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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Conserved Nonsense-Prone CpG Sites in Apoptosis-Regulatory Genes: Conditional Stop Signs on the Road to Cell Death
Yongzhong Zhao and Richard J. Epstein
Evolutionary Bioinformatics 2013:9 275-283
Original Research | Published on 14 Jul 2013

SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences
Kirill S. Antonets and Anton A. Nizhnikov
Evolutionary Bioinformatics 2013:9 263-273
Rapid Communication | Published on 11 Jul 2013

Effective Encoding for DNA Sequence Visualization Based on Nucleotide’s Ring Structure
A.T.M. Golam Bari, Mst. Rokeya Reaz, A.K.M. Tauhidul Islam, Ho-Jin Choi and Byeong-Soo Jeong
Evolutionary Bioinformatics 2013:9 251-261
Original Research | Published on 07 Jul 2013

Molecular Evolution and Functional Divergence of Soluble Starch Synthase Genes in Cassava (Manihot Esculenta Crantz)
Zefeng Yang, Yifan Wang, Shuhui Xu, Chenwu Xu and Changjie Yan
Evolutionary Bioinformatics 2013:9 239-249
Original Research | Published on 03 Jul 2013

rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection
Jan Irvahn, Sujay Chattopadhyay, Evgeni V. Sokurenko and Vladimir N. Minin
Evolutionary Bioinformatics 2013:9 235-238
Rapid Communication | Published on 12 Jun 2013

Comment on “The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway”
David Alvarez-Ponce, Montserrat Aguadé and Julio Rozas
Evolutionary Bioinformatics 2013:9 229-234
Letter to Editor | Published on 10 Jun 2013

Analysis of Synonymous Codon Usage Patterns in Seven Different Citrus Species
Chen Xu, Jing Dong, Chunfa Tong, Xindong Gong, Qiang Wen and Qiang Zhuge
Evolutionary Bioinformatics 2013:9 215-228
Original Research | Published on 23 May 2013

Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology
Dimitrios Vlachakis, Georgia Tsiliki, Athanasia Pavlopoulou, Maria G. Roubelakis, Spyridon Champeris Tsaniras and Sophia Kossida
Evolutionary Bioinformatics 2013:9 203-213
Review | Published on 16 May 2013

Top-Down Clustering for Protein Subfamily Identification
Eduardo P. Costa, Celine Vens and Hendrik Blockeel
Evolutionary Bioinformatics 2013:9 185-202
Original Research | Published on 06 May 2013

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

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