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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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Candidate Single Nucleotide Polymorphism Markers for Arsenic Responsiveness of Protein Targets
Raphael D. Isokpehi, Hari H.P. Cohly, Matthew N. Anyanwu, Rajendram V. Rajnarayanan, Paul B. Tchounwou, Udensi K. Udensi and Barbara E. Graham-Evans
Bioinformatics and Biology Insights 2010:4 99-111
Original Research | Published on 11 Oct 2010



An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces
Catherine H. Schein, Ovidiu Ivanciuc, Terumi Midoro-Horiuti, Randall M. Goldblum and Werner Braun
Bioinformatics and Biology Insights 2010:4 113-125
Review | Published on 11 Oct 2010



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



Comparative in Silico Analyses of Cpeb1–4 with Functional Predictions
Xiang-Ping Wang and Nigel G.F. Cooper
Bioinformatics and Biology Insights 2010:4 61-83
Original Research | Published on 30 Aug 2010



A Plausible Role for the Presence of Internal Shine-Dalgarno Sites
Lalit Ponnala
Bioinformatics and Biology Insights 2010:4 55-60
Original Research | Published on 28 Jun 2010



Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data
Christian Gorba and Florence Tama
Bioinformatics and Biology Insights 2010:4 43-54
Original Research | Published on 21 Jun 2010



Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach
Khader Shameer, Ganesan Pugalenthi, Krishna Kumar Kandaswamy, Ponnuthurai N. Suganthan, Govindaraju Archunan and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2010:4 33-42
Original Research | Published on 17 Jun 2010



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



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



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



Domain Organization of Long Autotransporter Signal Sequences
Jan A. Hiss and Gisbert Schneider
Bioinformatics and Biology Insights 2009:3 189-204
Original Research | Published on 14 Dec 2009



An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments
Haiyan Hu
Bioinformatics and Biology Insights 2009:3 179-187
Original Research | Published on 17 Nov 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



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



Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data
Haoyu Cheng, Lihua Jiang, Maoying Wu and Qi Liu
Bioinformatics and Biology Insights 2009:3 129-140
Original Research | Published on 21 Oct 2009



A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome
Marcin Kierczak, Krzysztof Ginalski, Michał Dramiński, Jacek Koronacki, Witold Rudnicki and Jan Komorowski
Bioinformatics and Biology Insights 2009:3 109-127
Original Research | Published on 05 Oct 2009



Graphical User Interfaces for Molecular Dynamics—Quo Vadis?
B. Knapp and W. Schreiner
Bioinformatics and Biology Insights 2009:3 103-107
Short Commentary | Published on 23 Sep 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



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



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



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



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



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



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



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



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



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



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



IMAGE: A New Tool for the Prediction of Transcription Factor Binding Sites
R. Casilli, A. Marongiu, S. Melchionna, P. Palazzari, R. Paparcone and V. Rosato
Bioinformatics and Biology Insights 2008:2 357-367
Published on 03 Oct 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



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



Designing Toxicogenomics Studies that use DNA Array Technology
Robert R. Delongchamp, Cruz Velasco, Varsha G. Desai, Taewon Lee and James C. Fuscoe
Bioinformatics and Biology Insights 2008:2 317-328
Published on 14 Aug 2008



Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae
Jesper Lundström, Johan Björkegren and Jesper Tegnér
Bioinformatics and Biology Insights 2008:2 307-316
Published on 14 Jul 2008



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



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



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



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



Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets
Angelica Lindlöf, Marcus Bräutigam, Aakash Chawade, Olof Olsson and Björn Olsson
Bioinformatics and Biology Insights 2008:2 215-237
Published on 01 May 2008



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



Effects of Feeding Periods of High Cholesterol and Saturated Fat Diet on Blood Biochemistry and Hydroxyproline Fractions in Rabbits
Mohamed A. K. Abdelhalim, N. J. Siddiqi, A. S. ALhomida and Mohammed S. Al- Ayed
Bioinformatics and Biology Insights 2008:2 95-100
Published on 22 Apr 2008



Topological Properties of Co-Occurrence Networks in Published Gene Expression Signatures
Heiko Muller and Francesco Acquati
Bioinformatics and Biology Insights 2008:2 203-213
Published on 17 Apr 2008



Borges Dilemma, Fundamental Laws, and Systems Biology
Ping Ao
Bioinformatics and Biology Insights 2008:2 201-202
Published on 10 Apr 2008



Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis
Kanaka Durga Kedarisetti, Scott Dick and Lukasz Kurgan
Bioinformatics and Biology Insights 2008:2 133-144
Published on 12 Mar 2008



Ontologies for Bioinformatics
Nadine Schuurman and Agnieszka Leszczynski
Bioinformatics and Biology Insights 2008:2 187-200
Published on 12 Mar 2008



Utility of Computational Methods to Identify the Apoptosis Machinery in Unicellular Eukaryotes
Pierre Marcel Durand and Theresa Louise Coetzer
Bioinformatics and Biology Insights 2008:2 101-117
Published on 12 Mar 2008



Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications
Choon-Peng Chng and Lee-Wei Yang
Bioinformatics and Biology Insights 2008:2 171-185
Published on 05 Mar 2008



Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives
Lee-Wei Yang and Choon-Peng Chng
Bioinformatics and Biology Insights 2008:2 25-45

Published on 04 Mar 2008



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



A New Test Statistic Based on Shrunken Sample Variance for Identifying Differentially Expressed Genes in Small Microarray Experiments
Akihiro Hirakawa, Yasunori Sato, Chikuma Hamada and Isao Yoshimura
Bioinformatics and Biology Insights 2008:2 145-156
Published on 29 Feb 2008



Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis
Zhenkang Xu, Laura Gutierrez, Matthew Hitchens, Steve Scherer, Amy K. Sater and Dan E. Wells
Bioinformatics and Biology Insights 2008:2 157-169
Published on 26 Feb 2008





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