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The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA
BMC Bioinformatics 2003 Sep 11, 4:41
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Correspondence    
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Research article    
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56.


Methodology article    
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Software    
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58.


Research    
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Rogozin IB, Thomson K, Csürös M, Carmel L, Koonin EV
Biology Direct 2008, 3:7 (17 March 2008)
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Software    
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
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Research    
Functional protein divergence in the evolution of Homo sapiens
Lopez-Bigas N, De S, Teichmann SA
Genome Biology 2008, 9:R33 (15 February 2008)
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61.


Proceedings    
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
Kim WY, Kang S, Kim BC, Oh J, Cho S, Bhak J, Choi JS
BMC Bioinformatics 2008, 9(Suppl 1):S20 (13 February 2008)
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62.


Research article    
Characterization of a newly developed chicken 44K Agilent microarray
Li X, Chiang HI, Zhu J, Dowd SE, Zhou H
BMC Genomics 2008, 9:60 (31 January 2008)
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63.


Research    
The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization
Kagan J, Sharon I, Beja O, Kuhn JC
Genome Biology 2008, 9:R20 (27 January 2008)
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64.


Research article    
Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes
Moreira D, Brochier-Armanet C
BMC Evolutionary Biology 2008, 8:12 (18 January 2008)
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65.


Research article    
The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae
Münsterkötter M, Steinberg G
BMC Genomics 2007, 8:473 (20 December 2007)
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66.


Method    
Direct selection and phage display of a Gram-positive secretome
Jankovic D, Collett MA, Lubbers MW, Rakonjac J
Genome Biology 2007, 8:R266 (13 December 2007)
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67.


Research article    
Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
Nanjo T, Sakurai T, Totoki Y, Toyoda A, Nishiguchi M, Kado T, Igasaki T, Futamura N, Seki M, Sakaki Y, Shinozaki K, Shinohara K
BMC Genomics 2007, 8:448 (3 December 2007)
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68.


Research    
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV
Biology Direct 2007, 2:33 (27 November 2007)
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69.


Database    
CoryneCenter An online resource for the integrated analysis of corynebacterial genome and transcriptome data
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A
BMC Systems Biology 2007, 1:55 (22 November 2007)
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70.


Research    
The distributions, mechanisms, and structures of metabolite-binding riboswitches
Barrick JE, Breaker RR
Genome Biology 2007, 8:R239 (12 November 2007)
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71.


Research article    
Poly-G/poly-C tracts in the genomes of Caenorhabditis
Zhao Y, O'Neil NJ, Rose AM
BMC Genomics 2007, 8:403 (7 November 2007)
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72.


Database    
CoryneRegNet 4.0 A reference database for corynebacterial gene regulatory networks
Baumbach J
BMC Bioinformatics 2007, 8:429 (6 November 2007)
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73.


Proceedings    
Towards validating the hypothesis of phylogenetic profiling
Loganantharaj R, Atwi M
BMC Bioinformatics 2007, 8(Suppl 7):S25 (1 November 2007)
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74.


Research article    
Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family
Livesay DR, Kidd PD, Eskandari S, Roshan U
BMC Bioinformatics 2007, 8:397 (17 October 2007)
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75.


Research article    
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing
Wittkop T, Baumbach J, Lobo FP, Rahmann S
BMC Bioinformatics 2007, 8:396 (17 October 2007)
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76.


Research article    
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
Irimia M, Rukov JL, Penny D, Roy SW
BMC Evolutionary Biology 2007, 7:188 (4 October 2007)
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Research article    
Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia
Larsen J, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen JE
BMC Evolutionary Biology 2007, 7:184 (3 October 2007)
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Research article    
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
Boekhorst J, Snel B
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Research article    
Uncovering the mutation-fixation correlation in short lineages
Vallender EJ, Lahn BT
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Research    
A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
Lillo F, Krakauer DC
Biology Direct 2007, 2:22 (18 September 2007)
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Research article    
The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe
Miranda-Saavedra D, Stark MJR, Packer JC, Vivares CP, Doerig C, Barton GJ
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Research article    
Global analysis of host response to induction of a latent bacteriophage
Osterhout RE, Figueroa IA, Keasling JD, Arkin AP
BMC Microbiology 2007, 7:82 (31 August 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
83.


Research article    
Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom
Kuramae EE, Robert V, Echavarri-Erasun C, Boekhout T
BMC Evolutionary Biology 2007, 7:134 (9 August 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
84.


Method    
Novel metrics for evaluating the functional coherence of protein groups via protein semantic network
Zheng B, Lu X
Genome Biology 2007, 8:R153 (31 July 2007)
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85.


