Evolutionary Bioinformatics

The 2006 NESCent Phyloinformatics Hackathon: A Field Report
Hilmar Lapp, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, Alisha Holloway, Toshiaki Katayama, Paul O. Lewis, Aaron J. Mackey, Brian I. Osborne, William H. Piel, Sergei L. Kosakovsky Pond, Art F.Y. Poon, Wei-Gang Qiu et al
Evolutionary Bioinformatics 2007:3 287-296
Published on 14 Dec 2007

Phylogenetic Study of the Evolution of PEP-Carboxykinase
Sanjukta Aich and Louis T.J. Delbaere
Evolutionary Bioinformatics 2007:3 333-340
Published on 11 Dec 2007

Efficient Tree Searches with Available Algorithms
Gonzalo Giribet
Evolutionary Bioinformatics 2007:3 341-356
Published on 12 Nov 2007

Structural Evolution of the ABC Transporter Subfamily B
Flanagan, J.U. and Huber, T.
Evolutionary Bioinformatics 2007:3 309-316
Published on 08 Nov 2007

An Insulin-Like Modular Basis for the Evolution of Glucose Transporters (GLUT) with Implications for Diabetes
Robert Root-Bernstein
Evolutionary Bioinformatics 2007:3 317-331
Published on 15 Oct 2007

Minimizing Contradictions on Circular Order of Phylogenic Trees
Marc Thuillard
Evolutionary Bioinformatics 2007:3 267-277
Published on 11 Oct 2007

Selection Effects on the Positioning of Genes and Gene Structures from the Interplay of Replication and Transcription in Bacterial Genomes
Kazuharu Arakawa and Masaru Tomita
Evolutionary Bioinformatics 2007:3 279-286
Published on 09 Oct 2007

Phylogenomic Analysis Reveals Extensive Phylogenetic Mosaicism in the Human GPCR Superfamily
Robin G. Allaby and Mathew Woodwark
Evolutionary Bioinformatics 2007:3 357-370
Published on 26 Sep 2007

Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens
Wendy Mok, Kelly Seto and Jon Stone
Evolutionary Bioinformatics 2007:3 263-266
Published on 26 Sep 2007

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach
Bor-Sen Chen and Wei-Sheng Wu
Evolutionary Bioinformatics 2007:3 245-262
Published on 26 Sep 2007

Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity
Mike Steel, Aki Mimoto and Arne Ø. Mooers
Evolutionary Bioinformatics 2007:3 237-244
Published on 25 Sep 2007

Genome Signatures, Self-Organizing Maps and Higher Order Phylogenies: A Parametric Analysis
Derek Gatherer
Evolutionary Bioinformatics 2007:3 211-236
Published on 17 Sep 2007

The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection
Kazuharu Arakawa and Masaru Tomita
Evolutionary Bioinformatics 2007:3 159-168
Published on 06 Sep 2007

Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians
Sumiko Anno, Takashi Abe, Koichi Sairyo, Susumu Kudo, Takushi Yamamoto, Koretsugu Ogata and Vijay K. Goel
Evolutionary Bioinformatics 2007:3 169-178
Published on 06 Sep 2007

Identifcation of Novel Retroid Agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis
Holly A. Basta, Alex J. Buzak and Marcella A. McClure
Evolutionary Bioinformatics 2007:3 179-195
Published on 06 Sep 2007

Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution
Agostinho Antunes and Maria João Ramos
Evolutionary Bioinformatics 2007:3 207-209
Published on 06 Sep 2007

Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions
Ekaterina Kotelnikova, Andrey Kalinin, Anton Yuryev, and Sergei Maslov
Evolutionary Bioinformatics 2007:3 197-206
Published on 08 Aug 2007

Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes
Nicola Vitulo, Alessandro Vezzi, Giulio Galla, Sandra Citterio, Giada Marino, Benedetto Ruperti, Monica Zermiani, Emidio Albertini, Giorgio Valle and Gianni Barcaccia
Evolutionary Bioinformatics 2007:3 121-158
Published on 08 Aug 2007

Environmental Quality, Developmental Plasticity and the Thrifty Phenotype: A Review of Evolutionary Models
Jonathan CK Wells
Evolutionary Bioinformatics 2007:3 109-120
Published on 19 Jun 2007

Choosing and Using Introns in Molecular Phylogenetics
Simon Creer
Evolutionary Bioinformatics 2007:3 99-108
Published on 14 Jun 2007

Fast Genes and Slow Clades: Comparative Rates of Molecular Evolution in Mammals
Olaf R. P. Bininda-Emonds
Evolutionary Bioinformatics 2007:3 59-85
Published on 31 May 2007

A Reduction Algorithm for Computing The Hybridization Number of Two Trees
Magnus Bordewich, Simone Linz, Katherine St. John and Charles Semple
Evolutionary Bioinformatics 2007:3 86-98
Published on 30 May 2007

An Improved Implementation of Codon Adaptation Index
Xuhua Xia
Evolutionary Bioinformatics 2007:3 53-58
Published on 17 May 2007

Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup
Ludovic Orlando, Catherine Hänni and Christophe J. Douady
Evolutionary Bioinformatics 2007:3 45-51
Published on 29 Mar 2007

Mlcoalsim: Multilocus Coalescent Simulations
Sebastian E. Ramos-Onsins and Thomas Mitchell-Olds
Evolutionary Bioinformatics 2007:3 41-44
Published on 02 Mar 2007

