-
1
-
-
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 21:2104-2105.
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
43049120226
-
Determining kinetics and affinities of protein interactions using a parallel real-Time label-free biosensor, the Octet
-
Abdiche Y, Malashock D, Pinkerton A, Pons J. 2008. Determining kinetics and affinities of protein interactions using a parallel real-Time label-free biosensor, the Octet. Anal Biochem. 377: 209-217.
-
(2008)
Anal Biochem.
, vol.377
, pp. 209-217
-
-
Abdiche, Y.1
Malashock, D.2
Pinkerton, A.3
Pons, J.4
-
3
-
-
84871832204
-
Pruning rogue taxa improves phylogenetic accuracy: An efficient algorithm and webservice
-
Aberer AJ, Krompass D, Stamatakis A. 2013. Pruning rogue taxa improves phylogenetic accuracy: An efficient algorithm and webservice. Syst Biol. 62:162-166.
-
(2013)
Syst Biol.
, vol.62
, pp. 162-166
-
-
Aberer, A.J.1
Krompass, D.2
Stamatakis, A.3
-
4
-
-
0030308089
-
On combining protein sequences and nucleic acid sequences in phylogenetic analysis: The homeobox protein case
-
Agosti D, Jacobs D, DeSalle R. 1996. On combining protein sequences and nucleic acid sequences in phylogenetic analysis: The homeobox protein case. Cladistics 12:65-82.
-
(1996)
Cladistics
, vol.12
, pp. 65-82
-
-
Agosti, D.1
Jacobs, D.2
DeSalle, R.3
-
5
-
-
79952389828
-
RIG-I- and MDA5-initiated innate immunity linked with adaptive immunity accelerates beta-cell death in fulminant type 1 diabetes
-
18 Co-Authors).
-
Aida K, Nishida Y, Tanaka S, et al.. (18 co-Authors). 2011. RIG-I- and MDA5-initiated innate immunity linked with adaptive immunity accelerates beta-cell death in fulminant type 1 diabetes. Diabetes 60:884-889.
-
(2011)
Diabetes
, vol.60
, pp. 884-889
-
-
Aida, K.1
Nishida, Y.2
Tanaka, S.3
-
6
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer 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
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
7
-
-
77956331627
-
Integrating common and rare genetic variation in diverse human populations
-
69 Co-Authors).
-
Altshuler DM, Gibbs RA, Peltonen L, et al.. (69 co-Authors). 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467:52-58.
-
(2010)
Nature
, vol.467
, pp. 52-58
-
-
Altshuler, D.M.1
Gibbs, R.A.2
Peltonen, L.3
-
8
-
-
80052014395
-
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes
-
Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60:685-699.
-
(2011)
Syst Biol.
, vol.60
, pp. 685-699
-
-
Anisimova, M.1
Gil, M.2
Dufayard, J.F.3
Dessimoz, C.4
Gascuel, O.5
-
9
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci U S A. 98:10037-10041.
-
(2001)
Proc Natl Acad Sci U S A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
11
-
-
67749111851
-
Mitochondrial antiviral signaling protein plays a major role in induction of the fish innate immune response against RNA and DNA viruses
-
Biacchesi S, LeBerre M, Lamoureux A, Louise Y, Lauret E, Boudinot P, Bremont M. 2009. Mitochondrial antiviral signaling protein plays a major role in induction of the fish innate immune response against RNA and DNA viruses. J Virol. 83:7815-7827.
-
(2009)
J Virol.
, vol.83
, pp. 7815-7827
-
-
Biacchesi, S.1
LeBerre, M.2
Lamoureux, A.3
Louise, Y.4
Lauret, E.5
Boudinot, P.6
Bremont, M.7
-
13
-
-
84859739224
-
Domain enhanced lookup time accelerated BLAST
-
Boratyn GM, Schaffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL. 2012. Domain enhanced lookup time accelerated BLAST. Biol Direct. 7:12.
-
(2012)
Biol Direct.
, vol.7
, pp. 12
-
-
Boratyn, G.M.1
Schaffer, A.A.2
Agarwala, R.3
Altschul, S.F.4
Lipman, D.J.5
Madden, T.L.6
-
14
-
-
79952154345
-
Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study
-
Buerki S, Forest F, Salamin N, Alvarez N. 2011. Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study. Syst Biol. 60:32-44.
-
(2011)
Syst Biol.
