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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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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)



Periodicity Detection Method for Small-Sample Time Series Datasets
Daisuke Tominaga
Bioinformatics and Biology Insights 2010:4 127-136
Methodology | Published on 22 Nov 2010



Software for Quantifying and Simulating Microsatellite Genotyping Error
Paul C.D. Johnson and Daniel T. Haydon
Bioinformatics and Biology Insights 2007:1 71-75
Published on 12 Nov 2007



affyPara - a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data
Markus Schmidberger, Esmeralda Vicedo and Ulrich Mansmann
Bioinformatics and Biology Insights 2009:3 83-87
Short Report | Published on 22 Jul 2009



Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies
R. Shyama Prasad Rao, Ole Thomsen Buus and Bernd Wollenweber
Bioinformatics and Biology Insights 2010:4 9-17
Original Research | Published on 17 Feb 2010



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



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



Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case
Hélène San Clemente, Rafael Pont-Lezica and Elisabeth Jamet
Bioinformatics and Biology Insights 2009:3 15-28
Original Research | Published on 18 Feb 2009



Gromita: A Fully Integrated Graphical User Interface to Gromacs 4
Diamantis Sellis, Dimitrios Vlachakis and Metaxia Vlassi
Bioinformatics and Biology Insights 2009:3 99-102
Software or Database Review | Published on 07 Sep 2009



Normalization and Gene p-Value Estimation: Issues in Microarray Data Processing
Katrin Fundel, Robert Küffner, Thomas Aigner and Ralf Zimmer
Bioinformatics and Biology Insights 2008:2 291-305
Published on 28 May 2008



Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization
Junilda Spirollari, Jason T.L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park and Bruce A. Shapiro
Bioinformatics and Biology Insights 2009:3 51-69
Original Research | Published on 03 Jun 2009



Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
Surendra S Negi and Werner Braun
Bioinformatics and Biology Insights 2009:3 71-81
Original Research | Published on 01 Jul 2009



Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences
Ralf Aurahs, Markus Göker, Guido W. Grimm, Vera Hemleben, Christoph Hemleben, Ralf Schiebel and Michal Kučera
Bioinformatics and Biology Insights 2009:3 155-177
Methodology | Published on 11 Nov 2009



Neuroinformatics: From Bioinformatics to Databasing the Brain
Thomas M. Morse
Bioinformatics and Biology Insights 2008:2 253-264
Published on 14 May 2008



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



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



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



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



Proteomic Analysis in Diabetic Cardiomyopathy using Bioinformatics Approach
Allam Appa Rao, Hanuman Thota, Ramamurthy Adapala, Suresh Babu Changalasetty, Ramachandra Sridhar Gumpeny, Annapurna Akula, Lalitha Saroja Thota, Siva Reddy Challa, M.R. Narasinga Rao and Undurti N. Das
Bioinformatics and Biology Insights 2008:2 1-4
Published on 21 Jan 2008



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



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



Expression of Metabolic, Tissue Remodeling, Oxidative Stress, and Inflammatory Pathways in Mammary Tissue During Involution in Lactating Dairy Cows
Paola Piantoni, Ping Wang, James K. Drackley, Walter L. Hurley and Juan J. Loor
Bioinformatics and Biology Insights 2010:4 85-97
Original Research | Published on 20 Sep 2010



Prediction of Functional Class of Proteins and Peptides Irrespective of Sequence Homology by Support Vector Machines
Zhi Qun Tang, Hong Huang Lin, Hai Lei Zhang, Lian Yi Han, Xin Chen and Yu Zong Chen
Bioinformatics and Biology Insights 2007:1 19-47
Published on 15 Oct 2007



Gene Expression Based Leukemia Sub‑Classification Using Committee Neural Networks
Mihir S. Sewak, Narender P. Reddy and Zhong-Hui Duan
Bioinformatics and Biology Insights 2009:3 89-98
Methodology | Published on 03 Sep 2009



Methodology for Constructing Problem Definitions in Bioinformatics
Amy M. Hauth and Gertraud Burger
Bioinformatics and Biology Insights 2008:2 239-251

Published on 24 Apr 2008



Effect of Diet Supplementation on the Expression of Bovine Genes Associated with Fatty Acid Synthesis and Metabolism
Sandeep J. Joseph, Kelly R. Robbins, Enrique Pavan, Scott l. Pratt, Susan K. Duckett and Romdhane Rekaya
Bioinformatics and Biology Insights 2010:4 19-31
Original Research | Published on 31 Mar 2010



