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: 1.404 (2015)

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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Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs
Feng-Chi Chen, Chia-Lin Pan and Hsuan-Yu Lin
Evolutionary Bioinformatics 2014:10 219-228
Original Research | Published on 10 Dec 2014

Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Muhammad Aslam, Ali Raza Awan, Naeem Aslam, Tanveer Hussain, Nasir Naveed, Salman Qadri, Usman Waheed and Muhammad Shoaib
Evolutionary Bioinformatics 2014:10 205-217
Original Research | Published on 07 Dec 2014

SWAMP: Sliding Window Alignment Masker for PAML
Peter W. Harrison, Gregory E. Jordan and Stephen H. Montgomery
Evolutionary Bioinformatics 2014:10 197-204
Technical Advance | Published on 01 Dec 2014

Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh
Samina Momtaz, Arafat Rahman, Munawar Sultana and M. Anwar Hossain
Evolutionary Bioinformatics 2014:10 187-196
Original Research | Published on 03 Nov 2014

Cloning and Expression Profiling of the Polycomb Gene, Retinoblastoma-related Protein from Tomato Solanum lycopersicum L.
Zainab M. Almutairi and Monther T. Sadder
Evolutionary Bioinformatics 2014:10 177-185
Original Research | Published on 23 Oct 2014

Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family
Nu Thi Ngoc Tang and Ly Le
Evolutionary Bioinformatics 2014:10 165-176
Original Research | Published on 21 Oct 2014

A New Method for Motif Mining in Biological Networks
Yuan Xu, Qiang Zhang and Changjun Zhou
Evolutionary Bioinformatics 2014:10 155-163
Methodology | Published on 01 Oct 2014

The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite
Diogo A Tschoeke, Gisele L Nunes, Rodrigo Jardim, Joana Lima, Aline SR Dumaresq, Monete R Gomes, Leandro de Mattos Pereira, Daniel R Loureiro, Patricia H Stoco, Herbert Leonel de Matos Guedes, Antonio Basilio de Miranda, Jeronimo Ruiz, André Pitaluga, Floriano P Silva Jr, Christian M Probst, Nicholas J Dickens, Jeremy C Mottram, Edmundo C Grisard and Alberto MR Dávila
Evolutionary Bioinformatics 2014:10 131-153
Original Research | Published on 23 Sep 2014

iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees
James A. Fordyce, Premal Shah and Benjamin M. Fitzpatrick
Evolutionary Bioinformatics 2014:10 127-130
Rapid Communication | Published on 03 Aug 2014

An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea
James T. Tambong, Renlin Xu, Cynthia-Anne Kaneza and Jean-Claude Nshogozabahizi
Evolutionary Bioinformatics 2014:10 115-125
Original Research | Published on 27 Jul 2014

Regulation of Human PAX6 Expression by miR-7
Maria Needhamsen, Robert B. White, Keith M. Giles, Sarah A. Dunlop and Meghan G. Thomas
Evolutionary Bioinformatics 2014:10 107-113
Original Research | Published on 14 Jul 2014

Influence of Modularity and Regularity on Disparity of Atelostomata Sea Urchins
Juan López-Sauceda, Juan Malda-Barrera, Alfredo Laguarda-Figueras, Francisco Solís-Marín and José L. Aragón
Evolutionary Bioinformatics 2014:10 97-105
Original Research | Published on 29 Jun 2014

Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
Yuhua Yao, Shoujiang Yan, Huimin Xu, Jianning Han, Xuying Nan, Ping-an He and Qi Dai
Evolutionary Bioinformatics 2014:10 87-96
Original Research | Published on 12 Jun 2014

Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates
Beatriz Mello and Carlos G. Schrago
Evolutionary Bioinformatics 2014:10 79-85
Original Research | Published on 07 May 2014

A Multistep Screening Method to Identify Genes Using Evolutionary Transcriptome of Plants
Chang-Kug Kim, Hye-Min Lim, Jong-Kuk Na, Ji-Weon Choi, Seong-Han Sohn, Soo-Chul Park, Young-Hwan Kim, Yong-Kab Kim and Dool-Yi Kim
Evolutionary Bioinformatics 2014:10 69-78
Original Research | Published on 21 Apr 2014

TreSpEx—Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information
Torsten H. Struck
Evolutionary Bioinformatics 2014:10 51-67
Original Research | Published on 31 Mar 2014

Phylogenetic Relationships of Some Filamentous Cyanoprokaryotic Species
Plamen Stoyanov, Dzhemal Moten, Rumen Mladenov, Balik Dzhambazov and Ivanka Teneva
Evolutionary Bioinformatics 2014:10 39-49
Original Research | Published on 23 Feb 2014

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection
Bor-Sen Chen and Shih-Ju Ho
Evolutionary Bioinformatics 2014:10 17-38
Original Research | Published on 16 Feb 2014