Why Bacteriophage Encode Exotoxins and other Virulence Factors
Stephen T. Abedon and Jeffrey T. LeJeune
Evolutionary Bioinformatics Online 2005:1 97-110
Published on 28 Feb 2007

On the Adaptive Design Rules of Biochemical Networks in Evolution
Bor-Sen Chen, Wan-Shian Wu, Wei-Sheng Wu and Wen-Hsiung Li
Evolutionary Bioinformatics 2007:3 27-39
Published on 28 Feb 2007

Improved Heuristics for Minimum-Flip Supertree Construction
Duhong Chen, Oliver Eulenstein, David Fernández-Baca and J.Gordon Burleigh
Evolutionary Bioinformatics 2006:2 347-356
Published on 28 Feb 2007

The identification of functional motifs in temporal gene expression analysis
Jiuzhou Song, Jaime Bjarnason and Michael G. Surette
Evolutionary Bioinformatics Online 2005:1 84-96
Published on 27 Feb 2007

Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes
Nadja Neumann, Daniel C. Jeffares and Anthony M. Poole
Evolutionary Bioinformatics 2006:2 23-34
Published on 27 Feb 2007

The Rv3799–Rv3807 Gene Cluster in Mycobacterium Tuberculosis Genome Corresponds to the ‘Ancient Conserved Region’ in CMN Mycolyltransferases
Hemalatha G. Ramulu, Adindla Swathi and Lalitha Guruprasad
Evolutionary Bioinformatics Online 2006:2 377-385
Original Research | Published on 27 Feb 2007

MySSP: Non-stationary evolutionary sequence simulation, including indels
Michael S. Rosenberg
Evolutionary Bioinformatics Online 2005:1 81-83
Published on 26 Feb 2007

Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances
Xuhua Xia
Evolutionary Bioinformatics 2006:2 333-345
Published on 26 Feb 2007

Estimation of Phylogeny Using a General Markov Model
Vivek Jayaswal, Lars S. Jermiin and John Robinson
Evolutionary Bioinformatics Online 2005:1 62-80
Published on 25 Feb 2007

Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction
Michael Höhl, Isidore Rigoutsos and Mark A. Ragan
Evolutionary Bioinformatics 2006:2 359-375
Published on 25 Feb 2007

Evolution of proteins and proteomes: a phylogenetics approach
Toni Gabaldón
Evolutionary Bioinformatics Online 2005:1 51-61
Published on 24 Feb 2007

Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations
Tai-Sung Lee, Steven J. Potts, Matthew J. McGinniss and Charles M. Strom
Evolutionary Bioinformatics 2006:2 321-332
Published on 24 Feb 2007

Arlequin (version 3.0): An integrated software package for population genetics data analysis
Laurent Excoffier, Guillaume Laval and Stefan Schneider
Evolutionary Bioinformatics Online 2005:1 47-50
Published on 23 Feb 2007

ALFRED: An Allele Frequency Database for Microevolutionary Studies
Haseena Rajeevan, Kei-Hoi Cheung, Rohit Gadagkar, Shannon Stein, Usha Soundararajan, Judith R Kidd, Andrew J Pakstis, Perry L Miller, and Kenneth K Kidd
Evolutionary Bioinformatics Online 2005:1 1-10
Published on 22 Feb 2007

A Fast and Specific Alignment Method for Minisatellite Maps
Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel and Eric Rivals
Evolutionary Bioinformatics 2006:2 303-320
Published on 22 Feb 2007

Phylogenetic biodiversity assessment based on systematic nomenclature
Ross H Crozier, Lisa J Dunnett and Paul-Michael Agapow
Evolutionary Bioinformatics Online 2005:1 11-36
Published on 21 Feb 2007

Genome Halving with an Outgroup
Chunfang Zheng, Qian Zhu and David Sankoff
Evolutionary Bioinformatics 2006:2 295-302
Published on 21 Feb 2007

Fast Structural Search in Phylogenetic Databases
Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel
Evolutionary Bioinformatics Online 2005:1 37-46
Published on 20 Feb 2007

Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny
Tanja Gernhard, Daniel Ford, Rutger Vos and Mike Steel
Evolutionary Bioinformatics 2006:2 285-293
Published on 20 Feb 2007

The Role of the Phylogenetic Diversity Measure, PD, in Bio-informatics: Getting the Definition Right
Daniel P. Faith
Evolutionary Bioinformatics 2006:2 277-283
Published on 19 Feb 2007

Co-evolutionary Rates of Functionally Related Yeast Genes
Leonardo Mariño-Ramírez, Olivier Bodenreider, Natalie Kantz and I. King Jordan
Evolutionary Bioinformatics 2006:2 271-276
Published on 18 Feb 2007

A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences
Guido W. Grimm, Susanne S. Renner, Alexandros Stamatakis and Vera Hemleben
Evolutionary Bioinformatics 2006:2 7-22
Published on 17 Feb 2007

Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges
Daniel P. Faith, Andrew M. Baker
Evolutionary Bioinformatics 2006:2 121-128
Published on 17 Feb 2007

Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype
Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Wei Zhang
Evolutionary Bioinformatics 2006:2 261-270
Published on 16 Feb 2007

Gaussian Quadrature Formulae for Arbitrary Positive Measures
Andrew D. Fernandes and William R. Atchley
Evolutionary Bioinformatics 2006:2 251-259
Published on 15 Feb 2007