-
1
-
-
84863524200
-
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
-
Bansal MS, Alm EJ, Kellis M (2012) Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28, i283-i291.
-
(2012)
Bioinformatics
, vol.28
, pp. i283-i291
-
-
Bansal, M.S.1
Alm, E.J.2
Kellis, M.3
-
3
-
-
3042840997
-
Computational inference of scenarios for alphaproteobacterial genome evolution
-
Boussau B, Karlberg EO, Frank AC, Legault B, Andersson SGE (2004) Computational inference of scenarios for alphaproteobacterial genome evolution. Proceedings of the National Academy of Sciences 101, 9722-9727.
-
(2004)
Proceedings of the National Academy of Sciences
, vol.101
, pp. 9722-9727
-
-
Boussau, B.1
Karlberg, E.O.2
Frank, A.C.3
Legault, B.4
Andersson, S.G.E.5
-
4
-
-
39849102478
-
Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation
-
Brocks JJ, Schaeffer P (2008) Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation. Geochimica et Cosmochimica Acta 72, 1396-1414.
-
(2008)
Geochimica et Cosmochimica Acta
, vol.72
, pp. 1396-1414
-
-
Brocks, J.J.1
Schaeffer, P.2
-
5
-
-
27144475394
-
Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea
-
Brocks JJ, Love GD, Summons RE, Knoll AH, Logan GA, Bowden SA (2005) Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea. Nature 437, 866-870.
-
(2005)
Nature
, vol.437
, pp. 866-870
-
-
Brocks, J.J.1
Love, G.D.2
Summons, R.E.3
Knoll, A.H.4
Logan, G.A.5
Bowden, S.A.6
-
6
-
-
0002168111
-
Phylogenetics: the theory and practice of phylogenetic systematics
-
Colless DH (1982) Phylogenetics: the theory and practice of phylogenetic systematics. Systematic Zoology 31, 100-104.
-
(1982)
Systematic Zoology
, vol.31
, pp. 100-104
-
-
Colless, D.H.1
-
7
-
-
77649177164
-
Jane: a new tool for the cophylogeny reconstruction problem
-
Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R (2010) Jane: a new tool for the cophylogeny reconstruction problem. Algorithms for Molecular Biology 5, 1-10.
-
(2010)
Algorithms for Molecular Biology
, vol.5
, pp. 1-10
-
-
Conow, C.1
Fielder, D.2
Ovadia, Y.3
Libeskind-Hadas, R.4
-
8
-
-
79954529507
-
ProtTest 3: fast selection of best-fit models of protein evolution
-
Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164-1165.
-
(2011)
Bioinformatics
, vol.27
, pp. 1164-1165
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
9
-
-
84885143535
-
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
-
Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF, Ley RE (2013) The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife, 2, 1-25.
-
(2013)
eLife
, vol.2
, pp. 1-25
-
-
Di Rienzi, S.C.1
Sharon, I.2
Wrighton, K.C.3
Koren, O.4
Hug, L.A.5
Thomas, B.C.6
Goodrich, J.K.7
Bell, J.T.8
Spector, T.D.9
Banfield, J.F.10
Ley, R.E.11
-
10
-
-
70449556446
-
2-Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications
-
Doughty DM, Hunter R, Summons RE, Newman DK (2009) 2-Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications. Geobiology 7, 524-532.
-
(2009)
Geobiology
, vol.7
, pp. 524-532
-
-
Doughty, D.M.1
Hunter, R.2
Summons, R.E.3
Newman, D.K.4
-
11
-
-
81055130186
-
The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1
-
Doughty DM, Coleman ML, Hunter RC, Sessions AL, Summons RE, Newman DK (2011) The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1. Proceedings of the National Academy of Sciences of the United States of America 108, E1045-E1051.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, pp. E1045-E1051
-
-
Doughty, D.M.1
Coleman, M.L.2
Hunter, R.C.3
Sessions, A.L.4
Summons, R.E.5
Newman, D.K.6
-
12
-
-
84895174793
-
Probing the Subcellular Localization of Hopanoid Lipids in Bacteria Using NanoSIMS
-
Doughty DM, Dieterle M, Sessions AL, Fischer WW, Newman DK (2014) Probing the Subcellular Localization of Hopanoid Lipids in Bacteria Using NanoSIMS. PLoS One 9, e84455.