, vol.60
, pp. 32-44
-
-
Buerki, S.1
Forest, F.2
Salamin, N.3
Alvarez, N.4
-
15
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17: 540-552.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
16
-
-
77649326700
-
MDA5 and PTPN2, two candidate genes for type 1 diabetes, modify pancreatic beta-cell responses to the viral by-product double-stranded RNA
-
Colli ML, Moore F, Gurzov EN, Ortis F, Eizirik DL. 2010. MDA5 and PTPN2, two candidate genes for type 1 diabetes, modify pancreatic beta-cell responses to the viral by-product double-stranded RNA. Hum Mol Genet. 19:135-146.
-
(2010)
Hum Mol Genet.
, vol.19
, pp. 135-146
-
-
Colli, M.L.1
Moore, F.2
Gurzov, E.N.3
Ortis, F.4
Eizirik, D.L.5
-
17
-
-
34548566074
-
Majority-rule supertrees
-
Cotton JA, Wilkinson M. 2007. Majority-rule supertrees. Syst Biol. 56: 445-452.
-
(2007)
Syst Biol.
, vol.56
, pp. 445-452
-
-
Cotton, J.A.1
Wilkinson, M.2
-
18
-
-
38649089789
-
The C-Terminal regulatory domain is the RNA 50-Triphosphate sensor of RIG-I
-
Cui S, Eisenacher K, Kirchhofer A, Brzozka K, Lammens A, Lammens K, Fujita T, Conzelmann KK, Krug A, Hopfner KP. 2008. The C-Terminal regulatory domain is the RNA 50-Triphosphate sensor of RIG-I. Mol Cell. 29:169-179.
-
(2008)
Mol Cell.
, vol.29
, pp. 169-179
-
-
Cui, S.1
Eisenacher, K.2
Kirchhofer, A.3
Brzozka, K.4
Lammens, A.5
Lammens, K.6
Fujita, T.7
Conzelmann, K.K.8
Krug, A.9
Hopfner, K.P.10
-
19
-
-
26444603772
-
Two rounds of whole genome duplication in the ancestral vertebrate
-
Dehal P, Boore JL. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3:e314.
-
(2005)
PLoS Biol.
, vol.3
-
-
Dehal, P.1
Boore, J.L.2
-
20
-
-
2242464840
-
The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins
-
87 Co-Authors).
-
Dehal P, Satou Y, Campbell RK, et al.. (87 co-Authors). 2002. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298:2157-2167.
-
(2002)
Science
, vol.298
, pp. 2157-2167
-
-
Dehal, P.1
Satou, Y.2
Campbell, R.K.3
-
21
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. 2007. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35:W522-W525.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
22
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
602 Co-Authors).
-
Dunham I, Kundaje A, Aldred SF, et al.. (602 co-Authors). 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Dunham, I.1
Kundaje, A.2
Aldred, S.F.3
-
23
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Gibbs RA, Hurles ME, McVean GA. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
Durbin, R.M.1
Abecasis, G.R.2
Altshuler, D.L.3
Auton, A.4
Brooks, L.D.5
Gibbs, R.A.6
Hurles, M.E.7
McVean, G.A.8
-
24
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
26
-
-
55549141879
-
How well can the accuracy of comparative protein structure models be predicted?
-
Eramian D, Eswar N, Shen MY, Sali A. 2008. How well can the accuracy of comparative protein structure models be predicted?. Protein Sci. 17: 1881-1893.
-
(2008)
Protein Sci.
, vol.17
, pp. 1881-1893
-
-
Eramian, D.1
Eswar, N.2
Shen, M.Y.3
Sali, A.4
-
27
-
-
75549090603
-
The Pfam protein families database
-
14 Co-Authors).
-
Finn RD, Mistry J, Tate J, et al.. (14 co-Authors). 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
-
28
-
-
0347383758
-
Modeller: Generation and refinement of homologybased protein structure models
-
Fiser A, Sali A. 2003. Modeller: Generation and refinement of homologybased protein structure models. Methods Enzymol. 374:461-491.
-
(2003)
Methods Enzymol.
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
-
29
-
-
72849115174
-
Origin and evolution of the adaptive immune system: Genetic events and selective pressures
-
Flajnik MF, Kasahara M. 2010. Origin and evolution of the adaptive immune system: Genetic events and selective pressures. Nat Rev Genet. 11:47-59.
-
(2010)
Nat Rev Genet.
