: Collodictyon--an ancient lineage in the tree of eukaryotes. Mol Biol Evol 2012, 29(6):1557-1568.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.6
, pp. 1557-1568
-
-
Zhao, S.1
Burki, F.2
Brate, J.3
Keeling, P.J.4
Klaveness, D.5
Shalchian-Tabrizi, K.6
-
3
-
-
84872263069
-
Squamamoeba japonica n. g. n. sp (Amoebozoa): A Deep-sea Amoeba from the Sea of Japan with a Novel Cell Coat Structure
-
Kudryavtsev A, Pawlowski J: Squamamoeba japonica n. g. n. sp (Amoebozoa): A Deep-sea Amoeba from the Sea of Japan with a Novel Cell Coat Structure. Protist 2013, 164(1):13-23.
-
(2013)
Protist
, vol.164
, Issue.1
, pp. 13-23
-
-
Kudryavtsev, A.1
Pawlowski, J.2
-
4
-
-
82155181725
-
Description of Paramoeba atlantica n. sp (Amoebozoa, Dactylopodida)- a Marine Amoeba from the Eastern Atlantic, with Emendation of the Dactylopodid Families
-
Kudryavtsev A, Pawlowski J, Hausmann K: Description of Paramoeba atlantica n. sp (Amoebozoa, Dactylopodida)- a Marine Amoeba from the Eastern Atlantic, with Emendation of the Dactylopodid Families. Acta Protozool 2011, 50(3):239-253.
-
(2011)
Acta Protozool
, vol.50
, Issue.3
, pp. 239-253
-
-
Kudryavtsev, A.1
Pawlowski, J.2
Hausmann, K.3
-
5
-
-
62649113993
-
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic supergroups
-
Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ: Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic supergroups. Proc Natl Acad Sci U S A 2009, 106(10):3859-3864.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.10
, pp. 3859-3864
-
-
Hampl, V.1
Hug, L.2
Leigh, J.W.3
Dacks, J.B.4
Lang, B.F.5
Simpson, A.G.B.6
Roger, A.J.7
-
6
-
-
77958043342
-
Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life
-
Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison HG, Sogin ML, Patterson DJ, Katz LA: Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol 2010, 59(5):518-533.
-
(2010)
Syst Biol
, vol.59
, Issue.5
, pp. 518-533
-
-
Parfrey, L.W.1
Grant, J.2
Tekle, Y.I.3
Lasek-Nesselquist, E.4
Morrison, H.G.5
Sogin, M.L.6
Patterson, D.J.7
Katz, L.A.8
-
7
-
-
84862884930
-
Turning the crown upside down: Gene tree parsimony roots the eukaryotic tree of life
-
Katz LA, Grant JR, Parfrey LW, Burleigh JG: Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst Biol 2012, 61(4):653-60.
-
(2012)
Syst Biol
, vol.61
, Issue.4
, pp. 653-660
-
-
Katz, L.A.1
Grant, J.R.2
Parfrey, L.W.3
Burleigh, J.G.4
-
9
-
-
84860120228
-
Hal: an automated pipeline for phylogenetic analyses of genomic data
-
Robbertse B, Yoder RJ, Boyd A, Reeves J, Spatafora JW: Hal: an automated pipeline for phylogenetic analyses of genomic data. PLoS Curr 2011, 3:RRN1213.
-
(2011)
PLoS Curr
, vol.3
-
-
Robbertse, B.1
Yoder, R.J.2
Boyd, A.3
Reeves, J.4
Spatafora, J.W.5
-
10
-
-
84858716366
-
Genomes-based phylogeny of the genus Xanthomonas
-
Rodriguez R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A: Genomes-based phylogeny of the genus Xanthomonas. Bmc Microbiology 2012, 12.
-
(2012)
Bmc Microbiology
, pp. 12
-
-
Rodriguez, R.L.M.1
Grajales, A.2
Arrieta-Ortiz, M.L.3
Salazar, C.4
Restrepo, S.5
Bernal, A.6
-
11
-
-
80051801316
-
The taming of an impossible child: A standardized all-in approach to the phylogeny of Hymenoptera using public database sequences
-
Peters RS, Meyer B, Krogmann L, Borner J, Meusemann K, Schutte K, Niehuis O, Misof B: The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences. Bmc Biol 2011, 9.
