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JOURNAL

Bioinformatics and Biology Insights


An international, peer reviewed, open access journal that focuses 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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Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
Apichat Suratanee, Kitiporn Plaimas
Bioinformatics and Biology Insights 2017:11 1177932217720405
Original Research | Published on 13 Jul 2017



CellTrans: An R Package to Quantify Stochastic Cell State Transitions
Thomas Buder, Andreas Deutsch, Michael Seifert, Anja Voss-Böhme
Bioinformatics and Biology Insights 2017:11 1177932217712241
Original Research | Published on 16 Jun 2017



A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major
Larissa Catharina, Carlyle Ribeiro Lima, Alexander Franca, Ana Carolina Ramos Guimarães, Marcelo Alves-Ferreira, Pierre Tuffery, Philippe Derreumaux, Nicolas Carels
Bioinformatics and Biology Insights 2017:11 1177932217712471
Methodology | Published on 12 Jun 2017



Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows
A Agrawal, MJ Khan, DE Graugnard, M Vailati-Riboni, SL Rodriguez-Zas, JS Osorio, JJ Loor
Bioinformatics and Biology Insights 2017:11 1177932217704667
Original Research | Published on 28 Apr 2017



In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms
Jaire Alves Ferreira Filho, Lucas Soares de Brito, André Pereira Leão, Alexandre Alonso Alves, Eduardo Fernandes Formighieri, Manoel Teixeira Souza
Bioinformatics and Biology Insights 2017:11 1177932217702388
Original Research | Published on 18 Apr 2017



PISMA: A Visual Representation of Motif Distribution in DNA Sequences
Rogelio Alcántara-Silva, Moisés Alvarado-Hermida, Gibrán Díaz-Contreras, Martha Sánchez-Barrios, Samantha Carrera, Silvia Carolina Galván
Bioinformatics and Biology Insights 2017:11 1177932217700907
Methodology | Published on 30 Mar 2017



An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of
Kamalakshi Devi, Lochana Patar, Mahendra K Modi, Priyabrata Sen
Bioinformatics and Biology Insights 2017:11 1177932217701735
Original Research | Published on 30 Mar 2017



Current Developments in Machine Learning Techniques in Biological Data Mining
Gerard G Dumancas, Indra Adrianto, Ghalib Bello, Mikhail Dozmorov
Bioinformatics and Biology Insights 2017:11 1177932216687545
Editorial | Published on 22 Mar 2017



Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships
Luca Ambrosino, Maria Luisa Chiusano
Bioinformatics and Biology Insights 2017:11 1177932217690136
Methodology | Published on 23 Feb 2017



Plasma MicroRNA Levels Following Resection of Metastatic Melanoma
Nicholas Latchana, Zachary B Abrams, J Harrison Howard, Kelly Regan, Naduparambil Jacob, Paolo Fadda, Alicia Terando, Joseph Markowitz, Doreen Agnese, Philip Payne, William E Carson
Bioinformatics and Biology Insights 2017:11 1177932217694837
Original Research | Published on 23 Feb 2017



Molecular Modeling and Phylogeny of the Krüppel-like Factor 4 (cKLF4) Protein from the Arabian Camel, Camelus dromedarius
Abdullah O. Alawad, Sultan N. Alharbi, Othman A. Alhazzaa, Faisal S. Alagrafi, Mohammad N. Alkhrayef, Ziyad A. Alhamdan, Abdullah D. Alenazi, Mohamed Hammad, Sami A. Alyahya, Hasan A. AlJohi and Ibrahim O. Alanazi
Bioinformatics and Biology Insights 2016:10 291-300
Original Research | Published on 21 Dec 2016



Integrating Epigenomics into the Understanding of Biomedical Insight
Yixing Han and Ximiao He
Bioinformatics and Biology Insights 2016:10 267-289
Review | Published on 04 Dec 2016



Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets
D. D. Shrimankar and S. R. Sathe
Bioinformatics and Biology Insights 2016:10 255-265
Methodology | Published on 30 Nov 2016



Clustering Algorithms: Their Application to Gene Expression Data
Jelili Oyelade, Itunuoluwa Isewon, Funke Oladipupo, Olufemi Aromolaran, Efosa Uwoghiren, Faridah Ameh, Moses Achas and Ezekiel Adebiyi
Bioinformatics and Biology Insights 2016:10 237-253
Review | Published on 30 Nov 2016



Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins
Ernesto J. Grasso, Adolfo E. Sottile and Carlos E. Coronel
Bioinformatics and Biology Insights 2016:10 225-236
Original Research | Published on 30 Oct 2016



An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters
Stephen A. Ramsey
Bioinformatics and Biology Insights 2015:Suppl. 4 59-69
Methodology | Published on 25 Oct 2016



Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks
Miklós Laczik, Jan Hendrickx, Anne-Clémence Veillard, Mustafa Tammoh, Sarah Marzi and Dominique Poncelet
Bioinformatics and Biology Insights 2016:10 209-224
Perspective | Published on 25 Oct 2016



Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum
Stefan Simm, Klaus-Dieter Scharf, Sridharan Jegadeesan, Maria Luisa Chiusano, Nurit Firon and Enrico Schleiff
Bioinformatics and Biology Insights 2016:10 185-207
Original Research | Published on 26 Sep 2016



Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha
Sudeesh Karumathil, Vijaya R. Dirisala, Uthpala Srinadh, Valaboju Nikhil, N. Satya Sampath Kumar and Rahul R. Nair
Bioinformatics and Biology Insights 2016:10 167-184
Original Research | Published on 22 Sep 2016



Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives – An In Silico Approach
Subhomoi Borkotoky, Chetan Kumar Meena and Ayaluru Murali
Bioinformatics and Biology Insights 2016:10 155-166
Original Research | Published on 29 Aug 2016



In Silico Structure Prediction of Human Fatty Acid Synthase–Dehydratase: A Plausible Model for Understanding Active Site Interactions
Arun John, Vetrivel Umashankar, A. Samdani, Manoharan Sangeetha, Subramanian Krishnakumar and Perinkulam Ravi Deepa
Bioinformatics and Biology Insights 2016:10 143-154
Original Research | Published on 14 Aug 2016



OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid
William L. Poehlman, Mats Rynge, Chris Branton, D. Balamurugan and Frank A. Feltus
Bioinformatics and Biology Insights 2016:10 133-141
Technical Advance | Published on 02 Aug 2016



Computational Identification of Novel Genes: Current and Future Perspectives
Steffen Klasberg, Tristan Bitard-Feildel and Ludovic Mallet
Bioinformatics and Biology Insights 2016:10 121-131
Review | Published on 01 Aug 2016



Phylogenetic and Structural Analysis of the Pluripotency Factor Sex-Determining Region Y box2 Gene of Camelus dromedarius (cSox2)
Abdullah Alawad, Sultan Alharbi, Othman Alhazzaa, Faisal Alagrafi, Mohammed Alkhrayef, Ziyad Alhamdan, Abdullah Alenazi, Hasan Al-Johi, Ibrahim O. Alanazi and Mohamed Hammad.
Bioinformatics and Biology Insights 2016:10 111-120
Original Research | Published on 26 Jul 2016



Cluster Analysis of Tumor Suppressor Genes in Canine Leukocytes Identifies Activation State
Julie-Anne Daly, Sally-Anne Mortlock, Rosanne M. Taylor and Peter Williamson
Bioinformatics and Biology Insights 2015:Suppl. 2 59-67
Review | Published on 19 Jul 2016



PIMADb: A Database of Protein–Protein Interactions in Huge Macromolecular Assemblies
Oommen K. Mathew and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2016:10 105-109
Original Research | Published on 19 Jul 2016