, vol.11
, pp. 47-59
-
-
Flajnik, M.F.1
Kasahara, M.2
-
30
-
-
77950806408
-
New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
-
(2010)
Syst Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
31
-
-
77955975654
-
Robustness of ancestral sequence reconstruction to phylogenetic uncertainty
-
Hanson-Smith V, Kolaczkowski B, Thornton JW. 2010. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Mol Biol Evol. 27:1988-1999.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 1988-1999
-
-
Hanson-Smith, V.1
Kolaczkowski, B.2
Thornton, J.W.3
-
32
-
-
33751549306
-
The immune gene repertoire encoded in the purple sea urchin genome
-
16 Co-Authors).
-
Hibino T, Loza-Coll M, Messier C, et al.. (16 co-Authors). 2006. The immune gene repertoire encoded in the purple sea urchin genome. Dev Biol. 300:349-365.
-
(2006)
Dev Biol.
, vol.300
, pp. 349-365
-
-
Hibino, T.1
Loza-Coll, M.2
Messier, C.3
-
33
-
-
33750976374
-
50-Triphosphate RNA is the ligand for RIG-I
-
12 Co-Authors).
-
Hornung V, Ellegast J, Kim S, et al.. (12 co-Authors). 2006. 50-Triphosphate RNA is the ligand for RIG-I. Science 314:994-997.
-
(2006)
Science
, vol.314
, pp. 994-997
-
-
Hornung, V.1
Ellegast, J.2
Kim, S.3
-
34
-
-
11144277878
-
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
-
Huelsenbeck J, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53:904-913.
-
(2004)
Syst Biol.
, vol.53
, pp. 904-913
-
-
Huelsenbeck, J.1
Rannala, B.2
-
35
-
-
81555204380
-
Structural basis of RNA recognition and activation by innate immune receptor RIG-I
-
Jiang F, Ramanathan A, Miller MT, Tang GQ, Gale M Jr, Patel SS, Marcotrigiano J. 2011. Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Nature 479:423-427.
-
(2011)
Nature
, vol.479
, pp. 423-427
-
-
Jiang, F.1
Ramanathan, A.2
Miller, M.T.3
Tang, G.Q.4
Gale Jr., M.5
Patel, S.S.6
Marcotrigiano, J.7
-
36
-
-
33646342149
-
Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses
-
18 Co-Authors).
-
Kato H, Takeuchi O, Sato S, et al.. (18 co-Authors). 2006. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses. Nature 441:101-105.
-
(2006)
Nature
, vol.441
, pp. 101-105
-
-
Kato, H.1
Takeuchi, O.2
Sato, S.3
-
37
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
-
(2008)
Brief Bioinform.
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
38
-
-
27144440523
-
IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction
-
Kawai T, Takahashi K, Sato S, Coban C, Kumar H, Kato H, Ishii KJ, Takeuchi O, Akira S. 2005. IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction. Nat Immunol. 6: 981-988.
-
(2005)
Nat Immunol.
, vol.6
, pp. 981-988
-
-
Kawai, T.1
Takahashi, K.2
Sato, S.3
Coban, C.4
Kumar, H.5
Kato, H.6
Ishii, K.J.7
Takeuchi, O.8
Akira, S.9
-
39
-
-
44649184070
-
A mixed branch length model of heterotachy improves phylogenetic accuracy
-
Kolaczkowski B, Thornton JW. 2008. A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol. 25: 1054-1066.
-
(2008)
Mol Biol Evol.
, vol.25
, pp. 1054-1066
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
40
-
-
34248159030
-
Suppression of longbranch attraction artefacts in the animal phylogeny using a site-heterogeneous model
-
Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of longbranch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 7:S4.
-
(2007)
BMC Evol Biol.
, vol.7
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
41
-
-
69949126557
-
PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
-
Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286-2288.
-
(2009)
Bioinformatics
, vol.25
, pp. 2286-2288
-
-
Lartillot, N.1
Lepage, T.2
Blanquart, S.3
-
42
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-Acid replacement process
-
Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-Acid replacement process. Mol Biol Evol. 21:1095-1109.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
43
-
-
67651232539
-
Structural basis of double-stranded RNA recognition by the RIG-I like receptor MDA5
-
Li X, Lu C, Stewart M, Xu H, Strong RK, Igumenova T, Li P. 2009. Structural basis of double-stranded RNA recognition by the RIG-I like receptor MDA5. Arch Biochem Biophys. 488:23-33.
