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Volume 3;  2009
Original Research
Control Design for Signal Transduction Networks
Chun-Liang Lin, Yuan-Wei Liu, Chia-Hua Chuang
Bioinform Biol Insights. 2009; 3: 1–14. Published online 2009 February 9.
PMCID:
PMC2684693
Abstract Full Text PDF–1.1M
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, Elisabeth Jamet
Bioinform Biol Insights. 2009; 3: 15–28. Published online 2009 February 18.
PMCID:
PMC2808182
Abstract Full Text PDF–1.5M Supplementary Material
Short Report
Sequence Analysis of the Full-length cDNA and Protein Structure Homology Modeling of FABP2 from Paralichthys Olivaceus
Xiaowu Chen, Zhiyi Shi
Bioinform Biol Insights. 2009; 3: 29–35. Published online 2009 June 4.
PMCID:
PMC2808173
Abstract Full Text PDF–1.4M
Original Research
Universal Features for the Classification of Coding and Non-coding DNA Sequences
Nicolas Carels, Ramon Vidal, Diego Frías
Bioinform Biol Insights. 2009; 3: 37–49. Published online 2009 June 3.
PMCID:
PMC2808180
Abstract Full Text PDF–906K
Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization
Junilda Spirollari, Jason T.L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park, Bruce A. Shapiro
Bioinform Biol Insights. 2009; 3: 51–69. Published online 2009 June 3.
PMCID:
PMC2808183
Abstract Full Text PDF–598K
Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
Surendra S Negi, Werner Braun
Bioinform Biol Insights. 2009; 3: 71–81. Published online 2009 July 1.
PMCID:
PMC2808184
Abstract Full Text PDF–8.8M
Short Report
affyPara—a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data
Markus Schmidberger, Esmeralda Vicedo, Ulrich Mansmann
Bioinform Biol Insights. 2009; 3: 83–87. Published online 2009 July 22.
PMCID:
PMC2808179
Abstract Full Text PDF–476K
Methodology
Gene Expression Based Leukemia Sub-Classification Using Committee Neural Networks
Mihir S. Sewak, Narender P. Reddy, Zhong-Hui Duan
Bioinform Biol Insights. 2009; 3: 89–98. Published online 2009 September 3.
PMCID:
PMC2808175
Abstract Full Text PDF–4.1M
Software or Data Base Review
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4
Diamantis Sellis, Dimitrios Vlachakis, Metaxia Vlassi
Bioinform Biol Insights. 2009; 3: 99–102. Published online 2009 September 7.
PMCID:
PMC2808185
Abstract Full Text PDF–2.2M
Short Commentary
Graphical User Interfaces for Molecular Dynamics—Quo Vadis?
B. Knapp, W. Schreiner
Bioinform Biol Insights. 2009; 3: 103–107. Published online 2009 September 23.
PMCID:
PMC2808181
Abstract Full Text PDF–552K
Original Research
A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome
Marcin Kierczak, Krzysztof Ginalski, Michał Dramiński, Jacek Koronacki, Witold Rudnicki, Jan Komorowski
Bioinform Biol Insights. 2009; 3: 109–127. Published online 2009 October 5.
PMCID:
PMC2808174
Abstract Full Text PDF–3.8M
Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data
Haoyu Cheng, Lihua Jiang, Maoying Wu, Qi Liu
Bioinform Biol Insights. 2009; 3: 129–140. Published online 2009 October 21.
PMCID:
PMC2808186
Abstract Full Text PDF–7.0M
Classifying Coding DNA with Nucleotide Statistics
Nicolas Carels, Diego Frías
Bioinform Biol Insights. 2009; 3: 141–154. Published online 2009 October 28.
PMCID:
PMC2808172
Abstract Full Text PDF–1.7M
Methodology
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, Michal Kučera
Bioinform Biol Insights. 2009; 3: 155–177. Published online 2009 November 11.
PMCID:
PMC2808177
Abstract Full Text PDF–8.2M Supplementary Material
Original Research
Domain Organization of Long Autotransporter Signal Sequences
Jan A. Hiss, Gisbert Schneider
Bioinform Biol Insights. 2009; 3: 189–204. Published online 2009 December 14.
PMCID:
PMC2805444
Abstract Full Text PDF–2.7M Supplementary Material
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