Bioinform Biol Insights Volume 6; 2012

Casey P. Shannon, Zsuzsanna Hollander, Janet Wilson-McManus, Robert Balshaw, Raymond T. Ng, Robert McMaster, Bruce M. McManus, Paul A. Keown, Scott J. Tebbutt

Bioinform Biol Insights. 2012; 6: 49–61. Published online 2012 April 10. doi: 10.4137/BBI.S9197

PMCID:: PMC3329187

Abstract Full Text PDF–825K Supplementary Material

Mining Gene Ontology Data with AGENDA

Guvanch Ovezmyradov, Qianhao Lu, Martin C. Göpfert

Bioinform Biol Insights. 2012; 6: 63–67. Published online 2012 April 18. doi: 10.4137/BBI.S9101

PMCID:: PMC3337784

Abstract Full Text PDF–1.1M

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, Thomas Dandekar

Bioinform Biol Insights. 2012; 6: 69–96. Published online 2012 April 23. doi: 10.4137/BBI.S9150

PMCID:: PMC3342025

Abstract Full Text PDF–2.0M Supplementary Material

Different Evolutionary Modifications as a Guide to Rewire Two-Component Systems

Beate Krueger, Torben Friedrich, Frank Förster, Jörg Bernhardt, Roy Gross, Thomas Dandekar

Bioinform Biol Insights. 2012; 6: 97–128. Published online 2012 May 3. doi: 10.4137/BBI.S9356

PMCID:: PMC3348925

Abstract Full Text PDF–5.7M Supplementary Material

The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes

André E.R. Soares, Carlos G. Schrago

Bioinform Biol Insights. 2012; 6: 129–143. Published online 2012 May 31. doi: 10.4137/BBI.S9677

PMCID:: PMC3370833

Abstract Full Text PDF–1.4M Supplementary Material

Methodology

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, Guido J.E.J. Hooiveld

Bioinform Biol Insights. 2012; 6: 145–154. Published online 2012 June 19. doi: 10.4137/BBI.S9529

PMCID:: PMC3388742

Abstract Full Text PDF–1.5M Supplementary Material

Review

DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements

Pieter Meysman, Kathleen Marchal, Kristof Engelen

Bioinform Biol Insights. 2012; 6: 155–168. Published online 2012 July 2. doi: 10.4137/BBI.S9426

PMCID:: PMC3399529

Abstract Full Text PDF–1.4M

Short Report

Simple F Test Reveals Gene-Gene Interactions in Case-Control Studies

Guanjie Chen, Ao Yuan, Jie Zhou, Amy R. Bentley, Adebowale Adeyemo, Charles N. Rotimi

Bioinform Biol Insights. 2012; 6: 169–176. Published online 2012 July 2. doi: 10.4137/BBI.S9867

PMCID:: PMC3399554

Abstract Full Text PDF–3.5M

Methodology

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, Charles N. Rotimi

Bioinform Biol Insights. 2012; 6: 177–185. Published online 2012 July 31. doi: 10.4137/BBI.S9966

PMCID:: PMC3418150

Abstract Full Text PDF–650K

Original Research

The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses

John Ellis, Stephen Goodswen, Paul J Kennedy, Stephen Bush

Bioinform Biol Insights. 2012; 6: 187–202. Published online 2012 September 3. doi: 10.4137/BBI.S9954

PMCID:: PMC3448498

Abstract Full Text PDF–1.2M

Integrative Structural Modelling of the Cardiac Thin Filament: Energetics at the Interface and Conservation Patterns Reveal a Spotlight on Period 2 of Tropomyosin

S Margaret Sunitha, John A. Mercer, James A. Spudich, Ramanathan Sowdhamini

Bioinform Biol Insights. 2012; 6: 203–223. Published online 2012 October 3. doi: 10.4137/BBI.S9798

PMCID:: PMC3468436

Abstract Full Text PDF–1.6M Supplementary Material

The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation

Santi Nurbaiti, Muhamad A. Martoprawiro, Akhmaloka, Rukman Hertadi

Bioinform Biol Insights. 2012; 6: 225–234. Published online 2012 October 30. doi: 10.4137/BBI.S9390

PMCID:: PMC3491847

Abstract Full Text PDF–2.7M

Software Review

BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks

Oksana Kohutyuk, Fadi Towfic, M. Heather West Greenlee, Vasant Honavar

Bioinform Biol Insights. 2012; 6: 235–246. Published online 2012 November 8. doi: 10.4137/BBI.S9728

PMCID:: PMC3498971

Abstract Full Text PDF–1.0M

Original Research

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, R. Sowdhamini

Bioinform Biol Insights. 2012; 6: 247–254. Published online 2012 November 12. doi: 10.4137/BBI.S9902

PMCID:: PMC3503467

Abstract Full Text PDF–2.6M

Homology Modeling and Molecular Dynamics Simulation Studies of a Marine Alkaline Protease

Xiaofeng Ji, Wei Wang, Yuan Zheng, Jianhua Hao, Mi Sun

Bioinform Biol Insights. 2012; 6: 255–263. Published online 2012 November 19. doi: 10.4137/BBI.S10663

PMCID:: PMC3511052

Abstract Full Text PDF–3.3M

A Fast Quad-Tree Based Two Dimensional Hierarchical Clustering

Priscilla Rajadurai, Swamynathan Sankaranarayanan

Bioinform Biol Insights. 2012; 6: 265–274. Published online 2012 November 19. doi: 10.4137/BBI.S10383

PMCID:: PMC3511054

Abstract Full Text PDF–976K

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, Bianca L. Garner

Bioinform Biol Insights. 2012; 6: 275–286. Published online 2012 November 21. doi: 10.4137/BBI.S7977

PMCID:: PMC3511254

Abstract Full Text PDF–844K

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, T. Dandekar

Bioinform Biol Insights. 2012; 6: 287–302. Published online 2012 December 3. doi: 10.4137/BBI.S10193

PMCID:: PMC3516044

Abstract Full Text PDF–2.1M

Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length

Alexander Bolshoy, Tatiana Tatarinova

Bioinform Biol Insights. 2012; 6: 317–327. Published online 2012 December 10. doi: 10.4137/BBI.S10525

PMCID:: PMC3528112

Abstract Full Text PDF–646K

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