-
(2009)
Arch Biochem Biophys.
, vol.488
, pp. 23-33
-
-
Li, X.1
Lu, C.2
Stewart, M.3
Xu, H.4
Strong, R.K.5
Igumenova, T.6
Li, P.7
-
44
-
-
67649413594
-
The RIG-I-like receptor LGP2 recognizes the termini of doublestranded RNA
-
Li X, Ranjith-Kumar CT, Brooks MT, Dharmaiah S, Herr AB, Kao C, Li P. 2009. The RIG-I-like receptor LGP2 recognizes the termini of doublestranded RNA. J Biol Chem. 284:13881-13891.
-
(2009)
J Biol Chem.
, vol.284
, pp. 13881-13891
-
-
Li, X.1
Ranjith-Kumar, C.T.2
Brooks, M.T.3
Dharmaiah, S.4
Herr, A.B.5
Kao, C.6
Li, P.7
-
45
-
-
28644432877
-
Very fast empirical prediction and rationalization of protein pKa values
-
Li H, Robertson AD, Jensen JH. 2005. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61:704-721.
-
(2005)
Proteins
, vol.61
, pp. 704-721
-
-
Li, H.1
Robertson, A.D.2
Jensen, J.H.3
-
46
-
-
79956314622
-
Immune signaling by RIG-I-like receptors
-
Loo YM, Gale M Jr. 2011. Immune signaling by RIG-I-like receptors. Immunity 34:680-692.
-
(2011)
Immunity
, vol.34
, pp. 680-692
-
-
Loo, Y.M.1
Gale Jr., M.2
-
47
-
-
79952325540
-
Crystal structure of RIG-I C-Terminal domain bound to blunt-ended double-strand RNA without 50 triphosphate
-
Lu C, Ranjith-Kumar CT, Hao L, Kao CC, Li P. 2011. Crystal structure of RIG-I C-Terminal domain bound to blunt-ended double-strand RNA without 50 triphosphate. Nucleic Acids Res. 39:1565-1575.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1565-1575
-
-
Lu, C.1
Ranjith-Kumar, C.T.2
Hao, L.3
Kao, C.C.4
Li, P.5
-
48
-
-
77955481642
-
The structural basis of 50 triphosphate double-stranded RNA recognition by RIG-I C-Terminal domain
-
Lu C, Xu H, Ranjith-Kumar CT, Brooks MT, Hou TY, Hu F, Herr AB, Strong RK, Kao CC, Li P. 2010. The structural basis of 50 triphosphate double-stranded RNA recognition by RIG-I C-Terminal domain. Structure 18:1032-1043.
-
(2010)
Structure
, vol.18
, pp. 1032-1043
-
-
Lu, C.1
Xu, H.2
Ranjith-Kumar, C.T.3
Brooks, M.T.4
Hou, T.Y.5
Hu, F.6
Herr, A.B.7
Strong, R.K.8
Kao, C.C.9
Li, P.10
-
49
-
-
80054685883
-
Structural insights into RNA recognition by RIG-I
-
Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM. 2011. Structural insights into RNA recognition by RIG-I. Cell 147:409-422.
-
(2011)
Cell
, vol.147
, pp. 409-422
-
-
Luo, D.1
Ding, S.C.2
Vela, A.3
Kohlway, A.4
Lindenbach, B.D.5
Pyle, A.M.6
-
50
-
-
27144440476
-
Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus
-
Meylan E, Curran J, Hofmann K,Moradpour D, BinderM, Bartenschlager R, Tschopp J. 2005. Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus. Nature 437: 1167-1172.
-
(2005)
Nature
, vol.437
, pp. 1167-1172
-
-
Meylan, E.1
Curran, J.2
Hofmann, K.3
Moradpour, D.4
Binder, M.5
Bartenschlager, R.6
Tschopp, J.7
-
51
-
-
0344243515
-
Reanalysis of Murphy et al..'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees
-
Misawa K, Nei M. 2003. Reanalysis of Murphy et al..'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J Mol Evol. 57(1 suppl), S290-S296.
-
(2003)
J Mol Evol.
, vol.571
, Issue.SUPPL.
-
-
Misawa, K.1
Nei, M.2
-
52
-
-
46949102571
-
Structure and function of LGP2, a DEX(D/H) helicase that regulates the innate immunity response
-
Murali A, Li X, Ranjith-Kumar CT, Bhardwaj K, Holzenburg A, Li P, Kao CC. 2008. Structure and function of LGP2, a DEX(D/H) helicase that regulates the innate immunity response. J Biol Chem. 283: 15825-15833.
