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Expansion of Biological Pathways Based on Evolutionary Inference

Li, Yang, Calvo, Sarah E., Gutman, Roee, Liu, Jun S., Mootha, Vamsi K.·2014·Cell
DOI 10.1016/j.cell.2014.05.034PMC PMC4171950
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Research works printed but not linked: 56

  1. Ashburner, 2000, Gene ontology: tool for the unification of biology, Nat. Genet., 25, 25, 10.1038/75556 · DOI · Paper page
  2. Balsa, 2012, NDUFA4 is a subunit of complex IV of the mammalian electron transport chain, Cell Metab., 16, 378, 10.1016/j.cmet.2012.07.015 · DOI
  3. Barker, 2005, Predicting functional gene links from phylogenetic-statistical analyses of whole genomes, PLoS Comput. Biol., 1, e3, 10.1371/journal.pcbi.0010003 · DOI
  4. Barker, 2007, Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes, Bioinformatics, 23, 14, 10.1093/bioinformatics/btl558 · DOI
  5. Baughman, 2011, Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter, Nature, 476, 341, 10.1038/nature10234 · DOI
  6. Bick, 2012, Evolutionary diversity of the mitochondrial calcium uniporter, Science, 336, 886, 10.1126/science.1214977 · DOI
  7. Blacque, 2005, Functional genomics of the cilium, a sensory organelle, Curr. Biol., 15, 935, 10.1016/j.cub.2005.04.059 · DOI
  8. Blacque, 2008, Intraflagellar transport: from molecular characterisation to mechanism, Front. Biosci., 13, 2633, 10.2741/2871 · DOI
  9. Dorfman, 1969, The isolation of adenylosuccinate synthetase mutants in yeast by selection for constitutive behavior in pigmented strains, Genetics, 61, 377, 10.1093/genetics/61.2.377 · DOI
  10. Dovey, 1984, Purine salvage in Schistosoma mansoni schistosomules, Mol. Biochem. Parasitol., 11, 157, 10.1016/0166-6851(84)90062-8 · DOI
  11. Duleh, 2010, WASH and the Arp2/3 complex regulate endosome shape and trafficking, Cytoskeleton (Hoboken), 67, 193, 10.1002/cm.20437 · DOI · Paper page
  12. Efimenko, 2005, Analysis of xbx genes in C. elegans, Development, 132, 1923, 10.1242/dev.01775 · DOI
  13. Gabaldón, 2005, Evolution of proteins and proteomes: a phylogenetics approach, Evol. Bioinform. Online, 1, 51, 10.1177/117693430500100004 · DOI
  14. Glazko, 2004, Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns, Genome Biol., 5, R32, 10.1186/gb-2004-5-5-r32 · DOI
  15. Hamming, 1950, Error detecting and error correcting codes, Bell Syst. Tech. J., 29, 147, 10.1002/j.1538-7305.1950.tb00463.x · DOI · Paper page
  16. Harbour, 2012, Recruitment of the endosomal WASH complex is mediated by the extended ‘tail’ of Fam21 binding to the retromer protein Vps35, Biochem. J., 442, 209, 10.1042/BJ20111761 · DOI · Paper page
  17. Hubert, 1985, Comparing partitions, J. Classif., 2, 193, 10.1007/BF01908075 · DOI · Paper page
  18. Inglis, 2006, Piecing together a ciliome, Trends Genet., 22, 491, 10.1016/j.tig.2006.07.006 · DOI
  19. Jamerson, 2012, Pathogenic Naegleria fowleri and non-pathogenic Naegleria lovaniensis exhibit differential adhesion to, and invasion of, extracellular matrix proteins, Microbiology, 158, 791, 10.1099/mic.0.055020-0 · DOI
  20. Jim, 2004, A cross-genomic approach for systematic mapping of phenotypic traits to genes, Genome Res., 14, 109, 10.1101/gr.1586704 · DOI
  21. Kanehisa, 2006, From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Res., 34, D354, 10.1093/nar/gkj102 · DOI
  22. Kanehisa, 2012, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res., 40, D109, 10.1093/nar/gkr988 · DOI · Paper page
  23. Kass, 1995, Bayes factors, J. Am. Stat. Assoc., 90, 773, 10.1080/01621459.1995.10476572 · DOI · Paper page
  24. Kensche, 2008, Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution, J. R. Soc. Interface, 5, 151, 10.1098/rsif.2007.1047 · DOI
  25. Li, 2004, Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene, Cell, 117, 541, 10.1016/S0092-8674(04)00450-7 · DOI
  26. Lim, 2010, The evolution, metabolism and functions of the apicoplast, Philos. Trans. R. Soc. Lond. B Biol. Sci., 365, 749, 10.1098/rstb.2009.0273 · DOI · Paper page
  27. Mimaki, 2012, Understanding mitochondrial complex I assembly in health and disease, Biochim. Biophys. Acta, 1817, 851, 10.1016/j.bbabio.2011.08.010 · DOI · Paper page
  28. Ogilvie, 2005, A molecular chaperone for mitochondrial complex I assembly is mutated in a progressive encephalopathy, J. Clin. Invest., 115, 2784, 10.1172/JCI26020 · DOI