Software    
PHIDIAS: a pathogen-host interaction data integration and analysis system
Xiang Z, Tian Y, He Y
Genome Biology 2007, 8:R150 (30 July 2007)
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86.


Research article    
Identification of gene targets against dormant phase Mycobacterium tuberculosis infections
Murphy DJ, Brown JR
BMC Infectious Diseases 2007, 7:84 (26 July 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
87.


Database    
TrED: the Trichophyton rubrum Expression Database
Yang J, Chen L, Wang L, Zhang W, Liu T, Jin Q
BMC Genomics 2007, 8:250 (25 July 2007)
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88.


Research    
Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes
Ogura Y, Ooka T, Asadulghani , Terajima J, Nougayrède JP, Kurokawa K, Tashiro K, Tobe T, Nakayama K, Kuhara S, Oswald E, Watanabe H, Hayashi T
Genome Biology 2007, 8:R138 (10 July 2007)
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89.


Research    
Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system
Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, Roy PJ, Miller DM
Genome Biology 2007, 8:R135 (5 July 2007)
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90.


Software    
Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization
Kim N, Lee C
BMC Bioinformatics 2007, 8:213 (20 June 2007)
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91.


Research article    
Transcriptome analysis of the venom gland of the Mexican scorpion Hadrurus gertschi (Arachnida: Scorpiones)
Schwartz EF, Diego-Garcia E, Rodríguez de la Vega RC, Possani LD
BMC Genomics 2007, 8:119 (16 May 2007)
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92.


Research article    
Structural and functional insights into Mimivirus ORFans
Saini HK, Fischer D
BMC Genomics 2007, 8:115 (9 May 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
93.


Research article    
An insight into the sialome of the oriental rat flea, Xenopsylla cheopis (Rots)
Andersen JF, Hinnebusch BJ, Lucas DA, Conrads TP, Veenstra TD, Pham VM, Ribeiro JMC
BMC Genomics 2007, 8:102 (16 April 2007)
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94.


Research article    
Modelling the evolution of the archaeal tryptophan synthase
Merkl R
BMC Evolutionary Biology 2007, 7:59 (10 April 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
95.


Methodology article    
Orthology prediction at scalable resolution by phylogenetic tree analysis
van der Heijden RTJM, Snel B, van Noort V, Huynen MA
BMC Bioinformatics 2007, 8:83 (8 March 2007)
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96.


Research article    
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM
BMC Bioinformatics 2007, 8:73 (5 March 2007)
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97.


Research    
Genome display tool: visualizing features in complex data sets
Viswanath L, Lu Y, Fox GE
Source Code for Biology and Medicine 2007, 2:1 (14 February 2007)
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98.


Research    
Phylogenetic signal and functional categories in Proteobacteria genomes
Comas I, Moya A, González-Candelas F
BMC Evolutionary Biology 2007, 7(Suppl 1):S7 (8 February 2007)
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99.


Research    
Intron Evolution and Information processing in the DNA polymerase gene in spirotrichous ciliates: A hypothesis for interconversion between DNA and RNA deletion
Chang WJ, Addis VM, Li AJ, Axelsson E, Ardell DH, Landweber LF
Biology Direct 2007, 2:6 (1 February 2007)
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100.


Method    
An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta
Wang J, Jemielity S, Uva P, Wurm Y, Gräff J, Keller L
Genome Biology 2007, 8:R9 (15 January 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
101.


Method    
Prediction of effective genome size in metagenomic samples
Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P
Genome Biology 2007, 8:R10 (15 January 2007)
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102.


Software    
DiscoverySpace: an interactive data analysis application
Robertson N, Oveisi-Fordorei M, Zuyderduyn SD, Varhol RJ, Fjell C, Marra M, Jones S, Siddiqui A
Genome Biology 2007, 8:R6 (8 January 2007)
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103.


Research article    
An annotated catalogue of salivary gland transcripts in the adult female mosquito, Ædes ægypti*
Ribeiro JMC, Arcà B, Lombardo F, Calvo E, Van My Phan , Chandra PK, Wikel SK
BMC Genomics 2007, 8:6 (4 January 2007)
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104.




Research    
Evolutionary conservation of domain-domain interactions
Itzhaki Z, Akiva E, Altuvia Y, Margalit H
Genome Biology 2006, 7:R125 (21 December 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
105.


Comment    
Did the last common ancestor have a biological membrane?
Jékely G
Biology Direct 2006, 1:35 (27 November 2006)
 [Abstract] [Full Text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
106.


Review    
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
Birkholtz LM, Bastien O, Wells G, Grando D, Joubert F, Kasam V, Zimmermann M, Ortet P, Jacq N, Saïdani N, Roy S, Hofmann-Apitius M, Breton V, Louw AI, Maréchal E
Malaria Journal 2006, 5:110 (17 November 2006)
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107.


