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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Correction to: “Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection”
Mathias Currat, Pascale Gerbault, Da Di, José M. Nunes and Alicia Sanchez-Mazas
Evolutionary Bioinformatics 2015:Suppl. 2 69-69
Correction | Published on 29 May 2016

Coevolution of RAC Small GTPases and their Regulators GEF Proteins
Alejandro Jiménez-Sánchez
Evolutionary Bioinformatics 2016:12 121-131
Original Research | Published on 17 May 2016

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee and Giri Narasimhan
Evolutionary Bioinformatics 2016:Suppl. 1 5-16
Review | Published on 12 May 2016

Phylogenetic and Structural Analysis of Polyketide Synthases in Aspergilli
Preetida J. Bhetariya, Madhvi Prajapati, Asani Bhaduri, Rahul Shubhra Mandal, Anupam Varma, Taruna Madan, Yogendra Singh and P. Usha Sarma
Evolutionary Bioinformatics 2016:12 109-119
Original Research | Published on 10 May 2016

Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.)
Ethan J. Andersen, Shaukat Ali, R. Neil Reese, Yang Yen, Surendra Neupane and Madhav P. Nepal
Evolutionary Bioinformatics 2016:12 99-108
Original Research | Published on 04 May 2016

Estimating Divergence Times and Substitution Rates in Rhizobia
Rim Chriki-Adeeb and Ali Chriki
Evolutionary Bioinformatics 2016:12 87-97
Original Research | Published on 03 May 2016

Human Dispersal Out of Africa: A Lasting Debate
Saioa López, Lucy van Dorp and Garrett Hellenthal
Evolutionary Bioinformatics 2015:Suppl. 2 57-68
Review | Published on 21 Apr 2016

Introductory Editorial: Evolutionary Genomics
Yuval Itan, Gur Pines and Pascale Gerbault
Evolutionary Bioinformatics 2015:Suppl. 2 53-55
Editorial | Published on 20 Apr 2016

Surprisingly Low Limits of Selection in Plant Domestication
Robin G. Allaby, James L. Kitchen and Dorian Q. Fuller
Evolutionary Bioinformatics 2015:Suppl. 2 41-51
Original Research | Published on 05 Apr 2016

Genome Sequencing and Evolutionary Analysis of Marine Gut Fungus Aspergillus sp. Z5 from Ligia oceanica
Xue Li, Jin-Zhong Xu, Wen-Jie Wang, Yi-Wang Chen, Dao-Qiong Zheng, Ya-Nan Di, Ping Li, Pin-Mei Wang and Yu-Dong Li
Evolutionary Bioinformatics 2016:Suppl. 1 1-4
Short Report | Published on 03 Apr 2016

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection
Mathias Currat, Pascale Gerbault, Da Di, José M. Nunes and Alicia Sanchez-Mazas
Evolutionary Bioinformatics 2015:Suppl. 2 27-39
Technical Advance | Published on 25 Feb 2016

Using UNIFORMAT and GENE[RATE] to Analyze Data with Ambiguities in Population Genetics
José Manuel Nunes
Evolutionary Bioinformatics 2015:Suppl. 2 19-26
Methodology | Published on 21 Feb 2016

Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups
Jean-Pierre Munyampundu, You-Ping Xu and Xin-Zhong Cai
Evolutionary Bioinformatics 2016:12 59-71
Original Research | Published on 10 Feb 2016

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing
Ramin Karimi and Andras Hajdu
Evolutionary Bioinformatics 2016:12 73-85
Technical Advance | Published on 10 Feb 2016

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data
Young-Joo Seol, Tae-Ho Lee, Dong-Suk Park and Chang-Kug Kim
Evolutionary Bioinformatics 2016:12 51-58
Original Research | Published on 01 Feb 2016

Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82
Yun Luo, Chen Huang, Julian Ye, Weijia Fang, Wanjun Gu, Zhiping Chen, Hui Li, XianJun Wang and Dazhi Jin
Evolutionary Bioinformatics 2016:12 41-49
Original Research | Published on 24 Jan 2016

Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales
Lu Zhang, Wei Wu, Hai-Fei Yan and Xue-Jun Ge
Evolutionary Bioinformatics 2015:Suppl. 1 81-91
Original Research | Published on 18 Jan 2016

Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection
Yoan Diekmann and José B. Pereira-Leal
Evolutionary Bioinformatics 2015:Suppl. 2 11-17
Original Research | Published on 18 Jan 2016

Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza
Yu-Chia Hsu, Chang-Sheng Wang, Yann-Rong Lin and Yong-Pei Wu
Evolutionary Bioinformatics 2016:12 29-40
Original Research | Published on 18 Jan 2016

A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1
Steven Reisman, Thomas Hatzopoulos, Konstantin Läufer, George K. Thiruvathukal, and Catherine Putonti
Evolutionary Bioinformatics 2016:12 23-27
Original Research | Published on 18 Jan 2016

Introductory Editorial: RNA: An Expanding View of Function and Evolution
Xinwei Han, Yuan Chen, Liuyang Wang, Wenwen Fang, Ning Zhang, Qiyun Zhu
Evolutionary Bioinformatics 2015:Suppl. 1 77-79
Editorial | Published on 14 Jan 2016

Genome-Wide Analysis of NBS-LRR Genes in Sorghum Genome Revealed Several Events Contributing to NBS-LRR Gene Evolution in Grass Species
Xiping Yang and Jianping Wang
Evolutionary Bioinformatics 2016:12 9-21
Original Research | Published on 14 Jan 2016

pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana
Luca Ambrosino, Hamed Bostan, Pasquale di Salle, Mara Sangiovanni, Alessandra Vigilante, and Maria L. Chiusano
Evolutionary Bioinformatics 2016:12 1-7
Software or Database Review | Published on 11 Jan 2016

Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry
Kirsten E. Beattie, Luna De Ferrari and John B. O. Mitchell
Evolutionary Bioinformatics 2015:11 267-274
Original Research | Published on 29 Dec 2015

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions
Yan-Cong Zhang and Kui Lin
Evolutionary Bioinformatics 2015:Suppl. 2 1-9
Original Research | Published on 17 Dec 2015

Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos)
Ruiyi Lin, Xiaoyong Du, Sixue Peng, Liubin Yang, Yunlong Ma, Yanzhang Gong and Shijun Li
Evolutionary Bioinformatics 2015:Suppl. 1 67-76
Original Research | Published on 01 Dec 2015

SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage
William A. Freyman
Evolutionary Bioinformatics 2015:11 263-266
Technical Advance | Published on 30 Nov 2015

Segmenting the Human Genome into Isochores
Paolo Cozzi, Luciano Milanesi and Giorgio Bernardi
Evolutionary Bioinformatics 2015:11 253-261
Methodology | Published on 25 Nov 2015

Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins
Sayaka Miura, Stephanie Tate and Sudhir Kumar
Evolutionary Bioinformatics 2015:11 245-251
Original Research | Published on 02 Nov 2015

Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting
Gisele Cristine de Souza Carrocini, Larissa Paola Rodrigues Venancio and Claudia Regina Bonini-Domingos
Evolutionary Bioinformatics 2015:11 239-244
Original Research | Published on 27 Oct 2015

In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum
Itunuoluwa Isewon, Jelili Oyelade, Benedikt Brors and Ezekiel Adebiyi
Evolutionary Bioinformatics 2015:11 231-238
Original Research | Published on 22 Oct 2015

Soft Computing Methods for Disulfide Connectivity Prediction
Alfonso E. Márquez-Chamorro and Jesús S. Aguilar-Ruiz
Evolutionary Bioinformatics 2015:11 223-229
Review | Published on 20 Oct 2015

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers?
Marc Thuillard and Didier Fraix-Burnet
Evolutionary Bioinformatics 2015:11 213-221
Original Research | Published on 13 Oct 2015

Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life
Da-Cheng Hao and Pei-Gen Xiao
Evolutionary Bioinformatics 2015:11 197-212
Review | Published on 04 Oct 2015

Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
Dahai Gao, Dennis C. Ko, Xinmin Tian, Guang Yang and Liuyang Wang
Evolutionary Bioinformatics 2015:Suppl. 1 57-65
Review | Published on 13 Sep 2015