-
(2011)
Bmc Biol
, pp. 9
-
-
Peters, R.S.1
Meyer, B.2
Krogmann, L.3
Borner, J.4
Meusemann, K.5
Schutte, K.6
Niehuis, O.7
Misof, B.8
-
12
-
-
60849123934
-
Mega-phylogeny approach for comparative biology: An alternative to supertree and supermatrix approaches
-
Smith SA, Beaulieu JM, Donoghue MJ: Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol 2009, 9:37.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 37
-
-
Smith, S.A.1
Beaulieu, J.M.2
Donoghue, M.J.3
-
13
-
-
0028239042
-
Proterozoic and early Cambrian protists: Evidence for accelerating evolutionary tempo
-
Knoll AH: Proterozoic and early Cambrian protists: evidence for accelerating evolutionary tempo. Proc Natl Acad Sci 1994, 91:6743-6750.
-
(1994)
Proc Natl Acad Sci
, vol.91
, pp. 6743-6750
-
-
Knoll, A.H.1
-
14
-
-
80052019696
-
Estimating the timing of early eukaryotic diversification with multigene molecular clocks
-
Parfrey LW, Lahr DJG, Knoll AH, Katz LA: Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Natl Acad Sci U S A 2011, 108(33):13624-13629.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.33
, pp. 13624-13629
-
-
Parfrey, L.W.1
Lahr, D.J.G.2
Knoll, A.H.3
Katz, L.A.4
-
15
-
-
75549086594
-
InParanoid 7: New algorithms and tools for eukaryotic orthology analysis
-
Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer ELL: InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 2010, 38:D196-D203.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Ostlund, G.1
Schmitt, T.2
Forslund, K.3
Kostler, T.4
Messina, D.N.5
Roopra, S.6
Frings, O.7
Sonnhammer, E.L.L.8
-
16
-
-
0141519279
-
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
-
Li L, Stoeckert CJ, Jr., Roos DS: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research 101101/gr1224503 2003, 13(9):2178-2189.
-
(2003)
Genome Research 101101/gr1224503
, vol.13
, Issue.9
, pp. 2178-2189
-
-
Li, L.1
Stoeckert Jr., C.J.2
Roos, D.S.3
-
17
-
-
33747765539
-
Eukaryotic organisms in Proterozoic oceans
-
Knoll AH, Javaux EJ, Hewitt D, Cohen P: Eukaryotic organisms in Proterozoic oceans. Philos Trans R Soc B-Biol Sci 2006, 361(1470):1023-1038.
-
(2006)
Philos Trans R Soc B-Biol Sci
, vol.361
, Issue.1470
, pp. 1023-1038
-
-
Knoll, A.H.1
Javaux, E.J.2
Hewitt, D.3
Cohen, P.4
-
18
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, W. Fish, W. Miller, E.W. Myers, and D.J. Lipman: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Fish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
19
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A: RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
21
-
-
77954270711
-
GUIDANCE: A web server for assessing alignment confidence scores
-
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T: GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res 2010, 38:W23-W28.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Penn, O.1
Privman, E.2
Ashkenazy, H.3
Landan, G.4
Graur, D.5
Pupko, T.6
-
22
-
-
84892565878
-
Gene discovery in the transcriptomes of three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora
-
Grant JR, Lahr D. J. G, Rey F, Gordon JI, Knight R, Molestina RE, Katz LA: Gene discovery in the transcriptomes of three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora. Protist Genomics 2012, 1:3-18.
-
(2012)
Protist Genomics
, vol.1
, pp. 3-18
-
-
Grant, J.R.1
Lahr, D.J.G.2
Rey, F.3
Gordon, J.I.4
Knight, R.5
Molestina, R.E.6
Katz, L.A.7
-
23
-
-
41149122001
-
Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within 9Amoebozoa9 upon removal of varying rate classes of SSU-rDNA
-
Tekle YI, Grant J, Anderson OR, Nerad TA, Cole JC, Patterson DJ, Katz LA: Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within 9Amoebozoa9 upon removal of varying rate classes of SSU-rDNA. Mol Phylogenet Evol 2008, 47(1):339-352.
