Arcady Mushegian sponsors free access to F1000 for Moscow State University, Moscow, Russian Federation. Supporting F1000's initiative to make itself available to scientists in all countries, including free access to developing countries (more details).

http://www.stowers-institute.org/labs/MushegianLab.asp

Broad phylogenomic sampling improves resolution of the animal tree of life. Dunn CW, Hejnol A, …, Martindale MQ, Giribet G Nature 2008 Apr 10 452(7188):745-9 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Sebastian Shimeld / Rafael Zardoya Dissenters | Arcady Mushegian Evaluated 24 Sep 2008 Defining genetic interaction. Mani R, St Onge RP, …, Giaever G, Roth FP Proc Natl Acad Sci U S A 2008 Mar 4 105(9):3461-6 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 16 Sep 2008 Reticulate representation of evolutionary and functional relationships between phage genomes. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R Mol Biol Evol 2008 Apr 25(4):762-77 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 9 Apr 2008 Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. Monier A, Claverie JM, Ogata H BMC Genomics 2007 8:456 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 9 Apr 2008 Natural history and evolutionary principles of gene duplication in fungi. Wapinski I, Pfeffer A, Friedman N, Regev A Nature 2007 Sep 6 449(7158):54-61 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Sebastian Shimeld / Arcady Mushegian / Audrey Gasch Evaluated 31 Oct 2007 The human disease network. Goh KI, Cusick ME, …, Vidal M, Barabási AL Proc Natl Acad Sci U S A 2007 May 22 104(21):8685-90 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 11 Jun 2007 In search of the biological significance of modular structures in protein networks. Wang Z, Zhang J PLoS Comput Biol 2007 Jun 3(6):e107 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 8 Jun 2007 Eukaryotic operon-like transcription of functionally related genes in Drosophila. Ben-Shahar Y, Nannapaneni K, …, Scheetz TE, Welsh MJ Proc Natl Acad Sci U S A 2007 Jan 2 104(1):222-7 [abstract on PubMed] [related articles] [FREE full text] Selected by | Aniko Naray-Fejes-Toth / Arcady Mushegian Evaluated 8 Feb 2007 Computational prediction of genomic functional cores specific to different microbes. Carbone A J Mol Evol 2006 Dec 63(6):733-46 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Arcady Mushegian Evaluated 2 Feb 2007 A segmentation gene in tribolium produces a polycistronic mRNA that codes for multiple conserved peptides. Savard J, Marques-Souza H, Aranda M, Tautz D Cell 2006 Aug 11 126(3):559-69 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Arcady Mushegian Evaluated 10 Oct 2006 Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks. Rahman SA, Schomburg D Bioinformatics 2006 Jul 15 22(14):1767-74 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 2 Oct 2006 Close sequence comparisons are sufficient to identify human cis-regulatory elements. Prabhakar S, Poulin F, …, Couronne O, Pennacchio LA Genome Res 2006 Jul 16(7):855-63 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Andrew S. McCallion Evaluated 20 Jul 2006 Modularity and community structure in networks. Newman ME Proc Natl Acad Sci U S A 2006 Jun 6 103(23):8577-82 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Ram Samudrala Evaluated 31 May 2006 A new type of stochastic dependence revealed in gene expression data. Klebanov L, Jordan C, Yakovlev A Stat Appl Genet Mol Biol 2006 5(1):Article7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Arcady Mushegian Evaluated 10 Apr 2006 The "robust yet fragile" nature of the Internet. Doyle JC, Alderson DL, …, Tanaka R, Willinger W Proc Natl Acad Sci U S A 2005 Oct 11 102(41):14497-502 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 8 Dec 2005 Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Kawano S, Hashimoto K, …, Goto S, Kanehisa M Bioinformatics 2005 Nov 1 21(21):3976-82 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 20 Sep 2005 Coevolution between nonhomologous but functionally similar proteins and their conserved partners in the Legionella pathogenesis system. Feldman M, Zusman T, Hagag S, Segal G Proc Natl Acad Sci U S A 2005 Aug 23 102(34):12206-11 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 