-
(2014)
PLoS One
, vol.9
, pp. e84455
-
-
Doughty, D.M.1
Dieterle, M.2
Sessions, A.L.3
Fischer, W.W.4
Newman, D.K.5
-
14
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology 59, 307-321.
-
(2010)
Systematic biology
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.-F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
15
-
-
0032943554
-
Hopanoid Biosynthesis and Function in Bacteria
-
Kannenberg EL, Poralla K (1999) Hopanoid Biosynthesis and Function in Bacteria. Naturwissenschaften 86, 168-176.
-
(1999)
Naturwissenschaften
, vol.86
, pp. 168-176
-
-
Kannenberg, E.L.1
Poralla, K.2
-
16
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9, 286-298.
-
(2008)
Briefings in Bioinformatics
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
17
-
-
84882520415
-
The geological succession of primary producers in the oceans
-
In. (eds Falkowski P, Knoll AH). Academic Press, Boston.
-
Knoll AH, Summons RE, Waldbauer JR, Zumberge JE (2007) The geological succession of primary producers in the oceans. In The Evolution of Primary Producers in the Sea. (eds Falkowski P, Knoll AH). Academic Press, Boston, pp. 133-164.
-
(2007)
The Evolution of Primary Producers in the Sea
, pp. 133-164
-
-
Knoll, A.H.1
Summons, R.E.2
Waldbauer, J.R.3
Zumberge, J.E.4
-
18
-
-
84877968008
-
The general stress response factor EcfG regulates expression of the C-2 hopanoid methylase HpnP in Rhodopseudomonas palustris TIE-1
-
Kulkarni G, Wu C-H, Newman DK (2013) The general stress response factor EcfG regulates expression of the C-2 hopanoid methylase HpnP in Rhodopseudomonas palustris TIE-1. Journal of bacteriology 195, 2490-2498.
-
(2013)
Journal of bacteriology
, vol.195
, pp. 2490-2498
-
-
Kulkarni, G.1
Wu, C.-H.2
Newman, D.K.3
-
19
-
-
7444255997
-
N2-fixing cyanobacteria supplied nutrient N for Cretaceous oceanic anoxic events
-
Kuypers MMM, van Breugel Y, Schouten S, Erba E, Sinninghe Damsté JS (2004) N2-fixing cyanobacteria supplied nutrient N for Cretaceous oceanic anoxic events. Geology 32, 853-856.
-
(2004)
Geology
, vol.32
, pp. 853-856
-
-
Kuypers, M.M.M.1
van Breugel, Y.2
Schouten, S.3
Erba, E.4
Sinninghe Damsté, J.S.5
-
20
-
-
33845873289
-
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
-
Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
21
-
-
47749096232
-
StochChar: a package of Mesquite modules for stochastic models of character evolution
-
Version 1.1.
-
Maddison W, Maddison D (2006) StochChar: a package of Mesquite modules for stochastic models of character evolution. Version 1.1.
-
(2006)
-
-
Maddison, W.1
Maddison, D.2
-
22
-
-
3042649996
-
Mesquite: a modular system for evolutionary analysis
-
Version 2.75.
-
Maddison W, Maddison D (2011) Mesquite: a modular system for evolutionary analysis. Version 2.75. http://mesquiteproject.org.
-
(2011)
-
-
Maddison, W.1
Maddison, D.2
-
23
-
-
84901470061
-
Tree farm package for mesquite
-
Version 2.75.
-
Maddison W, Maddison D, Midford P (2011) Tree farm package for mesquite. Version 2.75.
-
(2011)
-
-
Maddison, W.1
Maddison, D.2
Midford, P.3
-
24
-
-
50249154976
-
Tree thinking for all biology: the problem with reading phylogenies as ladders of progress
-
Omland KE, Cook LG, Crisp MD (2008) Tree thinking for all biology: the problem with reading phylogenies as ladders of progress. BioEssays 30, 854-867.
-
(2008)
BioEssays
, vol.30
, pp. 854-867
-
-
Omland, K.E.1
Cook, L.G.2
Crisp, M.D.3
-
25
-
-
0021149810
-
Effect of Temperature and pH on the Hopanoid Content of Bacillus acidocaldarius
-
Poralla K, Hartner T, Kannenberg E (1984) Effect of Temperature and pH on the Hopanoid Content of Bacillus acidocaldarius. FEMS Microbiology Letters 23, 253-256.