-
(2008)
Mol Phylogenet Evol
, vol.47
, Issue.1
, pp. 339-352
-
-
Tekle, Y.I.1
Grant, J.2
Anderson, O.R.3
Nerad, T.A.4
Cole, J.C.5
Patterson, D.J.6
Katz, L.A.7
-
24
-
-
20444463591
-
Williams BaP, Slamovits CH: Comparative genomics of microsporidia
-
Keeling PJ, Fast NM, Law JS, Williams BaP, Slamovits CH: Comparative genomics of microsporidia. Folia Parasitol (Praha) 2005, 52(1-2):8-14.
-
(2005)
Folia Parasitol (Praha)
, vol.52
, Issue.1-2
, pp. 8-14
-
-
Keeling, P.J.1
Fast, N.M.2
Law, J.S.3
-
25
-
-
0036406924
-
Microsporidia: Biology and evolution of highly reduced intracellular parasites
-
Keeling PJ, Fast NM: Microsporidia: Biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol 2002, 56:93-116.
-
(2002)
Annu Rev Microbiol
, vol.56
, pp. 93-116
-
-
Keeling, P.J.1
Fast, N.M.2
-
26
-
-
33749677661
-
Evolutionary status of Entamoeba
-
Dong JH, Wen JF, Xin DD, Lu SQ: Evolutionary status of Entamoeba. Chinese Sci Bull 2004, 49(17):1847-1853.
-
(2004)
Chinese Sci Bull
, vol.49
, Issue.17
, pp. 1847-1853
-
-
Dong, J.H.1
Wen, J.F.2
Xin, D.D.3
Lu, S.Q.4
-
27
-
-
39749201627
-
Broadly sampled multigene trees of eukaryotes
-
doi:10.1186/1471-2148-1188-1114
-
Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, Cole JC, Logsdon JM, Patterson DJ, Bhattacharya D, Katz LA: Broadly sampled multigene trees of eukaryotes. BMC Evol Biol 2008, 8(14):doi:10.1186/1471-2148-1188-1114.
-
(2008)
BMC Evol Biol
, vol.8
, Issue.14
-
-
Yoon, H.S.1
Grant, J.2
Tekle, Y.I.3
Wu, M.4
Chaon, B.C.5
Cole, J.C.6
Logsdon, J.M.7
Patterson, D.J.8
Bhattacharya, D.9
Katz, L.A.10
-
28
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web-servers
-
Stamatakis A, Hoover P, Rougemont J: A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008, 57:758-771.
-
(2008)
Syst Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
29
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
Abascal F, Zardoya R, Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics: 21(9):2104-2105.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
30
-
-
22744435955
-
Molecular phylogeny and classification of the lobose amoebae
-
Smirnov A, Nassonova E, Berney C, Fahrni J, Bolivar I, Pawlowski J: Molecular phylogeny and classification of the lobose amoebae. Protist 2005, 156(2):129-142.
-
(2005)
Protist
, vol.156
, Issue.2
, pp. 129-142
-
-
Smirnov, A.1
Nassonova, E.2
Berney, C.3
Fahrni, J.4
Bolivar, I.5
Pawlowski, J.6
-
31
-
-
79960855196
-
Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analyses of SSU-rDNA and actin genes
-
Lahr DJG, Grant J, Nguyen T, Lin JH, Katz LA: Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analyses of SSU-rDNA and actin genes. PLoS One 2011, 6(7).
-
(2011)
PLoS One
, vol.6
, Issue.7
-
-
Lahr, D.J.G.1
Grant, J.2
Nguyen, T.3
Lin, J.H.4
Katz, L.A.5
-
32
-
-
79955787125
-
Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists
-
Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D: Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists. Science 2011, 332(6030):714-717.
-
(2011)
Science
, vol.332
, Issue.6030
, pp. 714-717
-
-
Yoon, H.S.1
Price, D.C.2
Stepanauskas, R.3
Rajah, V.D.4
Sieracki, M.E.5
Wilson, W.H.6
Yang, E.C.7
Duffy, S.8
Bhattacharya, D.9
|