Molecular Shape Analysis-Guided Virtual Screening Platform for Adenosine Kinase Inhibitors
Savita Bhutoria, Ballari Das and Nanda Ghoshal
Bioinformatics and Biology Insights 2016:10 97-103
Original Research | Published on 18 Jul 2016



S2M: A Stochastic Simulation Model of Poliovirus Genetic State Transition
Carol L. Ecale Zhou
Bioinformatics and Biology Insights 2016:10 81-95
Methodology | Published on 27 Jun 2016



PDBparam: Online Resource for Computing Structural Parameters of Proteins
R. Nagarajan, A. Archana, A. Mary Thangakani, S. Jemimah, D. Velmurugan, and M. Michael Gromiha
Bioinformatics and Biology Insights 2016:10 73-80
Software or Database Review | Published on 14 Jun 2016



Genome Data Exploration Using Correspondence Analysis
Fredj Tekaia
Bioinformatics and Biology Insights 2016:10 59-72
Review | Published on 07 Jun 2016



Quality Assessment of Domesticated Animal Genome Assemblies
Stefan E. Seemann, Christian Anthon, Oana Palasca and Jan Gorodkin
Bioinformatics and Biology Insights 2015:Suppl. 4 49-58
Original Research | Published on 06 Jun 2016



Unmasking Upstream Gene Expression Regulators with miRNA-corrected mRNA Data
Stephanie Bollmann, Dengpan Bu, Jiaqi Wang and Massimo Bionaz
Bioinformatics and Biology Insights 2015:Suppl. 4 33-48
Original Research | Published on 29 May 2016



Introductory Editorial: Current Developments in RNA Sequence Analysis
Jianping Zhang, Shaolei Teng, Cuncong Zhong, Bo Wang, Jie Wu
Bioinformatics and Biology Insights 2015:Suppl. 1 61-63
Editorial | Published on 15 May 2016



Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets
Jelili Oyelade, Itunuoluwa Isewon, Solomon Rotimi and Ifeoluwa Okunoren
Bioinformatics and Biology Insights 2016:10 49-57
Original Research | Published on 12 May 2016



Machine Learning Data Imputation and Classification in a Multicohort Hypertension Clinical Study
William Seffens, Chad Evans, Minority Health-GRID Network and Herman Taylor
Bioinformatics and Biology Insights 2015:Suppl. 3 43-54
Original Research | Published on 09 May 2016



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



High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism
Joshua C. McCann, Tryon A. Wickersham and Juan J. Loor
Bioinformatics and Biology Insights 2014:8 109-125
Review | Published on 08 Jun 2014



The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins
Miguel Ponce de Leon, Antonio Basilio de Miranda, Fernando Alvarez-Valin and Nicolas Carels
Bioinformatics and Biology Insights 2014:8 93-108
Original Research | Published on 20 May 2014



Promise and Reality in the Expanding Field of Network Interaction Analysis: Metabolic Networks
Susanna Bazzani
Bioinformatics and Biology Insights 2014:8 83-91
Commentary | Published on 16 Apr 2014



Computational Insights of the Interaction among Sea Anemones Neurotoxins and Kv1.3 Channel
Angélica Sabogal-Arango, George E. Barreto, David Ramírez-Sánchez, Juan González-Mendoza, Viviana Barreto, Ludis Morales and Janneth González
Bioinformatics and Biology Insights 2014:8 73-81
Original Research | Published on 15 Apr 2014



An In Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638)
Arafat Rahman Oany, Tahmina Pervin Jyoti and Shah Adil Ishtiyaq Ahmad
Bioinformatics and Biology Insights 2014:8 65-72
Original Research | Published on 20 Mar 2014