Universal Features for the Classification of Coding and Non-Coding DNA Sequences
Nicolas Carels, Ramon Vidal and Diego Frías
Bioinformatics and Biology Insights 2009:3 37-49
Original Research | Published on 03 Jun 2009



Unsupervised Meta-Analysis on Diverse Gene Expression Datasets Allows Insight into Gene Function and Regulation
Julia C. Engelmann, Roland Schwarz, Steffen Blenk, Torben Friedrich, Philipp N. Seibel, Thomas Dandekar and Tobias Müller
Bioinformatics and Biology Insights 2008:2 265-280
Published on 26 May 2008



Identification of the RGG Box Motif in Shadoo: RNA-Binding and Signaling Roles?
Susan M. Corley and Jill E. Gready
Bioinformatics and Biology Insights 2008:2 383-400
Published on 19 Nov 2008



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



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



Classifying Coding DNA with Nucleotide Statistics
Nicolas Carels and Diego Frías
Bioinformatics and Biology Insights 2009:3 141-154
Original Research | Published on 28 Oct 2009



Beyond Field Effect: Analysis of Shrunken Centroids in Normal Esophageal Epithelia Detects Concomitant Esophageal Adenocarcinoma
Florin M. Selaru, Suna Wang, Jing Yin, Karsten Schulmann, Yan Xu, Yuriko Mori, Alexandru V. Olaru, Fumiaki Sato, James P. Hamilton, John M. Abraham, Paul Schneider, Bruce D. Greenwald, Jan Brabender and Stephen J. Meltzer
Bioinformatics and Biology Insights 2007:1 127-136
Published on 01 Feb 2008



Gene Copy Number Analysis for Family Data Using Semiparametric Copula Model
Ao Yuan, Guanjie Chen, Zhong-Cheng Zhou, George Bonney and Charles Rotimi
Bioinformatics and Biology Insights 2008:2 343-355

Published on 26 Sep 2008



An Improved Approach for Mapping Quantitative Trait Loci in a Pseudo-Testcross: Revisiting a Poplar Mapping Study
Song Wu, Jie Yang, Youjun Huang, Yao Li, Tongming Yin, Stan D. Wullschleger, Gerald A. Tuskan and Rongling Wu
Bioinformatics and Biology Insights 2010:4 1-8
Original Research | Published on 04 Feb 2010



Estimating the Fraction of Non-Coding RNAs in Mammalian Transcriptomes
Yurong Xin, Giulio Quarta, Hin Hark Gan and Tamar Schlick
Bioinformatics and Biology Insights 2008:2 75-94
Published on 01 Mar 2008



Identification and Investigation of Drosophila  Postsynaptic Density Homologs
Faith L.W. Liebl and David E. Featherstone
Bioinformatics and Biology Insights 2008:2 369-381
Published on 03 Nov 2008



Association Between a Prognostic Gene Signature and Functional Gene Sets
Manuela Hummel, Klaus H. Metzeler, Christian Buske, Stefan K. Bohlander and Ulrich Mansmann
Bioinformatics and Biology Insights 2008:2 329-341
Published on 22 Sep 2008



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



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



Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data
Wei-Sheng Wu and Bor-Sen Chen
Bioinformatics and Biology Insights 2007:1 137-145
Published on 16 Oct 2007



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



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



Peptide Vocabulary Analysis Reveals Ultra-Conservation and Homonymity in Protein Sequences
Derek Gatherer
Bioinformatics and Biology Insights 2007:1 101-126
Published on 12 Dec 2007



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



Control Design for Signal Transduction Networks
Chun-Liang Lin, Yuan-Wei Liu and Chia-Hua Chuang
Bioinformatics and Biology Insights 2009:3 1-14
Original Research | Published on 09 Feb 2009



Sequence Analysis of the Full-length cDNA and Protein Structure Homology Modeling of FABP2 from Paralichthys Olivaceus
Xiaowu Chen and Zhiyi Shi
Bioinformatics and Biology Insights 2009:3 29-35
Short Report | Published on 04 Jun 2009



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



The Use of Artificial Neural Networks in Prediction of Congenital CMV Outcome from Sequence Data
Ravit Arav-Boger, Yuval S. Boger, Charles B. Foster and Zvi Boger
Bioinformatics and Biology Insights 2008:2 281-289
Published on 29 May 2008



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





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