-
(1984)
FEMS Microbiology Letters
, vol.23
, pp. 253-256
-
-
Poralla, K.1
Hartner, T.2
Kannenberg, E.3
-
26
-
-
35448958031
-
Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph
-
Rashby SE, Sessions AL, Summons RE, Newman DK (2007) Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph. Proceedings of the National Academy of Sciences of the United States of America 104, 15099-15104.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, pp. 15099-15104
-
-
Rashby, S.E.1
Sessions, A.L.2
Summons, R.E.3
Newman, D.K.4
-
27
-
-
54549114449
-
Reassessing the first appearance of eukaryotes and cyanobacteria
-
Rasmussen B, Fletcher IR, Brocks JJ, Kilburn MR (2008) Reassessing the first appearance of eukaryotes and cyanobacteria. Nature 455, 1101-1104.
-
(2008)
Nature
, vol.455
, pp. 1101-1104
-
-
Rasmussen, B.1
Fletcher, I.R.2
Brocks, J.J.3
Kilburn, M.R.4
-
28
-
-
84894368911
-
Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche
-
Ricci JN, Coleman ML, Welander PV, Sessions AL, Summons RE, Spear JR, Newman DK (2014) Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche. The ISME Journal 8, 675-684.
-
(2014)
The ISME Journal
, vol.8
, pp. 675-684
-
-
Ricci, J.N.1
Coleman, M.L.2
Welander, P.V.3
Sessions, A.L.4
Summons, R.E.5
Spear, J.R.6
Newman, D.K.7
-
29
-
-
79960927427
-
Abundance and structural diversity of bacteriohopanepolyols in suspended particulate matter along a river to ocean transect
-
Sáenz JP, Eglinton TI, Summons RE (2011) Abundance and structural diversity of bacteriohopanepolyols in suspended particulate matter along a river to ocean transect. Organic Geochemistry 42, 774-780.
-
(2011)
Organic Geochemistry
, vol.42
, pp. 774-780
-
-
Sáenz, J.P.1
Eglinton, T.I.2
Summons, R.E.3
-
30
-
-
84873157581
-
Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event
-
Schirrmeister BE, de Vos JM, Antonelli A, Bagheri HC (2013) Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proceedings of the National Academy of Sciences of the United States of America 110, 1791-1796.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, pp. 1791-1796
-
-
Schirrmeister, B.E.1
de Vos, J.M.2
Antonelli, A.3
Bagheri, H.C.4
-
31
-
-
66649119126
-
Menaquinone as pool quinone in a purple bacterium
-
Schoepp-Cothenet B, Lieutaud C, Baymann F, Verméglio A, Friedrich T, Kramer DM, Nitschke W (2009) Menaquinone as pool quinone in a purple bacterium. Proceedings of the National Academy of Sciences of the United States of America 106, 8549-8554.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 8549-8554
-
-
Schoepp-Cothenet, B.1
Lieutaud, C.2
Baymann, F.3
Verméglio, A.4
Friedrich, T.5
Kramer, D.M.6
Nitschke, W.7
-
32
-
-
84880685461
-
Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins
-
Shih PM, Matzke NJ (2013) Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins. Proceedings of the National Academy of Sciences of the United States of America 110, 12355-12360.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, pp. 12355-12360
-
-
Shih, P.M.1
Matzke, N.J.2
-
33
-
-
84872589843
-
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
-
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences of the United States of America 110, 1053-1058.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, pp. 1053-1058
-
-
Shih, P.M.1
Wu, D.2
Latifi, A.3
Axen, S.D.4
Fewer, D.P.5
Talla, E.6
Calteau, A.7
Cai, F.8
Tandeau de Marsac, N.9
Rippka, R.10
Herdman, M.11
Sivonen, K.12
Coursin, T.13
Laurent, T.14
Goodwin, L.15
Nolan, M.16
Davenport, K.W.17
Han, C.S.18
Rubin, E.M.19
Eisen, J.A.20
Woyke, T.21
Gugger, M.22
Kerfeld, C.A.23
more..