  29. Ostrowski, 2002, A proteomic analysis of human cilia: identification of novel components, Mol. Cell Proteomics, 1, 451, 10.1074/mcp.M200037-MCP200 · DOI
  30. Pagliarini, 2008, A mitochondrial protein compendium elucidates complex I disease biology, Cell, 134, 112, 10.1016/j.cell.2008.06.016 · DOI · Paper page
  31. Pazour, 2005, Proteomic analysis of a eukaryotic cilium, J. Cell Biol., 170, 103, 10.1083/jcb.200504008 · DOI
  32. Pellegrini, 1999, Assigning protein functions by comparative genome analysis: protein phylogenetic profiles, Proc. Natl. Acad. Sci. USA, 96, 4285, 10.1073/pnas.96.8.4285 · DOI
  33. Perocchi, 2010, MICU1 encodes a mitochondrial EF hand protein required for Ca(2+) uptake, Nature, 467, 291, 10.1038/nature09358 · DOI
  34. Powell, 2012, eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges, Nucleic Acids Res., 40, D284, 10.1093/nar/gkr1060 · DOI
  35. Rao, 2005, Lack of heme synthesis in a free-living eukaryote, Proc. Natl. Acad. Sci. USA, 102, 4270, 10.1073/pnas.0500877102 · DOI
  36. Ruiz-Trillo, 2007, The origins of multicellularity: a multi-taxon genome initiative, Trends Genet., 23, 113, 10.1016/j.tig.2007.01.005 · DOI
  37. Sancak, 2013, EMRE is an essential component of the mitochondrial calcium uniporter complex, Science, 342, 1379, 10.1126/science.1242993 · DOI
  38. Smith, 2005, Robust method for proteome analysis by MS/MS using an entire translated genome: demonstration on the ciliome of Tetrahymena thermophila, J. Proteome Res., 4, 909, 10.1021/pr050013h · DOI
  39. Stolc, 2005, Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes, Proc. Natl. Acad. Sci. USA, 102, 3703, 10.1073/pnas.0408358102 · DOI
  40. Tabach, 2013, Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence, Nature, 493, 694, 10.1038/nature11779 · DOI
  41. Trachana, 2011, Orthology prediction methods: a quality assessment using curated protein families, BioEssays, 33, 769, 10.1002/bies.201100062 · DOI · Paper page
  42. Vafai, 2012, Mitochondrial disorders as windows into an ancient organelle, Nature, 491, 374, 10.1038/nature11707 · DOI
  43. Vert, 2002, A tree kernel to analyse phylogenetic profiles, Bioinformatics, 18, S276, 10.1093/bioinformatics/18.suppl_1.S276 · DOI
  44. von Mering, 2003, STRING: a database of predicted functional associations between proteins, Nucleic Acids Res., 31, 258, 10.1093/nar/gkg034 · DOI
  45. Wapinski, 2007, Automatic genome-wide reconstruction of phylogenetic gene trees, Bioinformatics, 23, i549, 10.1093/bioinformatics/btm193 · DOI
  46. Zhou, 2006, Inferring functional linkages between proteins from evolutionary scenarios, J. Mol. Biol., 359, 1150, 10.1016/j.jmb.2006.04.011 · DOI
  47. Chib, 1995, Marginal likelihood from the Gibbs output, J. Am. Stat. Assoc., 90, 1313, 10.1080/01621459.1995.10476635 · DOI
  48. Felsenstein, 1981, Evolutionary trees from DNA sequences: a maximum likelihood approach, J. Mol. Evol., 17, 368, 10.1007/BF01734359 · DOI · Paper page
  49. Ferguson, 1973, A Bayesian analysis of some nonparametric problems, Ann. Stat., 1, 209, 10.1214/aos/1176342360 · DOI
  50. Gelfand, 1990, Sampling-based approaches to calculating marginal densities, J. Am. Stat. Assoc., 85, 398, 10.1080/01621459.1990.10476213 · DOI · Paper page
  51. Liu, 1994, The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem, J. Am. Stat. Assoc., 89, 958, 10.1080/01621459.1994.10476829 · DOI
  52. Neal, 2000, Markov chain sampling methods for Dirichlet process mixture models, J. Comput. Graph. Stat., 9, 249, 10.1080/10618600.2000.10474879 · DOI
  53. Nilsson, 2009, Discovery of genes essential for heme biosynthesis through large-scale gene expression analysis, Cell Metab., 10, 119, 10.1016/j.cmet.2009.06.012 · DOI
  54. Parra, 2007, CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, 23, 1061, 10.1093/bioinformatics/btm071 · DOI
  55. Pitman, 1996, Some developments of the Blackwell-MacQueen urn scheme, Lecture Notes—Monograph Series, 30, 245, 10.1214/lnms/1215453576 · DOI
  56. Scott, 2002, Bayesian methods for hidden Markov models: recursive computing in the 21st century, J. Am. Stat. Assoc., 97, 337, 10.1198/016214502753479464 · DOI

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Metadata

Authors
Li, Y., Calvo, S. E., Gutman, R., Liu, J. S., & Mootha, V. K.
Venue
Cell
Publisher
Elsevier BV
Published
2014-07
Volume
158
Issue
1
Pages
213-225
ISSN
0092-8674
DOI
10.1016/j.cell.2014.05.034
PMC
PMC4171950
Cited by
122
References
0
Language
en
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