Netmes: Assessing Gene Network Inference Algorithms by Network-Based Measures
Gökmen Altay, Zeyneb Kurt, Matthias Dehmer and Frank Emmert-Streib
Evolutionary Bioinformatics 2014:10 1-9
Original Research | Published on 06 Feb 2014

RapidMic: Rapid Computation of the Maximal Information Coefficient
Dongming Tang, Mingwen Wang, Weifan Zheng and Hongjun Wang
Evolutionary Bioinformatics 2014:10 11-16
Short Report | Published on 06 Feb 2014

Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
Arindam RoyChoudhury
Evolutionary Bioinformatics 2013:9 499-509
Original Research | Published on 10 Dec 2013

A Comprehensive Phylogenetic Analysis of Deadenylases
Athanasia Pavlopoulou, Dimitrios Vlachakis, Nikolaos A.A. Balatsos and Sophia Kossida
Evolutionary Bioinformatics 2013:9 491-497
Original Research | Published on 02 Dec 2013

EASER: Ensembl Easy Sequence Retriever
Emanuel Maldonado, Imran Khan, Siby Philip, Vítor Vasconcelos and Agostinho Antunes
Evolutionary Bioinformatics 2013:9 487-490
Technical Advance | Published on 24 Nov 2013

Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinofiagellate Alexandrium Tamarense
Dahai Gao, Limei Qiu, Zhanhui Hou, Qingchun Zhang, Jianmin Wu, Qiang Gao and Linsheng Song
Evolutionary Bioinformatics 2013:9 479-485
Original Research | Published on 20 Nov 2013

Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq
Tae Young Yang and Seongmun Jeong
Evolutionary Bioinformatics 2013:9 467-478
Methodology | Published on 13 Nov 2013

The Origin of Parasitism Gene in Nematodes: Evolutionary Analysis Through the Construction of Domain Trees
Yizi Yang and Damin Luo
Evolutionary Bioinformatics 2013:9 453-466
Original Research | Published on 06 Nov 2013

Identification of New Aquaporin Genes and Single Nucleotide Polymorphism in Bread Wheat
B. Pandey, P. Sharma, D.M. Pandey, I. Sharma and R. Chatrath
Evolutionary Bioinformatics 2013:9 437-452
Original Research | Published on 03 Nov 2013

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics
Kevin M. Kocot, Mathew R. Citarella, Leonid L. Moroz and Kenneth M. Halanych
Evolutionary Bioinformatics 2013:9 429-435
Methodology | Published on 29 Oct 2013

Analysis of New Functional Profiles of Protein Isoforms Yielded by Ds Exonization in Rice
Ting-Ying Chien, Li-yu Daisy Liu, and Yuh-Chyang Charng
Evolutionary Bioinformatics 2013:9 417-427
Original Research | Published on 09 Oct 2013 | Video abstract

Prediction of Protein Essentiality by the Support Vector Machine with Statistical Tests
Chiou-Yi Hor, Chang-Biau Yang, Zih-Jie Yang and Chiou-Ting Tseng
Evolutionary Bioinformatics 2013:9 387-416
Original Research | Published on 03 Oct 2013

Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in Soybean
Achal Neupane, Madhav P. Nepal, Sarbottam Piya, Senthil Subramanian, Jai S. Rohila, R. Neil Reese and Benjamin V. Benson
Evolutionary Bioinformatics 2013:9 363-386
Original Research | Published on 22 Sep 2013

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
Daniel Garrigan
Evolutionary Bioinformatics 2013:9 343-353
Technical Advance | Published on 01 Sep 2013

SBEToolbox: A Matlab Toolbox for Biological Network Analysis
Kranti Konganti, Gang Wang, Ence Yang and James J. Cai
Evolutionary Bioinformatics 2013:9 355-362
Software or database review | Published on 01 Sep 2013

Analysis of Protein Thermostability Enhancing Factors in Industrially Important Thermus Bacteria Species
Benjamin Kumwenda, Derek Litthauer, Özlem Tastan Bishop, and Oleg Reva
Evolutionary Bioinformatics 2013:9 327-342
Original Research | Published on 18 Aug 2013

Conventional Simulation of Biological Sequences Leads to a Biased Assessment of Multi-Loci Phylogenetic Analysis
Barbara O. Aguiar and Carlos G. Schrago
Evolutionary Bioinformatics 2013:9 317-325
Original Research | Published on 13 Aug 2013

Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation
Timothy D. O'Connor and Nicholas I. Mundy
Evolutionary Bioinformatics 2013:9 301-316
Original Research | Published on 28 Jul 2013

Identification of Differentially Evolved Genes: An Alternative Approach to Detection of Accelerated Molecular Evolution from Genome-Wide Comparative Data
Kyu-Won Kim, David W. Burt, Heebal Kim and Seoae Cho
Evolutionary Bioinformatics 2013:9 285-299
Methodology | Published on 28 Jul 2013

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

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