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Arcady Mushegian
Stowers Institute for Medical Research, Kansas City, United States of America

Faculty Member: Genomics & Genetics > Bioinformatics [ since 29 January 2002 ]
[ Homepage ] [ Evaluations ]
Home page

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

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Evaluations

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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