Research article    
In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans
Yang HL, Zhu YZ, Qin JH, He P, Jiang XC, Zhao GP, Guo XK
BMC Genomics 2006, 7:293 (16 November 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
108.


Methodology article    
Integration of curated databases to identify genotype-phenotype associations
Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M
BMC Genomics 2006, 7:257 (12 October 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
109.


Research article    
Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags
Wang L, Ma L, Leng W, Liu T, Yu L, Yang J, Yang L, Zhang W, Zhang Q, Dong J, Xue Y, Zhu Y, Xu X, Wan Z, Ding G, Yu F, Tu K, Li Y, Li R, Shen Y, Jin Q
BMC Genomics 2006, 7:255 (11 October 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
110.


Software    
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
Treangen TJ, Messeguer X
BMC Bioinformatics 2006, 7:433 (5 October 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
111.


Research article    
Comparative assessment of performance and genome dependence among phylogenetic profiling methods
Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C
BMC Bioinformatics 2006, 7:420 (27 September 2006)
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112.


Hypothesis    
Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons
Baranov PV, Vestergaard B, Hamelryck T, Gesteland RF, Nyborg J, Atkins JF
Biology Direct 2006, 1:28 (13 September 2006)
 [Abstract] [Full Text] [PDF] [PubMed] [Related articles] [1 comment]
113.


Research article    
Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
Brockmann-Gretza O, Kalinowski J
BMC Genomics 2006, 7:230 (8 September 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
114.


Research article    
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
Haft DH, Paulsen IT, Ward N, Selengut JD
BMC Biology 2006, 4:29 (24 August 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
115.


Research article    
On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
Yin Y, Fischer D
BMC Evolutionary Biology 2006, 6:63 (16 August 2006)
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116.


Research article    
Cross genome comparisons of serine proteases in Arabidopsis and rice
Tripathi LP, Sowdhamini R
BMC Genomics 2006, 7:200 (9 August 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
117.


Research    
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
Ekman D, Light S, Björklund K, Elofsson A
Genome Biology 2006, 7:R45 (16 June 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
118.


Research article    
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M
Journal of Biology 2006, 5:11 (8 June 2006)
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119.


Methodology article    
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
Reiss DJ, Baliga NS, Bonneau R
BMC Bioinformatics 2006, 7:280 (2 June 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
120.




Research    
Similarity searches in genome-wide numerical data sets
Glazko G, Coleman M, Mushegian A
Biology Direct 2006, 1:13 (30 May 2006)
 [Abstract] [Full Text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
121.


Methodology article    
Improving the specificity of high-throughput ortholog prediction
Fulton DL, Li YY, Laird MR, Horsman BGS, Roche FM, Brinkman FSL
BMC Bioinformatics 2006, 7:270 (28 May 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
122.


Research article    
Phylogenomic analysis of the GIY-YIG nuclease superfamily
Dunin-Horkawicz S, Feder M, Bujnicki JM
BMC Genomics 2006, 7:98 (28 April 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
123.


Research    
Benchmarking ortholog identification methods using functional genomics data
Hulsen T, Huynen MA, de Vlieg J, Groenen PMA
Genome Biology 2006, 7:R31 (13 April 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
124.


Database    
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
Dehal PS, Boore JL
BMC Bioinformatics 2006, 7:201 (11 April 2006)
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125.


Research article    
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds
Sadreyev RI, Grishin NV
BMC Structural Biology 2006, 6:6 (20 March 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
126.


Database    
Domain-based small molecule binding site annotation
Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CWV
BMC Bioinformatics 2006, 7:152 (17 March 2006)
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127.




Research    
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV
Biology Direct 2006, 1:7 (16 March 2006)
 [Abstract] [Full Text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
128.


Methodology article    
Gene annotation and network inference by phylogenetic profiling
Wu J, Hu Z, DeLisi C
BMC Bioinformatics 2006, 7:80 (17 February 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
129.


Method    
Predicting genes for orphan metabolic activities using phylogenetic profiles
Chen L, Vitkup D
Genome Biology 2006, 7:R17 (15 February 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
130.


Research article    
EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): Implications for the evolution of green plants (Viridiplantae)
Simon A, Glöckner G, Felder M, Melkonian M, Becker B
BMC Plant Biology 2006, 6:2 (13 February 2006)
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131.


Research article    
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis
Tkaczuk KL, Obarska A, Bujnicki JM
BMC Evolutionary Biology 2006, 6:6 (24 January 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
132.


Methodology article    
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs
Powell BC, Hutchison CA
BMC Bioinformatics 2006, 7:31 (19 January 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
133.


