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JOURNAL

Evolutionary Bioinformatics


An international, peer reviewed, open access journal focusing on evolutionary bioinformatics.  The journal aims to support understanding of organismal form and function through use of molecular, genetic, genomic and proteomic data by giving due consideration to its evolutionary context.

Impact Factor: 1.500 (2016)

Editor in Chief: Dr. Dennis Wall

ISSN: 1176-9343

Processing Speed: High quality, constructive peer review and rapid editorial decision within an average of four weeks.



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A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests
Chiou-Yi Hor, Chang-Biau Yang, Chia-Hung Chang, Chiou-Ting Tseng and Hung-Hsin Chen
Evolutionary Bioinformatics 2013:9 163-184
Original Research | Published on 14 Apr 2013



Circulation of Human Respiratory Syncytial Virus Strains Among Hospitalized Children with Acute Lower Respiratory Infection in Malaysia
Mohammad Reza Etemadi, Zamberi Sekawi, Norlijah Othman, Munn-Sann Lye and Faezeh Yazdani Moghaddam
Evolutionary Bioinformatics 2013:9 151-161
Original Research | Published on 10 Apr 2013



Design of Synthetic Genetic Oscillators Using Evolutionary Optimization
Yen-Chang Chang, Chun-Liang Lin and Tanagorn Jennawasin
Evolutionary Bioinformatics 2013:9 137-150
Methodology | Published on 10 Mar 2013



EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes
Tanja Magoc, Derrick Wood and Steven L. Salzberg,
Evolutionary Bioinformatics 2013:9 127-136
Technical Advance | Published on 10 Mar 2013



CMCpy: Genetic Code-Message Coevolution Models in Python
Peter J. Becich, Brian P. Stark, Harish S. Bhat and David H. Ardell
Evolutionary Bioinformatics 2013:9 111-125
Technical Advance | Published on 27 Feb 2013



A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-off on Phenotype Robustness in Biological Networks Part I: Gene Regulatory Networks in Systems and Evolutionary Biology
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 43-68
Original Research | Published on 26 Feb 2013



A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Tradeoff on Phenotype Robustness in Biological Networks Part II: Ecological Networks
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 69-85
Original Research | Published on 26 Feb 2013



A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology
Bor-Sen Chen and Ying-Po Lin
Evolutionary Bioinformatics 2013:9 87-109
Original Research | Published on 26 Feb 2013



A Proximity-Based Method to Identify Genomic Regions Correlated with a Continuously Varying Environmental Variable
Cornelia Di Gaetano, Giuseppe Matullo, Alberto Piazza, Moreno Ursino and Mauro Gasparini
Evolutionary Bioinformatics 2013:9 29-42
Methodology | Published on 29 Jan 2013



TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats
Tomasz Gambin, Michał Startek, Krzysztof Walczak, Jarosław Paszek, Dariusz Grzebelus and Anna Gambin
Evolutionary Bioinformatics 2013:9 17-27
Database review | Published on 22 Jan 2013



The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway
Minghui Wang, Qishan Wang, Zhen Wang, Qingping Wang, Xiangzhe Zhang and Yuchun Pan
Evolutionary Bioinformatics 2013:9 1-16
Original Research | Published on 10 Jan 2013



Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus
Ence Yang, Amanda M. Hulse and James J. Cai
Evolutionary Bioinformatics 2012:8 623-644
Original Research | Published on 19 Nov 2012



A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence
Eli Reuveni and Alessandro Giuliani
Evolutionary Bioinformatics 2012:8 611-622
Methodology | Published on 14 Nov 2012



Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes
Payal Singh and Supratim Sengupta
Evolutionary Bioinformatics 2012:8 589-609
Original Research | Published on 06 Nov 2012



Genome-Wide Survey of Ds Exonization to Enrich Transcriptomes and Proteomes in Plants
Li-yu Daisy Liu and Yuh-Chyang Charng
Evolutionary Bioinformatics 2012:8 575-587
Original Research | Published on 08 Oct 2012 | Video abstract



Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana
Wanjun Gu, Chuanying Zhai, Xiaofei Wang, Xueying Xie, Gurunadh Parinandi, and Tong Zhou,
Evolutionary Bioinformatics 2012:8 565-574
Original Research | Published on 25 Sep 2012



Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses
Namrata Misra, Prasanna Kumar Panda, Bikram Kumar Parida and Barada Kanta Mishra
Evolutionary Bioinformatics 2012:8 545-564
Original Research | Published on 20 Sep 2012



Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection
Ulf Sorhannus
Evolutionary Bioinformatics 2012:8 535-544
Original Research | Published on 17 Sep 2012



Cloud Computing for Comparative Genomics with Windows Azure Platform
Insik Kim, Jae-Yoon Jung, Todd F. DeLuca, Tristan H. Nelson and Dennis P. Wall
Evolutionary Bioinformatics 2012:8 527-534
Technical Advance | Published on 30 Aug 2012



Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling
Thomas Meinel and Antje Krause
Evolutionary Bioinformatics 2012:8 489-525
Original Research | Published on 07 Aug 2012



Inference of Self-Regulated Transcriptional Networks by Comparative Genomics
Joseph P. Cornish, Fialelei Matthews, Julien R. Thomas and Ivan Erill
Evolutionary Bioinformatics 2012:8 449-461
Original Research | Published on 06 Aug 2012



TreeCmp: Comparison of Trees in Polynomial Time
Damian Bogdanowicz, Krzysztof Giaro and Borys Wróbel,
Evolutionary Bioinformatics 2012:8 475-487
Software review | Published on 06 Aug 2012



Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups
Julia Lambret-Frotté, Fernando Araújo Perini and Claudia Augusta de Moraes Russo
Evolutionary Bioinformatics 2012:8 463-473
Original Research | Published on 06 Aug 2012



The Chordate Proteome History Database
Anthony Levasseur, Julien Paganini, Jacques Dainat, Julie D. Thompson, Olivier Poch, Pierre Pontarotti and Philippe Gouret
Evolutionary Bioinformatics 2012:8 437-447
Original Research | Published on 01 Aug 2012



PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny
Runhua Lei, Thaine W. Rowley, Lifeng Zhu, Carolyn A. Bailey, Shannon E. Engberg, Mindy L. Wood, Mary C. Christman, George H. Perry, Edward E. Louis Jr and Guoqing Lu
Evolutionary Bioinformatics 2012:8 423-435
Software review | Published on 23 Jul 2012



Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX
Julien Paganini and Philippe Gouret
Evolutionary Bioinformatics 2012:8 417-421
Rapid Communication | Published on 05 Jul 2012



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



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





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