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Bioinformatics and Biology Insights

ISSN Print: 1177-9322

ISSN Online:

Website: http://www.la-press.com/bioinformatics-and-biology-insights-journal-j39

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Construction of a Computable Network Model for DNA Damage, Autophagy, Cell Death, and Senescence

Stephan Gebel,Rosemarie B. Lichtner,Brian Frushour,Walter K. Schlage

A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences

Nicolas Carels,Diego Frias

Knowledge Discovery in Variant Databases Using Inductive Logic Programming

Hoan Nguyen,Tien-Dao Luu,Olivier Poch,Julie D. Thompson

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,Volker Knoop

A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences

Riccardo Percudani

miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment

Bram Sebastian,Samuel E. Aggrey

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

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

Computational Small RNA Prediction in Bacteria

Jayavel Sridhar,Paramasamy Gunasekaran

A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences

Riccardo Percudani

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

DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements

Pieter Meysman, Kathleen Marchal and Kristof Engelen

Computational Small RNA Prediction in Bacteria

Jayavel Sridhar and Paramasamy Gunasekaran

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

Computational Design of Targeted Inhibitors of Polo-Like Kinase 1 (Plk1)

Krupa S. Jani and D.S. Dalafave

Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length

Alexander Bolshoy, and Tatiana Tatarinova

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. Sch fer, S. Rahlfs, A. Ouedraogo, K. Xiao, S. Sawadogo, B. Coulibaly, K. Becker and T. Dandekar

A Statistical Method without Training Step for the Classification of Coding Frame in Transcriptome Sequences

Nicolas Carels and Diego Frias

Gene Networks Driving Bovine Mammary Protein Synthesis During the Lactation Cycle

Massimo Bionaz and Juan J. Loor

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

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

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

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

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

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

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

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

Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data

Christian Gorba and Florence Tama

Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

Frank F rster, Daniela Beisser, Markus A. Grohme, Chunguang Liang, Brahim Mali, Alexander Matthias Siegl, Julia C. Engelmann, Alexander V. Shkumatov, Elham Schokraie, Tobias Müller, Martina Schn lzer, Ralph O. Schill, Marcus Frohme and Thomas Dandekar

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

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

Mouse Retinal Development: a Dark Horse Model for Systems Biology Research

Xia Zhang, Jeanne M. Serb and M. Heather West Greenlee

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

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

Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites

Wei-Sheng Wu

Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies

R. Shyama Prasad Rao, Ole Thomsen Buus and Bernd Wollenweber

Mining Gene Ontology Data with AGENDA

Guvanch Ovezmyradov, Qianhao Lu and Martin C. G pfert

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

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

The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation

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

A Plausible Role for the Presence of Internal Shine-Dalgarno Sites

Lalit Ponnala

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

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

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

Structural and Functional Insights on the Myosin Superfamily

Divya P. Syamaladevi, James A. Spudich,* and R. Sowdhamini*

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

Knowledge Discovery in Variant Databases Using Inductive Logic Programming

Hoan Nguyen, Tien-Dao Luu, Olivier Poch and Julie D. Thompson

Comparative in Silico Analyses of Cpeb1–4 with Functional Predictions

Xiang-Ping Wang and Nigel G.F. Cooper

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

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

Beate Krueger, Torben Friedrich, Frank F rster, J rg Bernhardt, Roy Gross and Thomas Dandekar

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