Research article    
Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
Danchin EGJ, Gouret P, Pontarotti P
BMC Evolutionary Biology 2006, 6:5 (18 January 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
134.


Research article    
Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus
Gaudermann P, Vogl I, Zientz E, Silva FJ, Moya A, Gross R, Dandekar T
BMC Microbiology 2006, 6:1 (9 January 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
135.


Software    
Ulysses - an application for the projection of molecular interactions across species
Kemmer D, Huang Y, Shah SP, Lim J, Brumm J, Yuen MMS, Ling J, Xu T, Wasserman WW, Ouellette BFF
Genome Biology 2005, 6:R106 (2 December 2005)
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136.


Research article    
Natural history of S-adenosylmethionine-binding proteins
Kozbial PZ, Mushegian AR
BMC Structural Biology 2005, 5:19 (14 October 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
137.


Software    
Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis
Enault F, Suhre K, Claverie JM
BMC Bioinformatics 2005, 6:247 (12 October 2005)
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138.


Research article    
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization
Reynaud EG, Andrade MA, Bonneau F, Ly TBN, Knop M, Scheffzek K, Pepperkok R
BMC Biology 2005, 3:21 (7 October 2005)
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139.


Research article    
Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution
Nandi S, Mehra N, Lynn AM, Bhattacharya A
BMC Genomics 2005, 6:116 (9 September 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
140.


Research article    
Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa
Bräutigam M, Lindlöf A, Zakhrabekova S, Gharti-Chhetri G, Olsson B, Olsson O
BMC Plant Biology 2005, 5:18 (1 September 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
141.


Methodology article    
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
Sperisen P, Pagni M
BMC Bioinformatics 2005, 6:216 (31 August 2005)
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142.


Research    
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria
Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR
Genome Biology 2005, 6:R70 (1 August 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
143.


Proceedings    
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
Fang H, Tong W, Perkins R, Shi L, Hong H, Cao X, Xie Q, Yim SH, Ward JM, Pitot HC, Dragan YP
BMC Bioinformatics 2005, 6(Suppl 2):S6 (15 July 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
144.


Research article    
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
Kosinski J, Feder M, Bujnicki JM
BMC Bioinformatics 2005, 6:172 (12 July 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
145.


Software    
AutoFACT: An Automatic Functional Annotation and Classification Tool
Koski LB, Gray MW, Lang BF, Burger G
BMC Bioinformatics 2005, 6:151 (16 June 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
146.


Research article    
A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts
Galperin MY
BMC Microbiology 2005, 5:35 (14 June 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
147.


Software    
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets
La D, Livesay DR
BMC Bioinformatics 2005, 6:116 (13 May 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
148.


Software    
ProGenExpress: Visualization of quantitative data on prokaryotic genomes
Watson M
BMC Bioinformatics 2005, 6:98 (13 April 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [2 comments]
149.


Research article    
Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold
Roßbach M, Daumke O, Klinger C, Wittinghofer A, Kaufmann M
BMC Structural Biology 2005, 5:7 (20 March 2005)
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150.


Research article    
A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement
Ravagnani A, Finan CL, Young M
BMC Genomics 2005, 6:39 (17 March 2005)
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151.




Research article    
A comprehensive update of the sequence and structure classification of kinases
Cheek S, Ginalski K, Zhang H, Grishin NV
BMC Structural Biology 2005, 5:6 (16 March 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
152.


Research    
The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum
Martin RE, Henry RI, Abbey JL, Clements JD, Kirk K
Genome Biology 2005, 6:R26 (2 March 2005)
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153.




Research article    
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site
Feder M, Bujnicki JM
BMC Genomics 2005, 6:21 (18 February 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
154.


Software    
GenomeViz: visualizing microbial genomes
Ghai R, Hain T, Chakraborty T
BMC Bioinformatics 2004, 5:198 (15 December 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
155.


Software    
PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms
Meereis F, Kaufmann M
BMC Bioinformatics 2004, 5:150 (15 October 2004)
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156.


Research article    
Duplicated genes evolve slower than singletons despite the initial rate increase
Jordan IK, Wolf YI, Koonin EV
BMC Evolutionary Biology 2004, 4:22 (6 July 2004)
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157.


Research    
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
Glazko GV, Mushegian AR
Genome Biology 2004, 5:R32 (27 April 2004)
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158.




Research    
The regulatory content of intergenic DNA shapes genome architecture
Nelson CE, Hersh BM, Carroll SB
Genome Biology 2004, 5:R25 (15 March 2004)
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159.




Research    
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA
Genome Biology 2004, 5:R7 (15 January 2004)
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