Postpartal Subclinical Endometritis Alters Transcriptome Profiles in Liver and Adipose Tissue of Dairy Cows
Haji Akbar, Felipe C. Cardoso, Susanne Meier, Christopher Burke, Scott McDougall, Murray Mitchell, Caroline Walker, Sandra L. Rodriguez-Zas, Robin E. Everts, Harris A. Lewin, John R. Roche and Juan J. Loor
Bioinformatics and Biology Insights 2014:8 45-63
Original Research | Published on 19 Feb 2014



Probing the Unknowns in Cytokinin-Mediated Immune Defense in Arabidopsis with Systems Biology Approaches
Muhammad Naseem, Meik Kunz and Thomas Dandekar
Bioinformatics and Biology Insights 2014:8 35-44
Methodology | Published on 13 Feb 2014



Longitudinal Analysis of Whole Blood Transcriptomes to Explore Molecular Signatures Associated With Acute Renal Allograft Rejection
Heesun Shin, Oliver Günther, Zsuzsanna Hollander, Janet E. Wilson-McManus, Raymond T. Ng, Robert Balshaw, Paul A. Keown, Robert McMaster, Bruce M. McManus, Nicole M. Isbel, Greg Knoll and Scott J. Tebbutt; for the PROOF Centre of Excellence Team
Bioinformatics and Biology Insights 2014:8 17-33
Original Research | Published on 22 Jan 2014



GeneSV – an Approach to Help Characterize Possible Variations in Genomic and Protein Sequences
Adam Zemla, Tanya Kostova, Rodion Gorchakov, Evgeniya Volkova, David W. C. Beasley, Jane Cardosa, Scott C. Weaver, Nikos Vasilakis and Pejman Naraghi-Arani
Bioinformatics and Biology Insights 2014:8 1-16
Original Research | Published on 08 Jan 2014



Three Dimensional Structure Prediction of Fatty Acid Binding Site on Human Transmembrane Receptor CD36
Zineb Tarhda, Oussama Semlali, Anas Kettani, Ahmed Moussa, Nada A. Abumrad and Azeddine Ibrahimi
Bioinformatics and Biology Insights 2013:7 369-373
Original Research | Published on 02 Dec 2013



ChIP-Seq Data Mining: Remarkable Differences in NRSF/REST Target Genes between Human ESC and ESC-Derived Neurons
Jun-ichi Satoh, Natsuki Kawana and Yoji Yamamoto
Bioinformatics and Biology Insights 2013:7 357-368
Original Research | Published on 01 Dec 2013



A Computational Assay to Design an Epitope-Based Peptide Vaccine Against Saint Louis Encephalitis Virus
Md. Anayet Hasan, Mehjabeen Hossain and Md. Jibran Alam
Bioinformatics and Biology Insights 2013:7 347-355
Original Research | Published on 24 Nov 2013



On Crowd-verification of Biological Networks
The sbv IMPROVER project team (in alphabetical order): Sam Ansari, Jean Binder, Stephanie Boue, Anselmo Di Fabio, William Hayes, Julia Hoeng, Anita Iskandar, Robin Kleiman, Raquel Norel, Bruce O'Neel, Manuel C. Peitsch, Carine Poussin, Dexter Pratt, Kahn Rhrissorrakrai, Walter K. Schlage, Gustavo Stolovitzky and Marja Talikka
Bioinformatics and Biology Insights 2013:7 307-325
Original Research | Published on 10 Oct 2013



Automatic Identification of Algal Community from Microscopic Images
Natchimuthu Santhi, Chinnaraj Pradeepa, Parthasarathy Subashini and Senthil Kalaiselvi
Bioinformatics and Biology Insights 2013:7 327-334
Original Research | Published on 10 Oct 2013



Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights
Diego Frias, Joana P. Monteiro-Cunha, Aline C. Mota-Miranda, Vagner S. Fonseca, Tulio de Oliveira, Bernardo Galvao-Castro, and Luiz C. J. Alcantara
Bioinformatics and Biology Insights 2013:7 335-345
Original Research | Published on 10 Oct 2013



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