Volume 4, issue 1, December 2004
52 articles in this issue
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Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications
Authors
- Johannes Berg
- Michael Lässig
- Andreas Wagner
- Content type: Research article
- Open Access
- Published: 27 November 2004
- Article: 51
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Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics
Authors (first, second and last of 5)
- Alex Mira
- Ravindra Pushker
- Francisco RodrÃguez-Valera
- Content type: Research article
- Open Access
- Published: 26 November 2004
- Article: 50
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Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens
Authors
- Hinrich Schulenburg
- Jonathan J Ewbank
- Content type: Research article
- Open Access
- Published: 22 November 2004
- Article: 49
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Good vs complementary genes for parasite resistance and the evolution of mate choice
Authors
- R Stephen Howard
- Curtis M Lively
- Content type: Research article
- Open Access
- Published: 19 November 2004
- Article: 48
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Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes
Authors
- Alexandra V Andreeva
- Mikhail A Kutuzov
- Content type: Research article
- Open Access
- Published: 19 November 2004
- Article: 47
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Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife
Authors
- Jean-François Manen
- Content type: Research article
- Open Access
- Published: 18 November 2004
- Article: 46
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Density-dependence and within-host competition in a semelparous parasite of leaf-cutting ants
Authors (first, second and last of 7)
- William OH Hughes
- Klaus S Petersen
- Jacobus J Boomsma
- Content type: Research article
- Open Access
- Published: 14 November 2004
- Article: 45
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A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land
Authors
- Fabia U Battistuzzi
- Andreia Feijao
- S Blair Hedges
- Content type: Research article
- Open Access
- Published: 09 November 2004
- Article: 44
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An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution
Authors (first, second and last of 4)
- Gustavo Glusman
- Amardeep Kaur
- Lee Rowen
- Content type: Research article
- Open Access
- Published: 04 November 2004
- Article: 43
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Adaptive evolution of transcription factor binding sites
Authors
- Johannes Berg
- Stana Willmann
- Michael Lässig
- Content type: Research article
- Open Access
- Published: 28 October 2004
- Article: 42
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The structurally constrained protein evolution model accounts for sequence patterns of the LβH superfamily
Authors
- Gustavo Parisi
- Julián Echave
- Content type: Research article
- Open Access
- Published: 22 October 2004
- Article: 41
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Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer
Authors (first, second and last of 5)
- Daniel L Nickrent
- Albert Blarer
- Frank E Anderson
- Content type: Research article
- Open Access
- Published: 20 October 2004
- Article: 40
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Evolutionary relationships of Aurora kinases: Implications for model organism studies and the development of anti-cancer drugs
Authors (first, second and last of 5)
- James R Brown
- Kristin K Koretke
- Denis R Patrick
- Content type: Research article
- Open Access
- Published: 12 October 2004
- Article: 39
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Characterization of an endogenous retrovirus class in elephants and their relatives
Authors
- Alex D Greenwood
- Claudia C Englbrecht
- Ross DE MacPhee
- Content type: Research article
- Open Access
- Published: 11 October 2004
- Article: 38
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Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements
Authors (first, second and last of 4)
- Ravi Shankar
- Deepak Grover
- Mitali Mukerji
- Content type: Research article
- Open Access
- Published: 04 October 2004
- Article: 37
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Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways
Authors (first, second and last of 4)
- Jibin Sun
- Rolf Daniel
- An-Ping Zeng
- Content type: Research article
- Open Access
- Published: 29 September 2004
- Article: 36
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Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
Authors
- Saša Stefanović
- Danny W Rice
- Jeffrey D Palmer
- Content type: Research article
- Open Access
- Published: 28 September 2004
- Article: 35
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Evolution of sexual asymmetry
Authors
- Tamás L Czárán
- Rolf F Hoekstra
- Content type: Research article
- Open Access
- Published: 21 September 2004
- Article: 34
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Reconstruction of ancestral protein sequences and its applications
Authors
- Wei Cai
- Jimin Pei
- Nick V Grishin
- Content type: Methodology article
- Open Access
- Published: 17 September 2004
- Article: 33
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Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models
Authors (first, second and last of 4)
- Georgy P Karev
- Yuri I Wolf
- Eugene V Koonin
- Content type: Research article
- Open Access
- Published: 09 September 2004
- Article: 32
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Evidence for positive selection on Mycobacterium tuberculosis within patients
Authors
- Mark M Tanaka
- Content type: Research article
- Open Access
- Published: 09 September 2004
- Article: 31
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Experimental evaluation of the relationship between lethal or non-lethal virulence and transmission success in malaria parasite infections
Authors (first, second and last of 6)
- REL Paul
- T Lafond
- JC Koella
- Content type: Research article
- Open Access
- Published: 08 September 2004
- Article: 30
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Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group
Authors (first, second and last of 6)
- Marinalva Martins-Pinheiro
- Rodrigo S Galhardo
- Carlos FM Menck
- Content type: Research article
- Open Access
- Published: 27 August 2004
- Article: 29
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A supertree approach to shorebird phylogeny
Authors
- Gavin H Thomas
- Matthew A Wills
- Tamás Székely
- Content type: Research article
- Open Access
- Published: 24 August 2004
- Article: 28
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Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes
Authors
- Mary E Cosner
- Linda A Raubeson
- Robert K Jansen
- Content type: Research article
- Open Access
- Published: 23 August 2004
- Article: 27
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Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III
Authors
- Sachiko Matsutani
- Content type: Research article
- Open Access
- Published: 09 August 2004
- Article: 26
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Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha)
Authors
- MyLo L Thao
- Linda Baumann
- Paul Baumann
- Content type: Research article
- Open Access
- Published: 03 August 2004
- Article: 25
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Function and evolution of the serotonin-synthetic bas-1 gene and other aromatic amino acid decarboxylase genes in Caenorhabditis
Authors
- Emily E Hare
- Curtis M Loer
- Content type: Research article
- Open Access
- Published: 02 August 2004
- Article: 24
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Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors
Authors (first, second and last of 4)
- Martin Irestedt
- Jon Fjeldså
- Per GP Ericson
- Content type: Research article
- Open Access
- Published: 30 July 2004
- Article: 23
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Duplicated genes evolve slower than singletons despite the initial rate increase
Authors
- I King Jordan
- Yuri I Wolf
- Eugene V Koonin
- Content type: Research article
- Open Access
- Published: 06 July 2004
- Article: 22
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Moderate mutation rate in the SARS coronavirus genome and its implications
Authors (first, second and last of 8)
- Zhongming Zhao
- Haipeng Li
- Yun-Xin Fu
- Content type: Research article
- Open Access
- Published: 28 June 2004
- Article: 21
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Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
Authors (first, second and last of 4)
- Tobias Müller
- Sven Rahmann
- Matthias Wolf
- Content type: Methodology article
- Open Access
- Published: 28 June 2004
- Article: 20
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Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
Authors (first, second and last of 4)
- Xiu-Feng Wan
- Dong Xu
- Jizhong Zhou
- Content type: Research article
- Open Access
- Published: 28 June 2004
- Article: 19
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RETRACTED ARTICLE: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
Authors
- Gangolf Jobb
- Arndt von Haeseler
- Korbinian Strimmer
- Content type: Software
- Open Access
- Published: 28 June 2004
- Article: 18
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Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics
Authors
- Sérgio L Pereira
- Allan J Baker
- Content type: Research article
- Open Access
- Published: 25 June 2004
- Article: 17
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Structure-function evolution of the Transforming acidic coiled coil genes revealed by analysis of phylogenetically diverse organisms
Authors (first, second and last of 4)
- Ivan H Still
- Ananthalakshmy K Vettaikkorumakankauv
- Ping Liang
- Content type: Research article
- Open Access
- Published: 18 June 2004
- Article: 16
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Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions
Authors
- Maile C Neel
- Michael P Cummings
- Content type: Research article
- Open Access
- Published: 08 June 2004
- Article: 15
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Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response
Authors
- Jesse D Bloom
- Christoph Adami
- Content type: Debate
- Open Access
- Published: 01 June 2004
- Article: 14
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Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
Authors
- Hunter B Fraser
- Aaron E Hirsh
- Content type: Debate
- Open Access
- Published: 27 May 2004
- Article: 13
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Adaptation of a South American malaria vector to laboratory colonization suggests faster-male evolution for mating ability
Authors
- José BP Lima
- Denise Valle
- Alexandre A Peixoto
- Content type: Research article
- Open Access
- Published: 06 May 2004
- Article: 12
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Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans
Authors
- Frédéric Delsuc
- Sergio F VizcaÃno
- Emmanuel JP Douzery
- Content type: Research article
- Open Access
- Published: 28 April 2004
- Article: 11
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A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry
Authors (first, second and last of 4)
- Victoria Nembaware
- Cathal Seoighe
- Chris Gehring
- Content type: Research article
- Open Access
- Published: 24 March 2004
- Article: 10
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Upstream plasticity and downstream robustness in evolution of molecular networks
Authors (first, second and last of 4)
- Sergei Maslov
- Kim Sneppen
- Koon-Kiu Yan
- Content type: Research article
- Open Access
- Published: 08 March 2004
- Article: 9
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The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters
Authors (first, second and last of 4)
- Elisabeth Arévalo
- Yong Zhu
- Joan E Strassmann
- Content type: Research article
- Open Access
- Published: 02 March 2004
- Article: 8
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The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer
Authors
- Mark van der Giezen
- Siân Cox
- Jorge Tovar
- Content type: Research article
- Open Access
- Published: 20 February 2004
- Article: 7
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Evolutionary and functional relationships within the DJ1 superfamily
Authors
- Sourav Bandyopadhyay
- Mark R Cookson
- Content type: Research article
- Open Access
- Published: 19 February 2004
- Article: 6
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Acetylcholinesterase alterations reveal the fitness cost of mutations conferring insecticide resistance
Authors (first, second and last of 7)
- Ming An Shi
- Andrée Lougarre
- Didier Fournier
- Content type: Research article
- Open Access
- Published: 06 February 2004
- Article: 5
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Mutations of acetylcholinesterase which confer insecticide resistance in Drosophila melanogaster populations
Authors (first, second and last of 5)
- Philippe Menozzi
- Ming An Shi
- Didier Fournier
- Content type: Research article
- Open Access
- Published: 05 February 2004
- Article: 4
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A scale invariant clustering of genes on human chromosome 7
Authors
- Wayne S Kendal
- Content type: Research article
- Open Access
- Published: 30 January 2004
- Article: 3