Evolutionary Bioinformatics

Determinants of Exon-Level Evolutionary Rates in Arabidopsis Species
Gideon C.-T. Wu, and Feng-Chi Chen
Evolutionary Bioinformatics 2012:8 389-415
Original Research | Published on 04 Jul 2012

Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species
Shu-Hsi Lin, Miwa Yoshimoto, Ping-Chiang Lyu, Chuan-Yi Tang and Masanori Arita
Evolutionary Bioinformatics 2012:8 373-387
Original Research | Published on 04 Jul 2012

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity
Sohta A. Ishikawa, Yuji Inagaki, and Tetsuo Hashimoto
Evolutionary Bioinformatics 2012:8 357-371
Original Research | Published on 25 Jun 2012

AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots
Muhammad Rashid, He Guangyuan, Yang Guangxiao, Javeed Hussain and Yan Xu
Evolutionary Bioinformatics 2012:8 321-355
Original Research | Published on 21 Jun 2012

Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors
Balasubramanian Nagarathnam, Singaravelu Kalaimathy, Veluchamy Balakrishnan and Ramanathan Sowdhamini
Evolutionary Bioinformatics 2012:8 229-259
Original Research | Published on 19 Jun 2012

Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion
Dapeng Wang, Yao Su, Xumin Wang, Hongxing Lei and Jun Yu
Evolutionary Bioinformatics 2012:8 301-319
Original Research | Published on 19 Jun 2012

MiIP: The Monomer Identification and Isolation Program
Christopher Bun, William Ziccardi, Jeffrey Doering and Catherine Putonti
Evolutionary Bioinformatics 2012:8 293-300
Software or database review | Published on 14 Jun 2012

PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences
Melissa M. Norström, Mattia C.F. Prosperi, Rebecca R. Gray, Annika C. Karlsson and Marco Salemi
Evolutionary Bioinformatics 2012:8 261-269
Short Report | Published on 11 Jun 2012

Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns
Jun Cao, and Feng Shi
Evolutionary Bioinformatics 2012:8 271-292
Original Research | Published on 11 Jun 2012

Mitochondrial Genetic Differentiation of Spirlin (Actinopterigii: Cyprinidae) in the South Caspian Sea basin of Iran
Mahvash Seifali, Aziz Arshad, Faezeh Yazdani Moghaddam, Hamid Reza Esmaeili, Bahram H. Kiabi, Siti Khalijah Daud and Mansour Aliabadian
Evolutionary Bioinformatics 2012:8 219-227
Original Research | Published on 21 May 2012

Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets
Carolina M. Voloch and Carlos G. Schrago
Evolutionary Bioinformatics 2012:8 207-218
Original Research | Published on 14 May 2012

Efficient Feature Selection and Multiclass Classification with Integrated Instance and Model Based Learning
Zhenqiu Liu, Halima Bensmail and Ming Tan
Evolutionary Bioinformatics 2012:8 197-205
Methodology | Published on 30 Apr 2012

Promoter Sequences Prediction Using Relational Association Rule Mining
Gabriela Czibula, Maria-Iuliana Bocicor and Istvan Gergely Czibula
Evolutionary Bioinformatics 2012:8 181-196
Original Research | Published on 23 Apr 2012

A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment
Valerio Freschi and Alessandro Bogliolo
Evolutionary Bioinformatics 2012:8 171-180
Original Research | Published on 02 Apr 2012

Selection of Marker Genes Using Whole-Genome DNA Polymorphism Analysis
Harry M. Bohle and Toni Gabaldón
Evolutionary Bioinformatics 2012:8 161-169
Methodology | Published on 19 Mar 2012

easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
David Rosenkranz
Evolutionary Bioinformatics 2012:8 151-159
Software or database review | Published on 14 Mar 2012 | Video abstract

Inferring the Phylogeny of Bovidae Using Mitochondrial DNA Sequences: Resolving Power of Individual Genes Relative to Complete Genomes
Ibrahim A. Arif, Mohammad A. Bakir and Haseeb A. Khan
Evolutionary Bioinformatics 2012:8 139-150
Original Research | Published on 20 Feb 2012

Construction of a Pig Physical Interactome Using Sequence Homology and a Comprehensive Reference Human Interactome
Felix Dreher, Atanas Kamburov and Ralf Herwig
Evolutionary Bioinformatics 2012:8 119-126
Short Report | Published on 24 Jan 2012

Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents
Leticia Loss-Oliveira, Barbara O. Aguiar and Carlos G. Schrago*
Evolutionary Bioinformatics 2012:8 127-137
Original Research | Published on 24 Jan 2012 | Highly accessed (previous month)

Interkingdom Gene Transfer May Contribute to the Evolution of Phytopathogenicity in Botrytis Cinerea
Bo Zhu, Qing Zhou, Guanlin Xie, Guoqing Zhang, Xiaowei Zhang, Yanli Wang, Gunchang Sun, Bin Li and Gulei Jin
Evolutionary Bioinformatics 2012:8 105-117
Original Research | Published on 11 Jan 2012

Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group
Nicolás Lavagnino, François Serra, Leonardo Arbiza, Hernán Dopazo and Esteban Hasson,
Evolutionary Bioinformatics 2012:8 89-104
Original Research | Published on 09 Jan 2012

BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization
Jing Hu and Xianghe Yan
Evolutionary Bioinformatics 2012:8 79-87
Methodology | Published on 05 Jan 2012

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data
Benjamin Linard, Ngoc Hoan Nguyen, Francisco Prosdocimi, Olivier Poch and Julie D. Thompson
Evolutionary Bioinformatics 2012:8 61-77
Original Research | Published on 21 Dec 2011

SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis
Dimosthenis Tsagrasoulis, Vasilis Danos,, Maria Kissa, Philip Trimpalis, V. Lila Koumandou, Amalia D. Karagouni, Athanasios Tsakalidis and Sophia Kossida
Evolutionary Bioinformatics 2012:8 47-60
Original Research | Published on 18 Dec 2011

LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes
Dapeng Wang, Yubin Zhang, Zhonghua Fan, Guiming Liu and Jun Yu
Evolutionary Bioinformatics 2012:8 39-46
Original Research | Published on 13 Dec 2011

Species Delimitation and Global Biosecurity
Laura M. Boykin, Karen F. Armstrong, Laura Kubatko and Paul De Barro
Evolutionary Bioinformatics 2012:8 1-37
Original Research | Published on 08 Dec 2011 | Video abstract

Evolution of Antifreeze Protein Genes in the Diatom Genus Fragilariopsis: Evidence for Horizontal Gene Transfer, Gene Duplication and Episodic Diversifying Selection
Ulf Sorhannus
Evolutionary Bioinformatics 2011:7 279-289
Original Research | Published on 15 Nov 2011

Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of Oncidium Gower Ramsey
Chen Xu, Xiaoning Cai, Quanzhan Chen, Hongxia Zhou, Yao Cai and Ailing Ben
Evolutionary Bioinformatics 2011:7 271-278
Original Research | Published on 14 Nov 2011

ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications
Sylvain Lespinats and Bernard Fertil
Evolutionary Bioinformatics 2011:7 257-270
Original Research | Published on 13 Nov 2011

In Silico Prediction of Evolutionarily Conserved GC-Rich Elements Associated with Antigenic Proteins of Plasmodium falciparum
Porkodi Panneerselvam, Praveen Bawankar, Surashree Kulkarni, and Swati Patankar
Evolutionary Bioinformatics 2011:7 235-255
Original Research | Published on 10 Nov 2011

On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2011:7 201-233
Original Research | Published on 01 Nov 2011

Characterization and Inference of Gene Gain/Loss Along Burkholderia Evolutionary History
Bo Zhu, Shengli Zhou, Miaomiao Lou, Jun Zhu, Bin Li, Guanlin Xie, GuLei Jin, and René De Mot
Evolutionary Bioinformatics 2011:7 191-200
Original Research | Published on 18 Oct 2011

Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction
Hafida Bouziane, Belhadri Messabih and Abdallah Chouarfia
Evolutionary Bioinformatics 2011:7 171-189
Original Research | Published on 10 Oct 2011

A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory
Xingqin Qi, Qin Wu, Yusen Zhang, Eddie Fuller and Cun-Quan Zhang
Evolutionary Bioinformatics 2011:7 149-158
Original Research | Published on 04 Oct 2011

A New Support Measure to Quantify the Impact of Local Optima in Phylogenetic Analyses
Grant Brammer, Seung-Jin Sul and Tiffani L. Williams
Evolutionary Bioinformatics 2011:7 159-170
Original Research | Published on 29 Sep 2011

