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JOURNAL

Bioinformatics and Biology Insights


An international, peer reviewed, open access journal that focusses on computational methods used in the analysis and annotation of structures, in additional to other areas of computational biology.  The journal also seeks to place computational biology within the broader context of biology.

Editor in Chief: Professor Erich Bornberg-Bauer

ISSN: 1177-9322

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



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Practical Approaches for Mining Frequent Patterns in Molecular Datasets
Stefan Naulaerts, Sandy Moens, Kristof Engelen, Wim Vanden Berghe, Bart Goethals, Kris Laukens and Pieter Meysman
Bioinformatics and Biology Insights 2016:10 37-47
Review | Published on 02 May 2016



Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions
Usman Sumo Friend Tambunan, Feimmy Ruth Pratiwi Sipahutar, Arli Aditya Parikesit and Djati Kerami
Bioinformatics and Biology Insights 2016:10 27-35
Original Research | Published on 28 Apr 2016



Use of Metatranscriptomics in Microbiome Research
Stavros Bashiardes, Gili Zilberman-Schapira and Eran Elinav
Bioinformatics and Biology Insights 2016:10 19-25
Review | Published on 20 Apr 2016



Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus
Devendra K. Rai, Paul Lawrence, Steve J. Pauszek, Maria E. Piccone, Nick J. Knowles and Elizabeth Rieder
Bioinformatics and Biology Insights 2015:Suppl. 2 43-58
Original Research | Published on 04 Apr 2016



RNA Sequencing in Schizophrenia
Xin Li and Shaolei Teng
Bioinformatics and Biology Insights 2015:Suppl. 1 53-60
Review | Published on 31 Mar 2016



Modeling Intercellular Communication as a Survival Strategy of Cancer Cells: An In Silico Approach on a Flexible Bioinformatics Framework
Maura Cárdenas-García, Pedro P. González-Pérez, Sara Montagna, Oscar Sánchez Cortés and Elena Hernández Caballero
Bioinformatics and Biology Insights 2016:10 5-18
Original Research | Published on 13 Mar 2016



Transcriptome Analysis in Domesticated Species: Challenges and Strategies
Jessica P. Hekman, Jennifer L. Johnson and Anna V. Kukekova
Bioinformatics and Biology Insights 2015:Suppl. 4 21-31
Review | Published on 16 Feb 2016



Visualization of Genome Diversity in German Shepherd Dogs
Sally-Anne Mortlock, Rachel Booth, Hamutal Mazrier, Mehar S. Khatkar and Peter Williamson
Bioinformatics and Biology Insights 2015:Suppl. 2 37-42
Original Research | Published on 10 Feb 2016



Nematode Sodium Calcium Exchangers: A Surprising Lack of Transport
Vishal Sharma and Damien M. O'Halloran
Bioinformatics and Biology Insights 2016:10 1-4
Short Commentary | Published on 01 Feb 2016



Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome
Laura C. Miller, Darrell O. Bayles, Eraldo L. Zanella and Kelly M. Lager
Bioinformatics and Biology Insights 2015:Suppl. 2 25-36
Original Research | Published on 24 Jan 2016



Evolutionary Character of Alternative Splicing in Plants
Chengjun Zhang, Hong Yang and Huizhao Yang
Bioinformatics and Biology Insights 2015:Suppl. 1 47-52
Concise Review | Published on 20 Jan 2016



Homology-Based Prediction of Potential Protein–Protein Interactions between Human Erythrocytes and Plasmodium falciparum
Gayatri Ramakrishnan, Narayanaswamy Srinivasan, Ponnan Padmapriya and Vasant Natarajan
Bioinformatics and Biology Insights 2015:9 195-206
Original Research | Published on 20 Dec 2015



Sequence Analysis and Evolutionary Studies of Reelin Proteins
Malini Manoharan, Sayyed Auwn Muhammad, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2015:9 187-193
Original Research | Published on 20 Dec 2015



DDA: A Novel Network-Based Scoring Method to Identify Disease–Disease Associations
Apichat Suratanee and Kitiporn Plaimas
Bioinformatics and Biology Insights 2015:9 175-186
Original Research | Published on 08 Dec 2015



A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor
Peter R. LoVerso and Feng Cui
Bioinformatics and Biology Insights 2015:9 165-174
Original Research | Published on 02 Dec 2015



Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells
Peter R. LoVerso, Christopher M. Wachter and Feng Cui
Bioinformatics and Biology Insights 2015:9 153-164
Original Research | Published on 25 Nov 2015



Advanced Applications of RNA Sequencing and Challenges
Yixing Han, Shouguo Gao, Kathrin Muegge, Wei Zhang and Bing Zhou
Bioinformatics and Biology Insights 2015:Suppl. 1 29-46
Review | Published on 15 Nov 2015