20 Sep 2005 Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. Nakao M, Barrero RA, …, Suwa M, Nakai K Nucleic Acids Res 2005 33(8):2355-63 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 13 Jul 2005 Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451. Erlacher MD, Lang K, …, Mankin AS, Polacek N Nucleic Acids Res 2005 33(5):1618-27 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Andrea Barta Evaluated 13 May 2005 An evolutionary and functional assessment of regulatory network motifs. Mazurie A, Bottani S, Vergassola M Genome Biol 2005 6(4):R35 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Charles Auffray Evaluated 12 May 2005 Evolutionary origins of genomic repertoires in bacteria. Lerat E, Daubin V, Ochman H, Moran NA PLoS Biol 2005 May 3(5):e130 [abstract on PubMed] [related articles] [FREE full text] Selected by | Mark D. Adams / Arcady Mushegian / Jonathan A. Eisen Evaluated 11 May 2005 Prokaryotic phylogenies inferred from protein structural domains. Deeds EJ, Hennessey H, Shakhnovich EI Genome Res 2005 Mar 15(3):393-402 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 21 Mar 2005 Evolutionary profiles from the QR factorization of multiple sequence alignments. Sethi A, O'Donoghue P, Luthey-Schulten Z Proc Natl Acad Sci U S A 2005 Mar 15 102(11):4045-50 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Anne-Catherine Dock-Bregeon Evaluated 17 Mar 2005 Computational inference of scenarios for alpha-proteobacterial genome evolution. Boussau B, Karlberg EO, …, Legault BA, Andersson SG Proc Natl Acad Sci U S A 2004 Jun 29 101(26):9722-7 [abstract on PubMed] [related articles] [FREE full text] Selected by | Daniel Kahn / Arcady Mushegian Evaluated 14 Mar 2005 Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. Sandelin A, Bailey P, …, Ericson J, Lenhard B BMC Genomics 2004 5(1):99 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 19 Jan 2005 Integrating the universal metabolism into a phylogenetic analysis. Cunchillos C, Lecointre G Mol Biol Evol 2005 Jan 22(1):1-11 [abstract on PubMed] [related articles] [FREE full text] Selected by | John Jaenike / Arcady Mushegian Evaluated 14 Dec 2004 Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A Proc Natl Acad Sci U S A 2004 Oct 19 101(42):15148-53 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 16 Nov 2004 Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, Yamashita R, …, Nakai K, Sugano S Genome Res 2004 Sep 14(9):1711-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 5 Oct 2004 Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Snel B, van Noort V, Huynen MA Nucleic Acids Res 2004 32(16):4725-31 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 5 Oct 2004 The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. Dutilh BE, Huynen MA, Bruno WJ, Snel B J Mol Evol 2004 May 58(5):527-39 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Jeffrey Lawrence / Arcady Mushegian Evaluated 11 Aug 2004 Functional evolution of the yeast protein interaction network. Kunin V, Pereira-Leal JB, Ouzounis CA Mol Biol Evol 2004 Jul 21(7):1171-6 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 11 Aug 2004 Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Lake JA, Rivera MC Mol Biol Evol 2004 Apr 21(4):681-90 [abstract on PubMed] [related articles] [FREE full text] Selected by | William Martin / Arcady Mushegian Evaluated 10 Aug 2004 Protein ranking: from local to global structure in the protein similarity network. Weston J, Elisseeff A, …, Leslie CS, Noble WS Proc Natl Acad Sci U S A 2004 Apr 27 101(17):6559-63 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Torsten Schwede Evaluated 22 Apr 2004 Self-regulated cleavage of the mitochondrial intramembrane-cleaving protease PARL yields Pbeta, a nuclear-targeted peptide. Sík A, Passer BJ, Koonin EV, Pellegrini L J Biol Chem 2004 Apr 9 279(15):15323-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 14 Apr 2004 Methanogenic Archaea and human periodontal disease. Lepp PW, Brinig MM, …, Armitage GC, Relman DA Proc Natl Acad Sci U S A 2004 Apr 20 101(16):6176-81 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Joe Heitman Evaluated 13 Apr 2004 Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Wolf YI, Rogozin IB, Koonin