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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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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



Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis
Venkatesan Nalini, Ramya Segu, Perinkulam Ravi Deepa, Vikas Khetan, Madavan Vasudevan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2013:7 289-306
Original Research | Published on 18 Sep 2013



Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1
Ajit K. Sharma, Abhilasha Mansukh, Ashok Varma, Nikhil Gadewal, and Sanjay Gupta
Bioinformatics and Biology Insights 2013:7 271-288
Original Research | Published on 26 Aug 2013



Bioinformatics Analysis of Transcriptome Dynamics During Growth in Angus Cattle Longissimus Muscle
Sonia J. Moisá, Daniel W. Shike, Daniel E. Graugnard, Sandra L. Rodriguez-Zas, Robin E. Everts, Harris A. Lewin, Dan B. Faulkner, Larry L. Berger and Juan J. Loor
Bioinformatics and Biology Insights 2013:7 253-270
Original Research | Published on 04 Aug 2013



Systematic Verification of Upstream Regulators of a Computable Cellular Proliferation Network Model on Non-Diseased Lung Cells Using a Dedicated Dataset
Vincenzo Belcastro, Carine Poussin, Stephan Gebel, Carole Mathis, Walter K. Schlage, Rosemarie B. Lichtner, Sibille Quadt-Humme, Sandra Wagner, Julia Hoeng and Manuel C. Peitsch
Bioinformatics and Biology Insights 2013:7 217-230
Original Research | Published on 23 Jul 2013



Association of Putative Members to Family of Mosquito Odorant Binding Proteins: Scoring Scheme Using Fuzzy Functional Templates and Cys Residue Positions
Malini Manoharan, Kannan Sankar, Bernard Offmann and Sowdhamini Ramanathan
Bioinformatics and Biology Insights 2013:7 231-251
Original Research | Published on 22 Jul 2013



Bioinformatics and Gene Network Analyses of the Swine Mammary Gland Transcriptome during Late Gestation
Wangsheng Zhao, Khuram Shahzad, Mingfeng Jiang, Daniel E. Graugnard, Sandra L. Rodriguez-Zas, Jun Luo, Juan J. Loor and Walter L. Hurley
Bioinformatics and Biology Insights 2013:7 193-216
Original Research | Published on 14 Jul 2013



A Modular Cell-Type Focused Inflammatory Process Network Model for Non-Diseased Pulmonary Tissue
Jurjen W. Westra, Walter K. Schlage, Arnd Hengstermann, Stephan Gebel, Carole Mathis, Ty Thomson, Ben Wong, Vy Hoang, Emilija Veljkovic, Michael Peck, Rosemarie B. Lichtner, Dirk Weisensee, Marja Talikka, Renee Deehan, Julia Hoeng and Manuel C. Peitsch
Bioinformatics and Biology Insights 2013:7 167-192
Original Research | Published on 20 Jun 2013



The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum
Markus A. Grohme, Brahim Mali, Weronika Welnicz, Stephanie Michel, Ralph O. Schill and Marcus Frohme
Bioinformatics and Biology Insights 2013:7 153-165
Original Research | Published on 26 May 2013



Association Between a Multi-Locus Genetic Risk Score and Inflammatory Bowel Disease
Pingzhao Hu, Aleixo M. Muise, Xiang Xing, John H. Brumell, Mark S. Silverberg and Wei Xu
Bioinformatics and Biology Insights 2013:7 143-152
Short Report | Published on 19 May 2013



miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment
Bram Sebastian and Samuel E. Aggrey
Bioinformatics and Biology Insights 2013:7 133-142
Original Research | Published on 02 Apr 2013



Knowledge Discovery in Variant Databases Using Inductive Logic Programming
Hoan Nguyen, Tien-Dao Luu, Olivier Poch and Julie D. Thompson
Bioinformatics and Biology Insights 2013:7 119-131
Original Research | Published on 18 Mar 2013



Construction of a Computable Network Model for DNA Damage, Autophagy, Cell Death, and Senescence
Stephan Gebel, Rosemarie B. Lichtner, Brian Frushour, Walter K. Schlage, Vy Hoang, Marja Talikka, Arnd Hengstermann, Carole Mathis, Emilija Veljkovic, Michael Peck, Manuel C. Peitsch, Renee Deehan, Julia Hoeng and Jurjen W. Westra
Bioinformatics and Biology Insights 2013:7 97-117
Original Research | Published on 07 Mar 2013



Computational Small RNA Prediction in Bacteria
Jayavel Sridhar and Paramasamy Gunasekaran
Bioinformatics and Biology Insights 2013:7 83-95
Review | Published on 07 Mar 2013



Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study
Janneth González, Angela Gálvez, Ludis Morales, George E. Barreto, Francisco Capani, Omar Sierra and Yolima Torres
Bioinformatics and Biology Insights 2013:7 73-82
Original Research | Published on 27 Feb 2013



A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences
Riccardo Percudani
Bioinformatics and Biology Insights 2013:7 55-72
Original Research | Published on 24 Feb 2013



A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences
Nicolas Carels and Diego Frias
Bioinformatics and Biology Insights :7 35-54
Original Research | Published on 23 Jan 2013



PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation
Henning Lenz and Volker Knoop
Bioinformatics and Biology Insights 2013:7 1-19
Technical Advance | Published on 10 Jan 2013



Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets Towards Prediction of Novel Serum Biomarkers
Madhu Beta, Nalini Venkatesan, Madavan Vasudevan, Umashankar Vetrivel, Vikas Khetan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2013:7 21-34
Original Research | Published on 09 Jan 2013



Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length
Alexander Bolshoy, and Tatiana Tatarinova
Bioinformatics and Biology Insights 2012:6 317-327
Original Research | Published on 10 Dec 2012



Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR- Supported in silico Modeling
J. Zirkel, A. Cecil, F. Schäfer, S. Rahlfs, A. Ouedraogo, K. Xiao, S. Sawadogo, B. Coulibaly, K. Becker and T. Dandekar
Bioinformatics and Biology Insights 2012:6 287-302
Original Research | Published on 03 Dec 2012



Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium
Baraka S. Williams, Raphael D. Isokpehi, Andreas N. Mbah, Antoinesha L. Hollman, Christina O. Bernard, Shaneka S. Simmons, Wellington K. Ayensu and Bianca L. Garner
Bioinformatics and Biology Insights 2012:6 275-286
Original Research | Published on 21 Nov 2012



A Fast Quad-Tree Based Two Dimensional Hierarchical Clustering
Priscilla Rajadurai and Swamynathan Sankaranarayanan
Bioinformatics and Biology Insights 2012:6 265-274
Original Research | Published on 19 Nov 2012



Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease
Xiaofeng Ji, Wei Wang, Yuan Zheng, Jianhua Hao and Mi Sun
Bioinformatics and Biology Insights 2012:6 255-263
Original Research | Published on 19 Nov 2012



Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships
Divya P. Syamaladevi, Margaret S Sunitha, S. Kalaimathy, Chandrashekar C. Reddy, Mohammed Iftekhar, Shaik N. Pasha and R. Sowdhamini
Bioinformatics and Biology Insights 2012:6 247-254
Original Research | Published on 12 Nov 2012



BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks
Oksana Kohutyuk, Fadi Towfic, M. Heather West Greenlee and Vasant Honavar
Bioinformatics and Biology Insights 2012:6 235-246
Software or database review | Published on 08 Nov 2012



The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation
Santi Nurbaiti, Muhamad A. Martoprawiro, Akhmaloka and Rukman Hertadi
Bioinformatics and Biology Insights 2012:6 225-234
Original Research | Published on 30 Oct 2012



Integrative Structural Modelling of the Cardiac Thin Filament: Energetics at the Interface and Conservation Patterns Reveal a Spotlight on Period 2 of Tropomyosin
Margaret Sunitha S, John A. Mercer, James A. Spudich, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2012:6 203-223
Original Research | Published on 03 Oct 2012 | Video abstract



The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses
John Ellis, Stephen Goodswen, Paul J Kennedy and Stephen Bush
Bioinformatics and Biology Insights 2012:6 187-202
Original Research | Published on 03 Sep 2012



Simultaneous Analysis of Common and Rare Variants in Complex Traits: Application to SNPs (SCARVAsnp)
Guanjie Chen, Ao Yuan, Yanxun Zhou, Amy R. Bentley, Jie Zhou, Weiping Chen, Daniel Shriner, Adebowale Adeyemo and Charles N. Rotimi
Bioinformatics and Biology Insights 2012:6 177-185
Methodology | Published on 31 Jul 2012



Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies
Guanjie Chen, Ao Yuan, Jie Zhou, Amy R. Bentley, Adebowale Adeyemo and Charles N. Rotimi
Bioinformatics and Biology Insights 2012:6 169-176
Short Report | Published on 02 Jul 2012



DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements
Pieter Meysman, Kathleen Marchal and Kristof Engelen
Bioinformatics and Biology Insights 2012:6 155-168
Review | Published on 02 Jul 2012



An Integrated Statistical Approach to Compare Transcriptomics Data Across Experiments: A Case Study on the Identification of Candidate Target Genes of the Transcription Factor PPARα
Mohammad Ohid Ullah, Michael Müller and Guido J.E.J. Hooiveld
Bioinformatics and Biology Insights 2012:6 145-154
Methodology | Published on 19 Jun 2012