-
34
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Systematic biology 51, 492-508.
-
(2002)
Systematic biology
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
35
-
-
0036139287
-
CONSEL: for assessing the confidence of phylogenetic tree selection
-
Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247.
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasegawa, M.2
-
36
-
-
0027951531
-
Rooting molecular trees: problems and strategies
-
Smith AB (1994) Rooting molecular trees: problems and strategies. Biological Journal of Linnean Society 51, 279-292.
-
(1994)
Biological Journal of Linnean Society
, vol.51
, pp. 279-292
-
-
Smith, A.B.1
-
37
-
-
0033527055
-
2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis
-
Summons RE, Jahnke LL, Hope JM, Logan GA (1999) 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature 400, 554-557.
-
(1999)
Nature
, vol.400
, pp. 554-557
-
-
Summons, R.E.1
Jahnke, L.L.2
Hope, J.M.3
Logan, G.A.4
-
38
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic biology 56, 564-577.
-
(2007)
Systematic biology
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
39
-
-
33748559766
-
Improved inverse PCR scheme for metagenome walking
-
Uchiyama T, Watanabe K (2006) Improved inverse PCR scheme for metagenome walking. BioTechniques 41, 183-188.
-
(2006)
BioTechniques
, vol.41
, pp. 183-188
-
-
Uchiyama, T.1
Watanabe, K.2
-
40
-
-
84859442912
-
Biosynthesis of the biomarker okenone: χ-ring formation
-
Vogl K, Bryant D (2012) Biosynthesis of the biomarker okenone: χ-ring formation. Geobiology 10, 205-215.
-
(2012)
Geobiology
, vol.10
, pp. 205-215
-
-
Vogl, K.1
Bryant, D.2
-
41
-
-
70349088644
-
Hopanoids play a role in membrane integrity and pH homeostasis in Rhodopseudomonas palustris TIE-1
-
Welander PV, Hunter RC, Zhang L, Sessions AL, Summons RE, Newman DK (2009) Hopanoids play a role in membrane integrity and pH homeostasis in Rhodopseudomonas palustris TIE-1. Journal of bacteriology 191, 6145-6156.
-
(2009)
Journal of bacteriology
, vol.191
, pp. 6145-6156
-
-
Welander, P.V.1
Hunter, R.C.2
Zhang, L.3
Sessions, A.L.4
Summons, R.E.5
Newman, D.K.6
-
42
-
-
77952728544
-
Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes
-
Welander PV, Coleman ML, Sessions AL, Summons RE, Newman DK (2010) Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes. Proceedings of the National Academy of Sciences of the United States of America 107, 8537-8542.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 8537-8542
-
-
Welander, P.V.1
Coleman, M.L.2
Sessions, A.L.3
Summons, R.E.4
Newman, D.K.5
-
43
-
-
84856659509
-
Identification and characterization of Rhodopseudomonas palustris TIE-1 hopanoid biosynthesis mutants
-
Welander PV, Doughty DM, Wu C-H, Mehay S, Summons RE, Newman DK (2012) Identification and characterization of Rhodopseudomonas palustris TIE-1 hopanoid biosynthesis mutants. Geobiology 10, 163-177.
-
(2012)
Geobiology
, vol.10
, pp. 163-177
-
-
Welander, P.V.1
Doughty, D.M.2
Wu, C.-H.3
Mehay, S.4
Summons, R.E.5
Newman, D.K.6
-
45
-
-
85003048684
-
Methylation at the C-2 position of hopanoids increases rigidity in native bacterial membranes
-
[Epub ahead of print].
-
Wu C-H, Bialecka-Fornal M, Newman DK (2015) Methylation at the C-2 position of hopanoids increases rigidity in native bacterial membranes. eLife. doi: 10.7554/eLife.05663 [Epub ahead of print].
-
(2015)
eLife
-
-
Wu, C.-H.1
Bialecka-Fornal, M.2
Newman, D.K.3
-
46
-
-
84862814389
-
Molecular phylogenetics: principles and practice
-
Yang Z, Rannala B (2012) Molecular phylogenetics: principles and practice. Nature Reviews Genetics 13, 303-314.
-
(2012)
Nature Reviews Genetics
, vol.13
, pp. 303-314
-
-
Yang, Z.1
Rannala, B.2
|