Volume 2

Evolutionary Bioinformatics

Volume 2

1

The Role of the Phylogenetic Diversity Measure, PD, in Bio-Informatics: Getting the Definition Right

Faith, Daniel P.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 646 KB

english, 2006

2

Spectral Analysis of Sequence Variability in Basic-Helix-loop-helix (bHLH) Protein Domains

Wang, Zhi, Atchley, William R.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 734 KB

english, 2006

3

MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution

Cai, James J., Smith, David K., Xia, Xuhua, Yuen, Kwok-yung

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 170 KB

english, 2006

4

Improved Heuristics for Minimum-Flip Supertree Construction

Chen, Duhong, Eulenstein, Oliver, Fernández-Baca, David, Burleigh, J. Gordon

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 600 KB

english, 2006

5

3'UTR-located ALU Elements: Donors of Potetial miRNA Target Sites and Mediators of Network miRNA-based Regulatory Interactions

Daskalova, Evelina, Baev, Vesselin, Rusinov, Ventsislav, Minkov, Ivan

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 441 KB

english, 2006

6

A New Effective Method for Estimating Missing Values in the Sequence Data Prior to Phylogenetic Analysis

Diallo, Abdoulaye Baniré, Lapointe, François-Joseph, Makarenkov, Vladimir

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 474 KB

english, 2006

7

Evolution, Bioinformatics and Evolutionary Bioinformatics Online

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 102 KB

english, 2006

8

Phylogenetic Diversity (PD) and Biodiversity Conservation: Some Bioinformatics Challenges

Faith, Daniel P., Baker, Andrew M.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 577 KB

english, 2006

9

Unravelling Selection Shifts among Foot-and-Mouth Disease virus (FMDV) Serotypes

Tully, Damien C., Fares, Mario A.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 2.93 MB

english, 2006

10

Gaussian Quadrature Formulae for Arbitrary Positive Measures

Fernandes, Andrew D., Atchley, William R.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.47 MB

english, 2006

11

Finding Common Protein Interaction Patterns Across Organisms

Gerke, Mirco, Bornberg-Bauer, Erich, Jiang, Xiaoyi, Fuellen, Georg

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 305 KB

english, 2006

12

Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny

Gernhard, Tanja, Ford, Daniel, Vos, Rutger, Steel, Mike

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 607 KB

english, 2006

13

Functionality and the Evolution of Marginal Stability in Proteins: Inferences from Lattice Simulations

Williams, Paul D., Pollock, David D., Goldstein, Richard A.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 357 KB

english, 2006

14

A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

Grimm, Guido W., Renner, Susanne S., Stamatakis, Alexandros, Hemleben, Vera

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 4.33 MB

english, 2006

15

The Rv3799-Rv3807 Gene Cluster in Mycobacterium Tuberculosis Genome Corresponds to the ‘Ancient Conserved Region’ in CMN Mycolyltransferases

Ramulu, Hemalatha G., Swathi, Adindla, Guruprasad, Lalitha

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 899 KB

english, 2006

16

Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction

Höhl, Michael, Rigoutsos, Isidore, Ragan, Mark A.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 5.31 MB

english, 2006

17

Co-Evolutionary Rates of Functionally Related Yeast Genes

Mariño-Ramírez, Leonardo, Bodenreider, Olivier, Kantz, Natalie, Jordan, I. King

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 430 KB

english, 2006

18

Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make

Levasseur, Claudine, Lapointe, François-Joseph

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 174 KB

english, 2006

19

Assessing the Applicability of the GTR Nucleotide Substitution Model through Simulations

Gatto, Laurent, Catanzaro, Daniele, Milinkovitch, Michel C.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 614 KB

english, 2006

20

Coevolution of Exploiter Specialization and Victim Mimicry can be Cyclic and Saltational

Norrström, Niclas, Getz, Wayne M., Holmgren, Noél

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 264 KB

english, 2006

21

Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes

Neumann, Nadja, Jeffares, Daniel C., Poole, Anthony M.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 3.06 MB

english, 2006

22

LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates from Molecular Phylogenies

Rabosky, Daniel L.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 263 KB

english, 2006

23

A Fast and Specific Alignment Method for Minisatellite Maps

Bérard, Sèverine, Nicolas, François, Buard, Jérôme, Gascuel, Olivier, Rivals, Eric

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 671 KB

english, 2006

24

Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden

Ewing, Greg, Rodrigo, Allen

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 821 KB

english, 2006

25

Sources of Variation in Ancestral Sequence Reconstruction for HIV-1 Envelope Genes

Ross, Howard A., Nickle, David C., Liu, Yi, Heath, Laura, Jensen, Mark A., Rodrigo, Allen G., Mullins, James I.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 863 KB

english, 2006

26

Genome Halving with an Outgroup

Zheng, Chunfang, Zhu, Qian, Sankoff, David

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.71 MB

english, 2006

27

Modelling Prokaryote Gene Content

Spencer, Matthew, Susko, Edward, Roger, Andrew J.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 607 KB

english, 2006

28

Using Minimum Bootstrap support for Splits to Construct Confidence Regions for Trees

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.14 MB

english, 2006

29

Positional Homology in Bacterial Genomes

Burgetz, Ingrid J., Shariff, Salimah, Pang, Andy, Tillier*, Elisabeth R. M.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 323 KB

english, 2006

30

Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype

Zhang, Xiang-Sun, Wang, Rui-Sheng, Wu, Ling-Yun, Zhang, Wei

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.22 MB

english, 2006

31

PIRSF Family Classification System for Protein Functional and Evolutionary Analysis

Nikolskaya, Anastasia N., Arighi, Cecilia N., Huang, Hongzhan, Barker, Winona C., Wu, Cathy H.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 972 KB

english, 2006

32

Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 3.19 MB

english, 2006

33

CoMET: A Mesquite Package for Comparing Models of Continuous Character Evolution on Phylogenies

Lee, Chunghau, Blay, Sigal, Mooers, Arne Ø., Singh, Ambuj, Oakley, Todd H.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 330 KB

english, 2006

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