-
(2008)
J Biol Chem.
, vol.283
, pp. 15825-15833
-
-
Murali, A.1
Li, X.2
Ranjith-Kumar, C.T.3
Bhardwaj, K.4
Holzenburg, A.5
Li, P.6
Kao, C.C.7
-
53
-
-
27544437635
-
Genomic scans for selective sweeps using SNP data
-
Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. 2005. Genomic scans for selective sweeps using SNP data. Genome Res. 15:1566-1575.
-
(2005)
Genome Res.
, vol.15
, pp. 1566-1575
-
-
Nielsen, R.1
Williamson, S.2
Kim, Y.3
Hubisz, M.J.4
Clark, A.G.5
Bustamante, C.6
-
54
-
-
33750984771
-
RIG-I-mediated antiviral responses to single-stranded RNA bearing 50-phosphates
-
Pichlmair A, Schulz O, Tan CP, Naslund TI, LiljestromP,Weber F, Reis e Sousa C. 2006. RIG-I-mediated antiviral responses to single-stranded RNA bearing 50-phosphates. Science 314:997-1001.
-
(2006)
Science
, vol.314
, pp. 997-1001
-
-
Pichlmair, A.1
Schulz, O.2
Tan, C.P.3
Naslund, T.I.4
Liljestrom, P.5
Weber, F.6
Reise Sousa, C.7
-
55
-
-
64549126847
-
The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA
-
Pippig DA, Hellmuth JC, Cui S, Kirchhofer A, Lammens K, Lammens A, Schmidt A, Rothenfusser S, Hopfner KP. 2009. The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA. Nucleic Acids Res. 37:2014-2025.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2014-2025
-
-
Pippig, D.A.1
Hellmuth, J.C.2
Cui, S.3
Kirchhofer, A.4
Lammens, K.5
Lammens, A.6
Schmidt, A.7
Rothenfusser, S.8
Hopfner, K.P.9
-
56
-
-
55549114663
-
50-Triphosphate-siRNA: Turning gene silencing and Rig-I activation against melanoma
-
31 Co-Authors).
-
Poeck H, Besch R, Maihoefer C, et al.. (31 co-Authors). 2008. 50-Triphosphate-siRNA: Turning gene silencing and Rig-I activation against melanoma. Nat Med. 14:1256-1263.
-
(2008)
Nat Med.
, vol.14
, pp. 1256-1263
-
-
Poeck, H.1
Besch, R.2
Maihoefer, C.3
-
57
-
-
74049126045
-
Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production
-
18 Co-Authors).
-
Poeck H, Bscheider M, Gross O, et al.. (18 co-Authors). 2010. Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production. Nat Immunol. 11: 63-69.
-
(2010)
Nat Immunol.
, vol.11
, pp. 63-69
-
-
Poeck, H.1
Bscheider, M.2
Gross, O.3
-
58
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
59
-
-
78651345652
-
The RCSB protein data bank: Redesigned web site and web services
-
15 Co-Authors).
-
Rose PW, Beran B, Bi C, et al.. (15 co-Authors). 2011. The RCSB protein data bank: Redesigned web site and web services. Nucleic Acids Res. 39:D392-D401.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Rose, P.W.1
Beran, B.2
Bi, C.3
-
60
-
-
0034065724
-
Ab initio gene finding in Drosophila genomic DNA
-
Salamov AA, Solovyev VV. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10:516-522.
-
(2000)
Genome Res.
, vol.10
, pp. 516-522
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
61
-
-
55949083181
-
Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting
-
Sarkar D, Desalle R, Fisher PB. 2008. Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting. Proc Natl Acad Sci U S A. 105:17040-17045.
-
(2008)
Proc Natl Acad Sci U S A.
, vol.105
, pp. 17040-17045
-
-
Sarkar, D.1
Desalle, R.2
Fisher, P.B.3
-
62
-
-
76549109497
-
LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses
-
Satoh T, Kato H, Kumagai Y, Yoneyama M, Sato S, Matsushita K, Tsujimura T, Fujita T, Akira S, Takeuchi O. 2010. LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses. Proc Natl Acad Sci U S A. 107:1512-1517.
-
(2010)
Proc Natl Acad Sci U S A.