EV Genome Res 2004 Jan 14(1):29-36 [abstract on PubMed] [related articles] [FREE full text] Selected by | Nick Grishin / Arcady Mushegian / Alejandro Sanchez-Alvarado Evaluated 11 Mar 2004 Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Pe'er I, Felder CE, …, Sussman JL, Beckmann JS Proteins 2004 Jan 1 54(1):20-40 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Eaton E. Lattman / Arcady Mushegian Evaluated 23 Jan 2004 Genome-scale approaches to resolving incongruence in molecular phylogenies. Rokas A, Williams BL, King N, Carroll SB Nature 2003 Oct 23 425(6960):798-804 [abstract on PubMed] [related articles] [full text] [order article] Selected by | William Martin / Arcady Mushegian / Guenter Theissen Evaluated 27 Nov 2003 Finding evolutionary relations beyond superfamilies: fold-based superfamilies. Matsuda K, Nishioka T, …, Kawabata T, Go N Protein Sci 2003 Oct 12(10):2239-51 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 27 Nov 2003 Statistical significance for genomewide studies. Storey JD, Tibshirani R Proc Natl Acad Sci U S A 2003 Aug 5 100(16):9440-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Daniel Kahn Evaluated 27 Aug 2003 Tracing the evolution of RNA structure in ribosomes. Caetano-Anollés G Nucleic Acids Res 2002 Jun 1 30(11):2575-87 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 29 Jul 2003 Functional fingerprints of folds: evidence for correlated structure-function evolution. Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI J Mol Biol 2003 Feb 7 326(1):1-9 [abstract on PubMed] [related articles] [order article] Selected by | Janet Thornton / Arcady Mushegian Evaluated 30 Apr 2003 The riboswitch-mediated control of sulfur metabolism in bacteria. Epshtein V, Mironov AS, Nudler E Proc Natl Acad Sci U S A 2003 Apr 29 100(9):5052-6 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 25 Apr 2003 Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Levesque M, Shasha D, …, Surette MG, Benfey PN Curr Biol 2003 Jan 21 13(2):129-33 [abstract on PubMed] [related articles] [order article] Selected by | Arcady Mushegian Evaluated 3 Feb 2003 Using machine vision to analyze and classify Caenorhabditis elegans behavioral phenotypes quantitatively. Baek JH, Cosman P, …, Silver J, Schafer WR J Neurosci Methods 2002 Jul 30 118(1):9-21 [abstract on PubMed] [related articles] [order article] Selected by | Arcady Mushegian Evaluated 3 Jan 2003 Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Kondo N, Nikoh N, …, Shimada M, Fukatsu T Proc Natl Acad Sci U S A 2002 Oct 29 99(22):14280-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Yvonne Graeser Evaluated 22 Oct 2002 Transitive functional annotation by shortest-path analysis of gene expression data. Zhou X, Kao MC, Wong WH Proc Natl Acad Sci U S A 2002 Oct 1 99(20):12783-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 30 Aug 2002 A global analysis of Caenorhabditis elegans operons. Blumenthal T, Evans D, …, Kiraly M, Kim SK Nature 2002 Jun 20 417(6891):851-4 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Jonathan Hodgkin / Arcady Mushegian / Miles Wilkinson Evaluated 11 Jul 2002 Connected gene neighborhoods in prokaryotic genomes. Rogozin IB, Makarova KS, …, Szekely LA, Koonin EV Nucleic Acids Res 2002 May 15 30(10):2212-23 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 12 Jun 2002 An efficient algorithm for large-scale detection of protein families. Enright AJ, Van Dongen S, Ouzounis CA Nucleic Acids Res 2002 Apr 1 30(7):1575-84 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 2 May 2002 The evolutionary position of nematodes. Blair JE, Ikeo K, Gojobori T, Hedges SB BMC Evol Biol 2002 Apr 8 2:7 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Oliver Hobert Evaluated 2 May 2002 How many named species are valid? Alroy J Proc Natl Acad Sci U S A 2002 Mar 19 99(6):3706-11 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian Evaluated 22 Mar 2002 Genomes in flux: the evolution of archaeal and proteobacterial gene content. Snel B, Bork P, Huynen MA Genome Res 2002 Jan 12(1):17-25 [abstract on PubMed] [related articles] [FREE full text] Selected by | Arcady Mushegian / Christos Ouzounis / Eugene Koonin Evaluated 5 Feb 2002

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