Single-Domain Parvulins Constitute a Specific Marker for Recently Proposed Deep-Branching Archaeal Subgroups
Christoph Lederer, Dominik Heider, Johannes van den Boom, Daniel Hoffmann, Jonathan W. Mueller and Peter Bayer
Evolutionary Bioinformatics 2011:7 135-148
Original Research | Published on 19 Sep 2011

IONS: Identification of Orthologs by Neighborhood and Similarity—an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts
Marie-Line Seret and Philippe V. Baret
Evolutionary Bioinformatics 2011:7 123-133
Methodology | Published on 30 Aug 2011

Phylogenomics-Based Reconstruction of Protozoan Species Tree
Kary A.C.S. Ocaña, and Alberto M.R. Dávila
Evolutionary Bioinformatics 2011:7 107-121
Original Research | Published on 31 Jul 2011

Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method
Abdelmonaem Messaoudi, Hatem Belguith and Jeannette Ben Hamida
Evolutionary Bioinformatics 2011:7 99-105
Original Research | Published on 28 Jun 2011

Functional Evolution of BRCT Domains from Binding DNA to Protein
Zi-Zhang Sheng, Yu-Qi Zhao, and Jing-Fei Huang
Evolutionary Bioinformatics 2011:7 87-97
Original Research | Published on 12 Jun 2011

How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling
Sylvain Lespinats, Delphine Grando, Eric Maréchal, Mohamed-Ali Hakimi, Olivier Tenaillon and Olivier Bastien
Evolutionary Bioinformatics 2011:7 61-85
Original Research | Published on 07 Jun 2011

Structurama: Bayesian Inference of Population Structure
John P. Huelsenbeck, Peter Andolfatto and Edna T. Huelsenbeck
Evolutionary Bioinformatics 2011:7 55-59
Short Report | Published on 02 Jun 2011

Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family
V. Mallika, K.C. Sivakumar and E.V. Soniya
Evolutionary Bioinformatics 2011:7 41-53
Original Research | Published on 29 May 2011

A Monte Carlo Method for Assessing the Quality of Duplication-Aware Alignment Algorithms
Valerio Freschi and Alessandro Bogliolo
Evolutionary Bioinformatics 2011:7 31-40
Original Research | Published on 10 May 2011

Phylogenetic Analysis of Kindlins Suggests Subfunctionalization of an Ancestral Unduplicated Kindlin into Three Paralogs in Vertebrates
Ammad Aslam Khan, Axel Janke, Takashi Shimokawa and Hongquan Zhang
Evolutionary Bioinformatics 2011:7 7-19
Original Research | Published on 22 Mar 2011

FORS-D Analysis in P. falciparum can Differentiate Classes of Genes Under Selection
Atish Kathpal, Balakota Reddy Patakottu and Swati Patankar
Evolutionary Bioinformatics 2011:7 21-29
Original Research | Published on 20 Mar 2011

SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data
Young Jun Jeon, Sang Hyun Park, Sung Min Ahn and Hee Joung Hwang
Evolutionary Bioinformatics 2011:7 1-6
Software or database review | Published on 10 Mar 2011

Cost-Effective Cloud Computing: A Case Study Using the Comparative Genomics Tool, Roundup
Parul Kudtarkar, Todd F. DeLuca, Vincent A. Fusaro, Peter J. Tonellato and Dennis P. Wall
Evolutionary Bioinformatics 2010:6 197-203
Short Report | Published on 22 Dec 2010

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences
Kessy Abarenkov, Leho Tedersoo, R. Henrik Nilsson, Kai Vellak, Irja Saar, Vilmar Veldre, Erast Parmasto, Marko Prous, Anne Aan, Margus Ots, Olavi Kurina, Ivika Ostonen, Janno Jõgeva, Siim Halapuu, Kadri Põldmaa, Märt Toots, Jaak Truu, Karl-Henrik Larsson and Urmas Kõljalg
Evolutionary Bioinformatics 2010:6 189-196
Software or database review | Published on 16 Dec 2010

Where Does the Alignment Score Distribution Shape Come from?
Philippe Ortet and Olivier Bastien
Evolutionary Bioinformatics 2010:6 159-187
Original Research | Published on 12 Dec 2010