The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes
André E.R. Soares and Carlos G. Schrago
Bioinformatics and Biology Insights 2012:6 129-143
Original Research | Published on 31 May 2012



Different Evolutionary Modifications as a Guide to Rewire Two-Component Systems
Beate Krueger, Torben Friedrich, Frank Förster, Jörg Bernhardt, Roy Gross and Thomas Dandekar
Bioinformatics and Biology Insights 2012:6 97-128
Original Research | Published on 03 May 2012



Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations
Frank Förster, Daniela Beisser, Markus A. Grohme, Chunguang Liang, Brahim Mali, Alexander Matthias Siegl, Julia C. Engelmann, Alexander V. Shkumatov, Elham Schokraie, Tobias Müller, Martina Schnölzer, Ralph O. Schill, Marcus Frohme and Thomas Dandekar
Bioinformatics and Biology Insights 2012:6 69-96
Original Research | Published on 23 Apr 2012



Mining Gene Ontology Data with AGENDA
Guvanch Ovezmyradov, Qianhao Lu and Martin C. Göpfert
Bioinformatics and Biology Insights 2012:6 63-67
Original Research | Published on 18 Apr 2012



White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection
Casey P. Shannon, Zsuzsanna Hollander,Janet Wilson-McManus, Robert Balshaw, Raymond T. Ng, Robert McMaster, Bruce M. McManus, Paul A. Keown, and Scott J. Tebbutt
Bioinformatics and Biology Insights 2012:6 49-61
Original Research | Published on 10 Apr 2012



Molecular Modelling of Oligomeric States of DmOR83b, an Olfactory Receptor in D. melanogaster
K. Harini and R. Sowdhamini
Bioinformatics and Biology Insights 2012:6 33-47
Original Research | Published on 26 Mar 2012



Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1)
Krupa S. Jani and D.S. Dalafave
Bioinformatics and Biology Insights 2012:6 23-31
Original Research | Published on 20 Feb 2012



Structural and Functional Insights on the Myosin Superfamily
Divya P. Syamaladevi, James A. Spudich,* and R. Sowdhamini*
Bioinformatics and Biology Insights 2012:6 11-21
Review | Published on 01 Feb 2012 | Highly accessed (previous month)



A Novel Approach for the Simultaneous Analysis of Common and Rare Variants in Complex Traits
Ao Yuan, Guanjie Chen, Yanxun Zhou, Amy Bentley and Charles Rotimi
Bioinformatics and Biology Insights 2012:6 1-9
Methodology | Published on 22 Jan 2012



Functional Annotation Analytics of Rhodopseudomonas palustris Genomes
Shaneka S. Simmons, Raphael D. Isokpehi, Shyretha D. Brown, Donee L. McAllister, Charnia C. Hall, Wanaki M. McDuffy, Tamara L. Medley, Udensi K. Udensi, Rajendram V. Rajnarayanan, Wellington K. Ayensu and Hari H.P. Cohly
Bioinformatics and Biology Insights 2011:5 115-129
Original Research | Published on 21 Sep 2011



Mouse Retinal Development: a Dark Horse Model for Systems Biology Research
Xia Zhang, Jeanne M. Serb and M. Heather West Greenlee
Bioinformatics and Biology Insights 2011:5 99-113
Review | Published on 22 May 2011



Gene Networks Driving Bovine Mammary Protein Synthesis During the Lactation Cycle
Massimo Bionaz and Juan J. Loor
Bioinformatics and Biology Insights 2011:5 83-98
Original Research | Published on 04 May 2011



Amino Acid Features of P1B-ATPase Heavy Metal Transporters Enabling Small Numbers of Organisms to Cope with Heavy Metal Pollution
E. Ashrafi, A. Alemzadeh, M. Ebrahimi, E. Ebrahimie, N. Dadkhodaei and M. Ebrahimi
Bioinformatics and Biology Insights 2011:5 59-82
Original Research | Published on 17 Apr 2011



Identification of Drought-Responsive Universal Stress Proteins in Viridiplantae
Raphael D. Isokpehi, Shaneka S. Simmons, Hari H.P. Cohly, Stephen I.N. Ekunwe, Gregorio B. Begonia and Wellington K. Ayensu
Bioinformatics and Biology Insights 2011:5 41-58
Original Research | Published on 07 Feb 2011



Conceptual Aspects of Large Meta-Analyses with Publicly Available Microarray Data: A Case Study in Oncology
Markus Schmidberger, Sabine Lennert and Ulrich Mansmann
Bioinformatics and Biology Insights 2011:5 13-39
Case report | Published on 23 Jan 2011





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