, vol.107
, pp. 1512-1517
-
-
Satoh, T.1
Kato, H.2
Kumagai, Y.3
Yoneyama, M.4
Sato, S.5
Matsushita, K.6
Tsujimura, T.7
Fujita, T.8
Akira, S.9
Takeuchi, O.10
-
63
-
-
55249091610
-
PhySIC-IST: Cleaning source trees to infer more informative supertrees
-
Scornavacca C, Berry V, Lefort V, Douzery EJ, Ranwez V. 2008. PhySIC-IST: Cleaning source trees to infer more informative supertrees. BMC Bioinformatics 9:413.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 413
-
-
Scornavacca, C.1
Berry, V.2
Lefort, V.3
Douzery, E.J.4
Ranwez, V.5
-
64
-
-
24144461689
-
Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3
-
Seth RB, Sun L, Ea CK, Chen ZJ. 2005. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3. Cell 122:669-682.
-
(2005)
Cell
, vol.122
, pp. 669-682
-
-
Seth, R.B.1
Sun, L.2
Ea, C.K.3
Chen, Z.J.4
-
65
-
-
0035173378
-
DbSNP: The NCBI database of genetic variation
-
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29:308-311.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
Smigielski, E.M.6
Sirotkin, K.7
-
66
-
-
67649415364
-
Identification of loss of function mutations in human genes encoding RIG-I and MDA5: Implications for resistance to type I diabetes
-
Shigemoto T, Kageyama M, Hirai R, Zheng J, Yoneyama M, Fujita T. 2009. Identification of loss of function mutations in human genes encoding RIG-I and MDA5: Implications for resistance to type I diabetes. J Biol Chem. 284:13348-13354.
-
(2009)
J Biol Chem.
, vol.284
, pp. 13348-13354
-
-
Shigemoto, T.1
Kageyama, M.2
Hirai, R.3
Zheng, J.4
Yoneyama, M.5
Fujita, T.6
-
68
-
-
33745240931
-
A genomewide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region
-
14 Co-Authors).
-
Smyth DJ, Cooper JD, Bailey R, et al.. (14 co-Authors). 2006. A genomewide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet. 38:617-619.
-
(2006)
Nat Genet.
, vol.38
, pp. 617-619
-
-
Smyth, D.J.1
Cooper, J.D.2
Bailey, R.3
-
69
-
-
0035527373
-
Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?
-
Sullivan J, Swofford DL. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?. Syst Biol. 50:723-729.
-
(2001)
Syst Biol.
, vol.50
, pp. 723-729
-
-
Sullivan, J.1
Swofford, D.L.2
-
70
-
-
3042545431
-
On inconsistency of the neighborjoining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled
-
Susko E, Inagaki Y, Roger AJ. 2004. On inconsistency of the neighborjoining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol Biol Evol. 21: 1629-1642.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1629-1642
-
-
Susko, E.1
Inagaki, Y.2
Roger, A.J.3
-
71
-
-
0037058983
-
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
-
Suzuki Y, Glazko GV, Nei M. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U. S. A. 99:16138-16143.
-
(2002)
Proc Natl Acad Sci U. S. A.
, vol.99
, pp. 16138-16143
-
-
Suzuki, Y.1
Glazko, G.V.2
Nei, M.3
-
72
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
Swofford DL,Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol. 50:525-539.
-
(2001)
Syst Biol.
, vol.50
, pp. 525-539
-
-
Swofford, D.L.1
Waddell, P.J.2
Huelsenbeck, J.P.3
Foster, P.G.4
Lewis, P.O.5
Rogers, J.S.6
-
73
-
-
0024313579
-
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
-
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
74
-
-
67650510680
-
Solution structures of cytosolic RNA sensor MDA5 and LGP2 C-Terminal domains: Identification of the RNA recognition loop in RIG-I-like receptors
-
11 Co-Authors).
-
Takahasi K, Kumeta H, Tsuduki N, et al.. (11 co-Authors). 2009. Solution structures of cytosolic RNA sensor MDA5 and LGP2 C-Terminal domains: Identification of the RNA recognition loop in RIG-I-like receptors. J Biol Chem. 284:17465-17474.
-
(2009)
J Biol Chem.
, vol.284
, pp. 17465-17474
-
-
Takahasi, K.1
Kumeta, H.2
Tsuduki, N.3
-
75
-
-
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. Syst Biol. 56:564-577.
-
(2007)
Syst Biol.