In Silico Characterization of Functional Divergence of Two Cathelicidin Variants in Indian Sheep
Kamaljeet K. Dhaliwal, Jaspreet S. Arora, Chandra S. Mukhopadhyay and Prem P. Dubey
Evolutionary Bioinformatics 2015:11 189-196
Published on 01 Sep 2015

How Many Genes are Needed to Resolve Phylogenetic Incongruence?
Bin Ai and Ming Kang
Evolutionary Bioinformatics 2015:11 185-188
Rapid Communication | Published on 10 Aug 2015

Genome-wide Identification of WRKY Genes in the Desert Poplar Populus euphratica and Adaptive Evolution of the Genes in Response to Salt Stress
Jianchao Ma, Jing Lu, Jianmei Xu, Bingbing Duan, Xiaodong He and Jianquan Liu
Evolutionary Bioinformatics 2015:Suppl. 1 47-55
Review | Published on 05 Aug 2015

A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups
Insung Ahn, Jin-Hwa Jang, Ha-Yeon Kim, Ji-Hae Lee, and Hyeon Seok Son
Evolutionary Bioinformatics 2015:11 179-183
Original Research | Published on 27 Jul 2015

Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme
Bor-Sen Chen, Kun-Wei Tsai and Cheng-Wei Li
Evolutionary Bioinformatics 2015:11 155-178
Original Research | Published on 19 Jul 2015

Effective Population Size and Signatures of Selection Using Bovine 50K SNP Chips in Korean Native Cattle (Hanwoo)
Yi Li and Jong-Joo Kim
Evolutionary Bioinformatics 2015:11 143-153
Original Research | Published on 08 Jul 2015

The Origin of Land Plants: A Phylogenomic Perspective
Bojian Zhong, Linhua Sun and David Penny
Evolutionary Bioinformatics 2015:11 137-141
Consise Review | Published on 08 Jul 2015

De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae)
Lei Wang, Zhengkun Wang, Jianbing Chen, Chunyan Liu, Wanlong Zhu, Liuyang Wang and Lihua Meng
Evolutionary Bioinformatics 2015:Suppl. 1 39-45
Original Research | Published on 08 Jul 2015

MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data
David Gutiérrez-Avilés and Cristina Rubio-Escudero
Evolutionary Bioinformatics 2015:11 121-135
Original Research | Published on 23 Jun 2015

RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.
Zhili Zhou, Huancheng Ma, Kevin Lin, Youjie Zhao, Yuan Chen, Zhi Xiong, Liuyang Wang and Bin Tian
Evolutionary Bioinformatics 2015:Suppl. 1 27-37
Original Research | Published on 23 Jun 2015

MITOSCISSOR: A Useful Tool for Auto-Assembly of Mitogenomic Datasets in the Evolutionary Analysis of Fishes
Zheng Sun, Yuanzhi Cheng and Junbin Zhang
Evolutionary Bioinformatics 2015:11 115-120
Technical Advance | Published on 14 Jun 2015

Molecular Evolutionary Analysis of β-Defensin Peptides in Vertebrates
Jianbo Tu, Diyan Li, Qingqing Li, Long Zhang, Qing Zhu, Uma Gaur, Xiaolan Fan, Huailiang Xu, Yongfang Yao, Xiaoling Zhao and Mingyao Yang
Evolutionary Bioinformatics 2015:11 105-114
Original Research | Published on 01 Jun 2015

TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing
Etienne Kornobis, Luis Cabellos, Fernando Aguilar, Cristina Frías-López, Julio Rozas, Jesús Marco and Rafael Zardoya
Evolutionary Bioinformatics 2015:11 97-104
Technical Advance | Published on 24 May 2015

Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution
Kuangyu Wang, Shuhui Yu, Xiang Ji, Clemens Lakner, Alexander Griffing and Jeffrey L. Thorne
Evolutionary Bioinformatics 2015:11 85-96
Original Research | Published on 29 Apr 2015

BIR Pipeline for Preparation of Phylogenomic Data
Surendra Kumar, Anders K. Krabberød, Ralf S. Neumann, Katerina Michalickova, Sen Zhao, Xiaoli Zhang and Kamran Shalchian-Tabrizi
Evolutionary Bioinformatics 2015:11 79-83
Methodology | Published on 27 Apr 2015

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