Development and Application of a Genetic Algorithm for Variable Optimization and Predictive Modeling of Five-Year Mortality Using Questionnaire Data
Lucas J. Adams, Ghalib Bello and Gerard G. Dumancas
Bioinformatics and Biology Insights 2015:Suppl. 3 31-41
Original Research | Published on 08 Nov 2015



Gene Coexpression Networks in Human Brain Developmental Transcriptomes Implicate the Association of Long Noncoding RNAs with Intellectual Disability
Brian L. Gudenas and Liangjiang Wang
Bioinformatics and Biology Insights 2015:Suppl. 1 21-27
Original Research | Published on 27 Oct 2015



Application of Functional Genomics for Bovine Respiratory Disease Diagnostics
Aswathy N. Rai, William B. Epperson and Bindu Nanduri
Bioinformatics and Biology Insights 2015:Suppl. 2 13-23
Review | Published on 22 Oct 2015



Machine Learning Methods for Predicting HLA–Peptide Binding Activity
Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, Donna L. Mendrick and Huixiao Hong
Bioinformatics and Biology Insights 2015:Suppl. 3 21-29
Review | Published on 11 Oct 2015 | Video abstract



The Genetic Architecture of Domestication in Animals
Dominic Wright
Bioinformatics and Biology Insights 2015:Suppl. 4 11-20
Commentary | Published on 11 Oct 2015



B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data
Mikhail G. Dozmorov, Nicolas Dominguez, Krista Bean, Susan R. Macwana, Virginia Roberts, Edmund Glass, Judith A. James and Joel M. Guthridge
Bioinformatics and Biology Insights 2015:Suppl. 3 11-19
Original Research | Published on 08 Oct 2015



Genetics of Prion Disease in Cattle
Brenda M. Murdoch and Gordon K. Murdoch
Bioinformatics and Biology Insights 2015:Suppl. 4 1-10
Review | Published on 24 Sep 2015



The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology
Frank A. Feltus, Joseph R. Breen III, Juan Deng, Ryan S. Izard, Christopher A. Konger, Walter B. Ligon III, Don Preuss and Kuang-Ching Wang
Bioinformatics and Biology Insights 2015:Suppl. 1 9-19
Review | Published on 23 Sep 2015 | Video abstract



PPCheck: A Webserver for the Quantitative Analysis of Protein–Protein Interfaces and Prediction of Residue Hotspots
Anshul Sukhwal and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2015:9 141-151
Original Research | Published on 21 Sep 2015



Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form
Khadija Amine, Lamia Miri, Adil Naimi, Rachid Saile, Abderrahmane El Kharrim, Afaf Mikou and Anass Kettani
Bioinformatics and Biology Insights 2015:9 129-140
Original Research | Published on 13 Sep 2015



BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences
Martin Dahlö, Frédéric Haziza, Aleksi Kallio, Eija Korpelainen, Erik Bongcam-Rudloff and Ola Spjuth
Bioinformatics and Biology Insights 2015:9 125-128
Technical Advance | Published on 10 Sep 2015



Development and Validation of a Clinical Risk-Assessment Tool Predictive of All-Cause Mortality
Ghalib A. Bello, Gerard G. Dumancas and Chris Gennings
Bioinformatics and Biology Insights 2015:Suppl. 3 1-10
Original Research | Published on 01 Sep 2015



Antigenic Determinants of Possible Vaccine Escape by Porcine Circovirus Subtype 2b Viruses
Megan Constans, Marvin Ssemadaali, Oleksandr Kolyvushko and Sheela Ramamoorthy
Bioinformatics and Biology Insights 2015:Suppl. 2 1-12
Original Research | Published on 23 Aug 2015 | Video abstract



A Simple Rank Product Approach for Analyzing Two Classes
Tae Young Yang
Bioinformatics and Biology Insights 2015:9 119-123
Methodology | Published on 16 Jul 2015



High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism
Monica B. Assumpção, Fabiano C. Moreira, Igor G. Hamoy, Leandro Magalhães, Amanda Vidal, Adenilson Pereira, Rommel Burbano, André Khayat, Artur Silva, Sidney Santos, Samia Demachki, Ândrea Ribeiro-dos-Santos, and Paulo Assumpção
Bioinformatics and Biology Insights 2015:9 111-117
Original Research | Published on 06 Jul 2015



Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique
Hebatallah Hassan, Amr Badr and M. B. Abdelhalim
Bioinformatics and Biology Insights 2015:9 103-109
Original Research | Published on 05 Jul 2015



High-Throughput Sequencing of miRNAs Reveals a Tissue Signature in Gastric Cancer and Suggests Novel Potential Biomarkers
Sylvain Darnet, Fabiano C Moreira, Igor G Hamoy, Rommel Burbano, André Khayat, Aline Cruz, Leandro Magalhães, Artur Silva, Sidney Santos, Samia Demachki, Monica Assumpção, Paulo Assumpção, and Ândrea Ribeiro-dos-Santos
Bioinformatics and Biology Insights 2015:Suppl. 1 1-8
Original Research | Published on 28 Jun 2015