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
76
-
-
84863556835
-
Evolution and functional impact of rare coding variation from deep sequencing of human exomes
-
23 Co-Authors).
-
Tennessen JA, Bigham AW, OConnor TD, et al.. (23 co-Authors). 2012. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64-69.
-
(2012)
Science
, vol.337
, pp. 64-69
-
-
Tennessen, J.A.1
Bigham, A.W.2
Oconnor, T.D.3
-
77
-
-
80054948364
-
The selective footprints of viral pressures at the human RIG-I-like receptor family
-
Vasseur E, Patin E, Laval G, Pajon S, Fornarino S, Crouau-Roy B, Quintana-Murci L. 2011. The selective footprints of viral pressures at the human RIG-I-like receptor family. Hum Mol Genet. 20: 4462-4474.
-
(2011)
Hum Mol Genet.
, vol.20
, pp. 4462-4474
-
-
Vasseur, E.1
Patin, E.2
Laval, G.3
Pajon, S.4
Fornarino, S.5
Crouau-Roy, B.6
Quintana-Murci, L.7
-
78
-
-
77954386541
-
Structural and functional insights into 50-ppp RNA pattern recognition by the innate immune receptor RIG-I
-
12 Co-Authors).
-
Wang Y, Ludwig J, Schuberth C, et al.. (12 co-Authors). 2010. Structural and functional insights into 50-ppp RNA pattern recognition by the innate immune receptor RIG-I. Nat Struct Mol Biol. 17: 781-787.
-
(2010)
Nat Struct Mol Biol.
, vol.17
, pp. 781-787
-
-
Wang, Y.1
Ludwig, J.2
Schuberth, C.3
-
79
-
-
84872604349
-
Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5
-
Wu B, Peisley A, Richards C, Yao H, Zeng X, Lin C, Chu F, Walz T, Hur S. 2013. Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5. Cell 152:276-289.
-
(2013)
Cell
, vol.152
, pp. 276-289
-
-
Wu, B.1
Peisley, A.2
Richards, C.3
Yao, H.4
Zeng, X.5
Lin, C.6
Chu, F.7
Walz, T.8
Hur, S.9
-
80
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
81
-
-
0028820333
-
A new method of inference of ancestral nucleotide and amino acid sequences
-
Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
-
(1995)
Genetics
, vol.141
, pp. 1641-1650
-
-
Yang, Z.1
Kumar, S.2
Nei, M.3
-
82
-
-
16344378246
-
Bayes empirical bayes inference of amino acid sites under positive selection
-
Yang Z, Wong WS, Nielsen R. 2005. Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22: 1107-1118.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.2
Nielsen, R.3
-
83
-
-
23844438864
-
Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity
-
13 Co-Authors).
-
Yoneyama M, Kikuchi M, Matsumoto K, et al.. (13 co-Authors). 2005. Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity. J Immunol. 175: 2851-2858.
-
(2005)
J Immunol.
, vol.175
, pp. 2851-2858
-
-
Yoneyama, M.1
Kikuchi, M.2
Matsumoto, K.3
-
84
-
-
3242813113
-
The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses
-
Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S, Fujita T. 2004. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat Immunol. 5:730-737.
-
(2004)
Nat Immunol.
, vol.5
, pp. 730-737
-
-
Yoneyama, M.1
Kikuchi, M.2
Natsukawa, T.3
Shinobu, N.4
Imaizumi, T.5
Miyagishi, M.6
Taira, K.7
Akira, S.8
Fujita, T.9
-
85
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479.
-
(2005)
Mol Biol Evol.
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
-
86
-
-
0029917011
-
Linearization of the Bradford protein assay increases its sensitivity: Theoretical and experimental studies
-
Zor T, Selinger Z. 1996. Linearization of the Bradford protein assay increases its sensitivity: Theoretical and experimental studies. Anal Biochem. 236:302-308.
-
(1996)
Anal Biochem.
, vol.236
, pp. 302-308
-
-
Zor, T.1
Selinger, Z.2
-
87
-
-
66249094862
-
Origin and evolution of the RIG-I like RNA helicase gene family
-
Zou J, Chang M, Nie P, Secombes CJ. 2009. Origin and evolution of the RIG-I like RNA helicase gene family. BMC Evol Biol. 9:85.
-
(2009)
BMC Evol Biol.
, vol.9
, pp. 85
-
-
Zou, J.1
Chang, M.2
Nie, P.3
Secombes, C.J.4
|