Computational and in vitro Investigation of miRNA-Gene Regulations in Retinoblastoma Pathogenesis: miRNA Mimics Strategy
Nalini Venkatesan, Perinkulam Ravi Deepa, Vikas Khetan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2015:9 89-101
Original Research | Published on 12 May 2015



Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis and Ioannis Iliopoulos
Bioinformatics and Biology Insights 2015:9 75-88
Review | Published on 05 May 2015



Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists
Xiaoxi Dong, Anatoly Yambartsev, Stephen A. Ramsey, Lina D Thomas, Natalia Shulzhenko and Andrey Morgun
Bioinformatics and Biology Insights 2015:9 61-74
Review | Published on 29 Apr 2015



Cross-Disciplinary Detection and Analysis of Network Motifs
Ngoc Tam L. Tran, Luke DeLuccia, Aidan F. McDonald and Chun-Hsi Huang
Bioinformatics and Biology Insights 2015:9 49-60
Original Research | Published on 19 Apr 2015



An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences
Nicolas Carels and Miguel Ponce de Leon
Bioinformatics and Biology Insights 2015:9 37-47
Original Research | Published on 15 Apr 2015



A Systems Biology Approach Reveals the Dose- and Time-Dependent Effect of Primary Human Airway Epithelium Tissue Culture After Exposure to Cigarette Smoke In Vitro
Carole Mathis, Stephan Gebel, Carine Poussin, Vincenzo Belcastro, Alain Sewer, Dirk Weisensee, Arnd Hengstermann, Sam Ansari, Sandra Wagner, Manuel C. Peitsch and Julia Hoeng
Bioinformatics and Biology Insights 2015:9 19-35
Original Research | Published on 09 Mar 2015



Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum
Stefan Simm, Sotirios Fragkostefanakis, Puneet Paul, Mario Keller, Jens Einloft, Klaus-Dieter Scharf and  Enrico Schleiff
Bioinformatics and Biology Insights 2015:9 1-17
Original Research | Published on 09 Feb 2015



POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
Khader Shameer, Mahantesha BN Naika, Oommen K. Mathew, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2014:8 209-214
Original Research | Published on 21 Dec 2014



Computational Methods for CLIP-seq Data Processing
Paula H. Reyes-Herrera and Elisa Ficarra
Bioinformatics and Biology Insights 2014:8 199-207
Review | Published on 01 Oct 2014



Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes
Sony Malhotra and R. Sowdhamini
Bioinformatics and Biology Insights 2014:8 193-198
Original Research | Published on 10 Sep 2014



Integrated Analysis of Dysregulated miRNA-gene Expression in HMGA2-silenced Retinoblastoma Cells
Nalini Venkatesan, PR Deepa, Madavan Vasudevan, Vikas Khetan, Ashwin M Reddy and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2014:8 177-191
Original Research | Published on 04 Sep 2014



Computational Identification of Dengue Virus MicroRNA-Like Structures and their Cellular Targets
Maicol Ospina-Bedoya, Natalia Campillo-Pedroza, Juan P. Franco-Salazar and Juan C. Gallego-Gómez
Bioinformatics and Biology Insights 2014:8 169-176
Short Report | Published on 14 Aug 2014



In Silico Studies of Medicinal Compounds Against Hepatitis C Capsid Protein from North India
Shilu Mathew, Muhammad Faheem, Govindaraju Archunan, Muhammad Ilyas, Nargis Begum, Syed Jahangir, Ishtiaq Qadri, Mohammad Al Qahtani and Shiny Mathew
Bioinformatics and Biology Insights 2014:8 159-168
Original Research | Published on 23 Jun 2014



Identification of Chicken Pulmonary miRNAs Targeting PB1, PB1-F2, and N40 Genes of Highly Pathogenic Avian Influenza Virus H5N1 In Silico
Amod Kumar, Muhasin Asaf V.N., Ashwin Ashok Raut, Richa Sood and Anamika Mishra
Bioinformatics and Biology Insights 2014:8 135-145
Original Research | Published on 12 Jun 2014



DOR – a Database of Olfactory Receptors – Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes
Balasubramanian Nagarathnam, Snehal D. Karpe, Krishnan Harini, Kannan Sankar, Mohammed Iftekhar, Durairaj Rajesh, Sadasivam Giji, Govidaraju Archunan, Veluchamy Balakrishnan, M. Michael Gromiha, Wataru Nemoto, Kazhuhiko Fukui and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2014:8 147-158
Original Research | Published on 12 Jun 2014



A Protocol for mtGenome Analysis on Large Sample Numbers
Igor G. Hamoy, André M. Ribeiro-dos-Santos, Luiz Alvarez, Silvanira Barbosa, Artur Silva, Sidney Santos, Leonor Gusmão and Ândrea Ribeiro-dos-Santos
Bioinformatics and Biology Insights 2014:8 127-134
Original Research | Published on 11 Jun 2014



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